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yong27/gist:1e18d3b07d4c7fe6b2366bfe642a3df3

Created August 26, 2016 01:49
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Pfeiffer syndrom quartet analysis
Raw
gistfile1.txt
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Pfeiffer syndrom quartet analysis"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%matplotlib inline\n",
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"##fileformat=VCFv4.1\r\n",
"##ApplyRecalibration=\"analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=/storage/gluster/insilico/data/GenomicsData/Series//ISDB11122GPL11154/apply_recalibrator/d2cd22743d3eea79f59dd21ebb84a0d7/SM.recal.snps.vcf.log help=false input=[(RodBinding name=input source=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/ISDB11122.snps.raw.vcf)] recal_file=(RodBinding name=recal_file source=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/ISDB11122.snps.VarRecal.recal) tranches_file=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/ISDB11122.snps.VarRecal.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 ignore_filter=null mode=SNP filter_mismatching_base_and_quals=false\"\r\n",
"##CombineVariants=\"analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=/storage/gluster/insilico/data/GenomicsData/Series//ISDB11122GPL11154/combine_variants/00e90c599e331929a09028693bed91f7/ISDB11122.SNPrecal.IndelFiltered.vcf.log help=false variant=[(RodBinding name=variant source=/tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/ISDB11122.indel.filtered.vcf), (RodBinding name=variant2 source=/tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/SM.recal.snps.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false\"\r\n",
"##FILTER=<ID=GATKStandard,Description=\"QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0\">\r\n",
"##FILTER=<ID=LowQual,Description=\"Low quality\">\r\n",
"##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description=\"Truth sensitivity tranche level for SNP model at VQS Lod: -5.6494 <= x < 1.6606\">\r\n",
"##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description=\"Truth sensitivity tranche level for SNP model at VQS Lod < -2277.7485\">\r\n",
"##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description=\"Truth sensitivity tranche level for SNP model at VQS Lod: -2277.7485 <= x < -5.6494\">\r\n",
"##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">\r\n",
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\r\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification\">\r\n",
"##INFO=<ID=ABHet,Number=1,Type=Float,Description=\"Allele Balance for hets (ref/(ref+alt))\">\r\n",
"##INFO=<ID=ABHom,Number=1,Type=Float,Description=\"Allele Balance for homs (A/(A+O))\">\r\n",
"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes, for each ALT allele, in the same order as listed\">\r\n",
"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">\r\n",
"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\r\n",
"##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description=\"Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities\">\r\n",
"##INFO=<ID=DB,Number=0,Type=Flag,Description=\"dbSNP Membership\">\r\n",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth; some reads may have been filtered\">\r\n",
"##INFO=<ID=DS,Number=0,Type=Flag,Description=\"Were any of the samples downsampled?\">\r\n",
"##INFO=<ID=Dels,Number=1,Type=Float,Description=\"Fraction of Reads Containing Spanning Deletions\">\r\n",
"##INFO=<ID=END,Number=1,Type=Integer,Description=\"Stop position of the interval\">\r\n",
"##INFO=<ID=FS,Number=1,Type=Float,Description=\"Phred-scaled p-value using Fisher's exact test to detect strand bias\">\r\n",
"##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description=\"Consistency of the site with at most two segregating haplotypes\">\r\n",
"##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description=\"Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation\">\r\n",
"##INFO=<ID=MLEAC,Number=A,Type=Integer,Description=\"Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed\">\r\n",
"##INFO=<ID=MLEAF,Number=A,Type=Float,Description=\"Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed\">\r\n",
"##INFO=<ID=MQ,Number=1,Type=Float,Description=\"RMS Mapping Quality\">\r\n",
"##INFO=<ID=MQ0,Number=1,Type=Integer,Description=\"Total Mapping Quality Zero Reads\">\r\n",
"##INFO=<ID=MQRankSum,Number=1,Type=Float,Description=\"Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities\">\r\n",
"##INFO=<ID=OND,Number=1,Type=Float,Description=\"Overall non-diploid ratio (alleles/(alleles+non-alleles))\">\r\n",
"##INFO=<ID=QD,Number=1,Type=Float,Description=\"Variant Confidence/Quality by Depth\">\r\n",
"##INFO=<ID=RPA,Number=.,Type=Integer,Description=\"Number of times tandem repeat unit is repeated, for each allele (including reference)\">\r\n",
"##INFO=<ID=RU,Number=1,Type=String,Description=\"Tandem repeat unit (bases)\">\r\n",
"##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description=\"Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias\">\r\n",
"##INFO=<ID=SB,Number=1,Type=Float,Description=\"Strand Bias\">\r\n",
"##INFO=<ID=STR,Number=0,Type=Flag,Description=\"Variant is a short tandem repeat\">\r\n",
"##INFO=<ID=VQSLOD,Number=1,Type=Float,Description=\"Log odds ratio of being a true variant versus being false under the trained gaussian mixture model\">\r\n",
"##INFO=<ID=culprit,Number=1,Type=String,Description=\"The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out\">\r\n",
"##INFO=<ID=set,Number=1,Type=String,Description=\"Source VCF for the merged record in CombineVariants\">\r\n",
"##SelectVariants=\"analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_SELECTEDVARIANTS.py/3aed2f246e8c0249ff8a031bd209dc10/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/tmp/generate_SELECTEDVARIANTS.py/3aed2f246e8c0249ff8a031bd209dc10/ISDB11122.variants.raw.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false regenotype=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false filter_mismatching_base_and_quals=false\"\r\n",
"##UnifiedGenotyper=\"analysis_type=UnifiedGenotyper input_file=[/storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322016/printreads/880ddadd1566253466a7e6761e854445/ISDBM322016.recal.bam, /storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322018/printreads/c3a712cdc76c431297effdb013de7bd2/ISDBM322018.recal.bam, /storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322017/printreads/b43e7abc909888a6a066fc3da4c305e7/ISDBM322017.recal.bam, /storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322015/printreads/8eb77fc396f7325f7da846402d1a6df9/ISDBM322015.recal.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_UNIFIEDGENOTYPER.py/dbe01e32e5f0143c1e3d62bfa4a46bd0/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=6 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT pcr_error_rate=1.0E-4 noSLOD=false annotateNDA=false min_base_quality_score=17 max_deletion_fraction=0.05 cap_max_alternate_alleles_for_indels=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 dbsnp=(RodBinding name=dbsnp source=/tmp/generate_UNIFIEDGENOTYPER.py/dbe01e32e5f0143c1e3d62bfa4a46bd0/dbsnp_135.b37.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[AlleleBalance, DepthOfCoverage, FisherStrand] excludeAnnotation=[] filter_mismatching_base_and_quals=false\"\r\n",
"##VariantFiltration=\"analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_VARIANT_FILTRATION.py/af94a8015760f0c3d105ae21bdcee583/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=/storage/gluster/insilico/data/GenomicsData/Series//ISDB11122GPL11154/variant_filtration/af94a8015760f0c3d105ae21bdcee583/ISDB11122.indel.filtered.vcf.log help=false variant=(RodBinding name=variant source=/tmp/generate_VARIANT_FILTRATION.py/af94a8015760f0c3d105ae21bdcee583/ISDB11122.indels.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0] filterName=[GATKStandard] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=true invalidatePreviousFilters=false filter_mismatching_base_and_quals=false\"\r\n",
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"##contig=<ID=GL000215.1,length=172545,assembly=b37>\r\n",
"##contig=<ID=GL000205.1,length=174588,assembly=b37>\r\n",
"##contig=<ID=GL000219.1,length=179198,assembly=b37>\r\n",
"##contig=<ID=GL000224.1,length=179693,assembly=b37>\r\n",
"##contig=<ID=GL000223.1,length=180455,assembly=b37>\r\n",
"##contig=<ID=GL000195.1,length=182896,assembly=b37>\r\n",
"##contig=<ID=GL000212.1,length=186858,assembly=b37>\r\n",
"##contig=<ID=GL000222.1,length=186861,assembly=b37>\r\n",
"##contig=<ID=GL000200.1,length=187035,assembly=b37>\r\n",
"##contig=<ID=GL000193.1,length=189789,assembly=b37>\r\n",
"##contig=<ID=GL000194.1,length=191469,assembly=b37>\r\n",
"##contig=<ID=GL000225.1,length=211173,assembly=b37>\r\n",
"##contig=<ID=GL000192.1,length=547496,assembly=b37>\r\n",
"##reference=file:///tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/human_g1k_v37.fasta\r\n",
"##source=SelectVariants\r\n",
"##SnpEffVersion=\"3.3c (build 2013-06-28), by Pablo Cingolani\"\r\n",
"##SnpEffCmd=\"SnpEff -t hg19 /tmp/generate_SNPEFF.py/98b17a7321fce5a67e5dcd5a1c24a311/ISDB11122.SNPrecal.IndelFiltered.vcf \"\r\n",
"##INFO=<ID=EFF,Number=.,Type=String,Description=\"Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon | GenotypeNum [ | ERRORS | WARNINGS ] )' \">\r\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tISDBM322015\tISDBM322016\tISDBM322017\tISDBM322018\r\n"
]
}
],
"source": [
"!head -n 135 Pfeiffer-quartet.vcf"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"데이터 로드하기. 135줄부터 로드해야 함."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>#CHROM</th>\n",
" <th>POS</th>\n",
" <th>ID</th>\n",
" <th>REF</th>\n",
" <th>ALT</th>\n",
" <th>QUAL</th>\n",
" <th>FILTER</th>\n",
" <th>INFO</th>\n",
" <th>FORMAT</th>\n",
" <th>ISDBM322015</th>\n",
" <th>ISDBM322016</th>\n",
" <th>ISDBM322017</th>\n",
" <th>ISDBM322018</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>1</td>\n",
" <td>14907</td>\n",
" <td>rs79585140</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>514.87</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.628;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:6,0:6:18:0,18,178</td>\n",
" <td>0/1:17,10:27:99:208,0,341</td>\n",
" <td>0/1:14,9:23:99:176,0,258</td>\n",
" <td>0/1:20,11:31:99:174,0,380</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>1</td>\n",
" <td>14930</td>\n",
" <td>rs75454623</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>780.25</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.644;AC=4;AF=0.500;AN=8;BaseQRankSum=-5...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:6,1:7:7:7,0,150</td>\n",
" <td>0/1:16,13:29:99:296,0,378</td>\n",
" <td>0/1:19,13:32:99:245,0,420</td>\n",
" <td>0/1:24,15:39:99:274,0,535</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>1</td>\n",
" <td>14948</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>47.48</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.846;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:10,0:10:24:0,24,228</td>\n",
" <td>0/0:32,0:32:81:0,81,734</td>\n",
" <td>0/1:28,6:34:79:79,0,549</td>\n",
" <td>0/1:41,6:47:8:8,0,850</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>1</td>\n",
" <td>15211</td>\n",
" <td>rs144718396</td>\n",
" <td>T</td>\n",
" <td>G</td>\n",
" <td>110.28</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.359;ABHom=1.00;AC=5;AF=0.625;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:1,1:2:17:17,0,17</td>\n",
" <td>0/1:3,5:8:8:76,0,8</td>\n",
" <td>1/1:0,1:1:3:23,3,0</td>\n",
" <td>0/1:1,4:5:14:36,0,14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>1</td>\n",
" <td>17538</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>A</td>\n",
" <td>151.64</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.735;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:2,0:2:6:0,6,80</td>\n",
" <td>0/1:10,2:13:51:51,0,138</td>\n",
" <td>0/0:23,1:24:0:0,0,418</td>\n",
" <td>0/1:14,8:22:99:139,0,243</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>1</td>\n",
" <td>63336</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>460.26</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.705;ABHom=1.00;AC=2;AF=0.333;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>0/1:31,15:46:99:340,0,308</td>\n",
" <td>0/1:25,9:34:99:159,0,394</td>\n",
" <td>0/0:52,0:52:90:0,90,830</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>1</td>\n",
" <td>63735</td>\n",
" <td>.</td>\n",
" <td>CCTA</td>\n",
" <td>C</td>\n",
" <td>193.23</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:6,2:4:6:116,6,0</td>\n",
" <td>0/1:8,4:8:99:128,0,301</td>\n",
" <td>0/0:18,2:15:30:0,30,666</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>1</td>\n",
" <td>69511</td>\n",
" <td>rs75062661</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>4293.01</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHom=0.982;AC=8;AF=1.00;AN=8;BaseQRankSum=2.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:2,171:173:99:2218,228,0</td>\n",
" <td>1/1:0,33:34:60:508,60,0</td>\n",
" <td>1/1:0,61:63:93:777,93,0</td>\n",
" <td>1/1:0,61:61:96:790,96,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>1</td>\n",
" <td>121009</td>\n",
" <td>rs1851943</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>35.27</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.636;ABHom=0.929;AC=1;AF=0.167;AN=6;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>0/0:11,0:11:33:0,33,436</td>\n",
" <td>0/0:6,1:7:18:0,18,240</td>\n",
" <td>0/1:7,4:11:70:70,0,229</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>1</td>\n",
" <td>133160</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>88.69</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.750;ABHom=0.841;AC=3;AF=0.500;AN=6;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:1,3:4:9:109,9,0</td>\n",
" <td>0/1:3,1:4:20:20,0,107</td>\n",
" <td>./.</td>\n",
" <td>0/0:1,0:1:3:0,3,40</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>1</td>\n",
" <td>546952</td>\n",
" <td>rs9438487</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>43.22</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:49,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:28,3,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>1</td>\n",
" <td>745347</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>59.16</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.702;ABHom=0.938;AC=3;AF=0.375;AN=8;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:3,1:4:13:13,0,60</td>\n",
" <td>0/0:15,1:16:8:0,8,212</td>\n",
" <td>0/1:4,4:8:71:75,0,71</td>\n",
" <td>0/1:13,2:15:13:13,0,203</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>1</td>\n",
" <td>745370</td>\n",
" <td>rs146246821</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>510.54</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:4,1:5:32:32,0,185</td>\n",
" <td>0/1:17,4:18:99:132,0,623</td>\n",
" <td>0/1:9,7:16:99:273,0,395</td>\n",
" <td>0/1:16,4:19:99:125,0,661</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>1</td>\n",
" <td>752566</td>\n",
" <td>rs3094315</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>118.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>1</td>\n",
" <td>752721</td>\n",
" <td>rs3131972</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>242.70</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,4:4:12:159,12,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>1</td>\n",
" <td>753405</td>\n",
" <td>rs61770173</td>\n",
" <td>C</td>\n",
" <td>A</td>\n",
" <td>432.40</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=31;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,14:14:24:221,24,0</td>\n",
" <td>1/1:0,8:8:12:111,12,0</td>\n",
" <td>1/1:0,9:9:15:138,15,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>1</td>\n",
" <td>753474</td>\n",
" <td>rs2073814</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>271.92</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHom=0.952;AC=6;AF=1.00;AN=6;DB;DP=15;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,3:3:9:118,9,0</td>\n",
" <td>1/1:0,6:7:9:83,9,0</td>\n",
" <td>1/1:0,5:5:9:108,9,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>1</td>\n",
" <td>758324</td>\n",
" <td>rs3131955</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>1</td>\n",
" <td>780027</td>\n",
" <td>rs2977613</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>1</td>\n",
" <td>808631</td>\n",
" <td>rs11240779</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>1853.99</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,7:7:21:223,21,0</td>\n",
" <td>1/1:0,16:16:48:602,48,0</td>\n",
" <td>1/1:0,13:13:36:457,36,0</td>\n",
" <td>1/1:0,16:16:48:611,48,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>1</td>\n",
" <td>808922</td>\n",
" <td>rs6594027</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>4960.01</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=222;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,43:43:96:1199,96,0</td>\n",
" <td>1/1:0,62:62:99:1304,102,0</td>\n",
" <td>1/1:0,58:58:93:1169,93,0</td>\n",
" <td>1/1:0,59:59:99:1288,102,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>1</td>\n",
" <td>808928</td>\n",
" <td>rs11240780</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>5605.01</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=234;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,48:48:99:1318,111,0</td>\n",
" <td>1/1:0,61:61:99:1456,114,0</td>\n",
" <td>1/1:0,63:63:99:1383,111,0</td>\n",
" <td>1/1:0,62:62:99:1448,114,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>1</td>\n",
" <td>809171</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>103.55</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.800;ABHom=0.936;AC=2;AF=0.250;AN=8;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:35,6:41:36:36,0,520</td>\n",
" <td>0/1:44,15:59:99:109,0,657</td>\n",
" <td>0/0:47,5:52:57:0,57,722</td>\n",
" <td>0/0:31,0:32:78:0,78,634</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>1</td>\n",
" <td>809732</td>\n",
" <td>rs147199422</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>44.02</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.865;ABHom=0.932;AC=1;AF=0.125;AN=8;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:64,10:74:80:80,0,2123</td>\n",
" <td>0/0:58,2:60:99:0,121,2171</td>\n",
" <td>0/0:42,4:46:17:0,17,1486</td>\n",
" <td>0/0:54,5:59:29:0,29,1912</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>1</td>\n",
" <td>809744</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>40.99</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.864;ABHom=0.950;AC=1;AF=0.125;AN=8;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:57,9:67:77:77,0,1851</td>\n",
" <td>0/0:57,2:60:99:0,115,2057</td>\n",
" <td>0/0:46,3:49:59:0,59,1686</td>\n",
" <td>0/0:53,3:56:74:0,74,1828</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>1</td>\n",
" <td>812267</td>\n",
" <td>rs7541694</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>385.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,3:3:9:95,9,0</td>\n",
" <td>1/1:0,5:5:15:175,15,0</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,3:3:9:99,9,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>1</td>\n",
" <td>812284</td>\n",
" <td>rs7545373</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>428.75</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,5:5:15:185,15,0</td>\n",
" <td>1/1:0,4:4:12:148,12,0</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>1</td>\n",
" <td>823790</td>\n",
" <td>rs143626389</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>38.82</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:75,6,0</td>\n",
" <td>./.</td>\n",
" <td>0/0:3,0:3:9:0,9,99</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>1</td>\n",
" <td>834832</td>\n",
" <td>rs4411087</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>48.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>1</td>\n",
" <td>849998</td>\n",
" <td>rs13303222</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300006</th>\n",
" <td>GL000225.1</td>\n",
" <td>198637</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>80.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,3:3:9:113,9,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300007</th>\n",
" <td>GL000225.1</td>\n",
" <td>198643</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>86.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,3:3:9:119,9,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300008</th>\n",
" <td>GL000225.1</td>\n",
" <td>202533</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>46.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300009</th>\n",
" <td>GL000225.1</td>\n",
" <td>203673</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>78.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,1:1:3:32,3,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300010</th>\n",
" <td>GL000192.1</td>\n",
" <td>99120</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>1132.79</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.594;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:37,35:72:99:680,0,597</td>\n",
" <td>0/1:30,11:41:99:211,0,460</td>\n",
" <td>0/1:15,13:28:99:285,0,257</td>\n",
" <td>0/0:45,0:45:99:0,123,1131</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300011</th>\n",
" <td>GL000192.1</td>\n",
" <td>99283</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>775.57</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.648;ABHom=0.800;AC=5;AF=0.625;AN=8;Bas...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:21,12:33:99:143,0,226</td>\n",
" <td>0/1:13,12:25:99:223,0,167</td>\n",
" <td>0/1:26,7:33:99:127,0,155</td>\n",
" <td>1/1:4,16:20:36:328,36,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300012</th>\n",
" <td>GL000192.1</td>\n",
" <td>99390</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>74.63</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.527;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:3,0:3:6:0,6,55</td>\n",
" <td>0/0:7,0:7:12:0,12,111</td>\n",
" <td>0/1:5,4:9:13:96,0,13</td>\n",
" <td>0/1:5,5:10:19:19,0,46</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300013</th>\n",
" <td>GL000192.1</td>\n",
" <td>100085</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>128.56</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.442;ABHom=1.00;AC=4;AF=0.667;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>0/1:2,1:3:19:19,0,66</td>\n",
" <td>0/1:1,4:5:11:120,0,11</td>\n",
" <td>1/1:0,1:1:3:28,3,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300014</th>\n",
" <td>GL000192.1</td>\n",
" <td>101228</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>493.56</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.378;ABHom=1.00;AC=5;AF=0.625;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:6,3:9:93:93,0,186</td>\n",
" <td>0/1:3,7:10:75:222,0,75</td>\n",
" <td>0/1:1,5:6:23:133,0,23</td>\n",
" <td>1/1:0,3:3:9:90,9,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300015</th>\n",
" <td>GL000192.1</td>\n",
" <td>101317</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>C</td>\n",
" <td>311.87</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.429;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:10,7:17:99:146,0,201</td>\n",
" <td>0/1:3,7:10:28:166,0,28</td>\n",
" <td>0/0:7,0:7:18:0,18,166</td>\n",
" <td>0/1:2,3:5:43:43,0,43</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300016</th>\n",
" <td>GL000192.1</td>\n",
" <td>107709</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>149.56</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.662;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:24,0:24:45:0,45,511</td>\n",
" <td>0/0:12,0:12:27:0,27,328</td>\n",
" <td>0/1:6,5:12:99:124,0,131</td>\n",
" <td>0/1:14,4:18:67:67,0,313</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300017</th>\n",
" <td>GL000192.1</td>\n",
" <td>111042</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>A</td>\n",
" <td>440.55</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.460;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:39,0:39:78:0,78,1000</td>\n",
" <td>0/0:24,0:24:45:0,45,579</td>\n",
" <td>0/1:9,11:20:45:310,0,45</td>\n",
" <td>0/1:8,9:17:99:172,0,133</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300018</th>\n",
" <td>GL000192.1</td>\n",
" <td>121717</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>286.55</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.663;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:45,0:45:51:0,51,470</td>\n",
" <td>0/0:29,0:29:51:0,51,463</td>\n",
" <td>0/1:20,7:27:87:87,0,281</td>\n",
" <td>0/1:17,12:29:99:241,0,209</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300019</th>\n",
" <td>GL000192.1</td>\n",
" <td>121977</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>1200.79</td>\n",
" <td>VQSRTrancheSNP99.00to99.90</td>\n",
" <td>ABHet=0.450;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:19,19:38:99:492,0,361</td>\n",
" <td>0/1:16,15:31:99:394,0,386</td>\n",
" <td>0/0:28,0:28:84:0,84,918</td>\n",
" <td>0/1:6,12:18:99:358,0,137</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300020</th>\n",
" <td>GL000192.1</td>\n",
" <td>131599</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>360.79</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.460;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:3,3:6:65:65,0,65</td>\n",
" <td>0/1:10,9:19:99:155,0,125</td>\n",
" <td>0/0:15,0:15:36:0,36,332</td>\n",
" <td>0/1:6,11:17:75:184,0,75</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300021</th>\n",
" <td>GL000192.1</td>\n",
" <td>139953</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>165.56</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.451;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:27,0:27:57:0,57,725</td>\n",
" <td>0/0:18,0:18:30:0,30,363</td>\n",
" <td>0/1:11,4:15:48:48,0,280</td>\n",
" <td>0/1:1,5:6:21:159,0,21</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300022</th>\n",
" <td>GL000192.1</td>\n",
" <td>139953</td>\n",
" <td>.</td>\n",
" <td>CTG</td>\n",
" <td>C</td>\n",
" <td>1104.53</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=-3.358;DP=66;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:7,18:20:51:677,51,0</td>\n",
" <td>0/1:9,6:10:33:204,0,33</td>\n",
" <td>0/1:8,7:10:19:280,0,19</td>\n",
" <td>0/0:6,0:6:9:0,9,141</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300023</th>\n",
" <td>GL000192.1</td>\n",
" <td>160087</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>157.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.625;ABHom=1.00;AC=6;AF=0.750;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:2,2:4:52:60,0,52</td>\n",
" <td>0/1:3,1:4:25:25,0,105</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>1/1:0,1:1:3:37,3,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300024</th>\n",
" <td>GL000192.1</td>\n",
" <td>197562</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>158.55</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=7;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,4:4:12:111,12,0</td>\n",
" <td>1/1:0,3:3:9:83,9,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300025</th>\n",
" <td>GL000192.1</td>\n",
" <td>212151</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>566.79</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.498;AC=4;AF=0.500;AN=8;BaseQRankSum=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:18,23:41:99:291,0,208</td>\n",
" <td>0/1:6,12:18:99:253,0,114</td>\n",
" <td>0/1:7,4:11:62:62,0,90</td>\n",
" <td>0/1:11,1:12:1:1,0,194</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300026</th>\n",
" <td>GL000192.1</td>\n",
" <td>216599</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>A</td>\n",
" <td>223.55</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.492;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:46,0:46:99:0,102,941</td>\n",
" <td>0/0:19,0:19:33:0,33,304</td>\n",
" <td>0/1:5,6:11:56:139,0,56</td>\n",
" <td>0/1:9,8:17:99:126,0,130</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300027</th>\n",
" <td>GL000192.1</td>\n",
" <td>228788</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>46.77</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHom=0.500;AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:2,2:4:6:78,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300028</th>\n",
" <td>GL000192.1</td>\n",
" <td>229867</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>2232.98</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHom=0.857;AC=8;AF=1.00;AN=8;DP=111;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:4,25:29:66:609,66,0</td>\n",
" <td>1/1:2,25:27:57:528,57,0</td>\n",
" <td>1/1:6,23:29:66:609,66,0</td>\n",
" <td>1/1:4,22:26:57:526,57,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300029</th>\n",
" <td>GL000192.1</td>\n",
" <td>272061</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>CT</td>\n",
" <td>125.59</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.375;AN=8;BaseQRankSum=-0.058;DP=33;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:5,0:4:9:0,9,93</td>\n",
" <td>0/1:5,4:7:12:107,0,12</td>\n",
" <td>0/1:9,2:3:18:53,0,18</td>\n",
" <td>0/1:6,1:4:17:17,0,69</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300030</th>\n",
" <td>GL000192.1</td>\n",
" <td>311575</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>248.50</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.333;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:2,0:2:3:0,3,39</td>\n",
" <td>0/1:3,6:9:93:212,0,93</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>0/0:5,0:5:15:0,15,181</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300031</th>\n",
" <td>GL000192.1</td>\n",
" <td>313293</td>\n",
" <td>.</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>174.79</td>\n",
" <td>VQSRTrancheSNP99.90to100.00</td>\n",
" <td>ABHet=0.640;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:42,16:58:55:55,0,587</td>\n",
" <td>0/0:34,0:34:42:0,42,447</td>\n",
" <td>0/1:26,10:36:57:57,0,367</td>\n",
" <td>0/1:19,21:40:99:106,0,367</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300032</th>\n",
" <td>GL000192.1</td>\n",
" <td>313701</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>120.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300033</th>\n",
" <td>GL000192.1</td>\n",
" <td>337826</td>\n",
" <td>.</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>489.51</td>\n",
" <td>PASS</td>\n",
" <td>AC=2;AF=0.250;AN=8;BaseQRankSum=-3.725;DP=62;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:18,0:18:51:0,51,855</td>\n",
" <td>0/0:13,0:13:39:0,39,695</td>\n",
" <td>0/1:5,10:15:99:438,0,228</td>\n",
" <td>0/1:13,3:16:99:102,0,647</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300034</th>\n",
" <td>GL000192.1</td>\n",
" <td>394140</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.7...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>300035</th>\n",
" <td>10</td>\n",
" <td>123256215</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>G</td>\n",
" <td>100.00</td>\n",
" <td>PASS</td>\n",
" <td>GENE=FGFR2;INHERITANCE=AD;MIM=101600</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>1/0:1,0:1:3:0,3,39</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>300036 rows × 13 columns</p>\n",
"</div>"
],
"text/plain": [
" #CHROM POS ID REF ALT QUAL \\\n",
"0 1 14907 rs79585140 A G 514.87 \n",
"1 1 14930 rs75454623 A G 780.25 \n",
"2 1 14948 . G A 47.48 \n",
"3 1 15211 rs144718396 T G 110.28 \n",
"4 1 17538 . C A 151.64 \n",
"5 1 63336 . C T 460.26 \n",
"6 1 63735 . CCTA C 193.23 \n",
"7 1 69511 rs75062661 A G 4293.01 \n",
"8 1 121009 rs1851943 C T 35.27 \n",
"9 1 133160 . G A 88.69 \n",
"10 1 546952 rs9438487 T C 43.22 \n",
"11 1 745347 . T C 59.16 \n",
"12 1 745370 rs146246821 TA T 510.54 \n",
"13 1 752566 rs3094315 G A 118.67 \n",
"14 1 752721 rs3131972 A G 242.70 \n",
"15 1 753405 rs61770173 C A 432.40 \n",
"16 1 753474 rs2073814 C G 271.92 \n",
"17 1 758324 rs3131955 T C 45.77 \n",
"18 1 780027 rs2977613 G T 47.01 \n",
"19 1 808631 rs11240779 G A 1853.99 \n",
"20 1 808922 rs6594027 G A 4960.01 \n",
"21 1 808928 rs11240780 C T 5605.01 \n",
"22 1 809171 . G A 103.55 \n",
"23 1 809732 rs147199422 T C 44.02 \n",
"24 1 809744 . A G 40.99 \n",
"25 1 812267 rs7541694 A G 385.67 \n",
"26 1 812284 rs7545373 C G 428.75 \n",
"27 1 823790 rs143626389 G A 38.82 \n",
"28 1 834832 rs4411087 G C 48.77 \n",
"29 1 849998 rs13303222 A G 45.77 \n",
"... ... ... ... ... .. ... \n",
"300006 GL000225.1 198637 . C T 80.98 \n",
"300007 GL000225.1 198643 . A G 86.98 \n",
"300008 GL000225.1 202533 . C T 46.77 \n",
"300009 GL000225.1 203673 . C T 78.22 \n",
"300010 GL000192.1 99120 . C T 1132.79 \n",
"300011 GL000192.1 99283 . T C 775.57 \n",
"300012 GL000192.1 99390 . C G 74.63 \n",
"300013 GL000192.1 100085 . A G 128.56 \n",
"300014 GL000192.1 101228 . T C 493.56 \n",
"300015 GL000192.1 101317 . A C 311.87 \n",
"300016 GL000192.1 107709 . G A 149.56 \n",
"300017 GL000192.1 111042 . C A 440.55 \n",
"300018 GL000192.1 121717 . G A 286.55 \n",
"300019 GL000192.1 121977 . G A 1200.79 \n",
"300020 GL000192.1 131599 . C G 360.79 \n",
"300021 GL000192.1 139953 . C G 165.56 \n",
"300022 GL000192.1 139953 . CTG C 1104.53 \n",
"300023 GL000192.1 160087 . C T 157.22 \n",
"300024 GL000192.1 197562 . T C 158.55 \n",
"300025 GL000192.1 212151 . G C 566.79 \n",
"300026 GL000192.1 216599 . C A 223.55 \n",
"300027 GL000192.1 228788 . G T 46.77 \n",
"300028 GL000192.1 229867 . C T 2232.98 \n",
"300029 GL000192.1 272061 . C CT 125.59 \n",
"300030 GL000192.1 311575 . C T 248.50 \n",
"300031 GL000192.1 313293 . G A 174.79 \n",
"300032 GL000192.1 313701 . T C 120.67 \n",
"300033 GL000192.1 337826 . TA T 489.51 \n",
"300034 GL000192.1 394140 . A G 45.26 \n",
"300035 10 123256215 . T G 100.00 \n",
"\n",
" FILTER \\\n",
"0 VQSRTrancheSNP99.00to99.90 \n",
"1 VQSRTrancheSNP99.00to99.90 \n",
"2 VQSRTrancheSNP99.90to100.00 \n",
"3 VQSRTrancheSNP99.90to100.00 \n",
"4 VQSRTrancheSNP99.00to99.90 \n",
"5 VQSRTrancheSNP99.90to100.00 \n",
"6 PASS \n",
"7 VQSRTrancheSNP99.90to100.00 \n",
"8 VQSRTrancheSNP99.00to99.90 \n",
"9 VQSRTrancheSNP99.00to99.90 \n",
"10 VQSRTrancheSNP99.90to100.00 \n",
"11 VQSRTrancheSNP99.90to100.00 \n",
"12 PASS \n",
"13 PASS \n",
"14 PASS \n",
"15 VQSRTrancheSNP99.90to100.00 \n",
"16 VQSRTrancheSNP99.00to99.90 \n",
"17 PASS \n",
"18 PASS \n",
"19 PASS \n",
"20 VQSRTrancheSNP99.00to99.90 \n",
"21 VQSRTrancheSNP99.00to99.90 \n",
"22 VQSRTrancheSNP99.90to100.00 \n",
"23 VQSRTrancheSNP99.90to100.00 \n",
"24 VQSRTrancheSNP99.90to100.00 \n",
"25 PASS \n",
"26 PASS \n",
"27 PASS \n",
"28 PASS \n",
"29 PASS \n",
"... ... \n",
"300006 PASS \n",
"300007 PASS \n",
"300008 PASS \n",
"300009 PASS \n",
"300010 VQSRTrancheSNP99.90to100.00 \n",
"300011 VQSRTrancheSNP99.90to100.00 \n",
"300012 VQSRTrancheSNP99.90to100.00 \n",
"300013 VQSRTrancheSNP99.00to99.90 \n",
"300014 VQSRTrancheSNP99.00to99.90 \n",
"300015 VQSRTrancheSNP99.90to100.00 \n",
"300016 VQSRTrancheSNP99.00to99.90 \n",
"300017 VQSRTrancheSNP99.00to99.90 \n",
"300018 VQSRTrancheSNP99.90to100.00 \n",
"300019 VQSRTrancheSNP99.00to99.90 \n",
"300020 VQSRTrancheSNP99.90to100.00 \n",
"300021 VQSRTrancheSNP99.90to100.00 \n",
"300022 PASS \n",
"300023 PASS \n",
"300024 VQSRTrancheSNP99.90to100.00 \n",
"300025 VQSRTrancheSNP99.90to100.00 \n",
"300026 VQSRTrancheSNP99.90to100.00 \n",
"300027 VQSRTrancheSNP99.90to100.00 \n",
"300028 VQSRTrancheSNP99.90to100.00 \n",
"300029 PASS \n",
"300030 PASS \n",
"300031 VQSRTrancheSNP99.90to100.00 \n",
"300032 PASS \n",
"300033 PASS \n",
"300034 PASS \n",
"300035 PASS \n",
"\n",
" INFO FORMAT \\\n",
"0 ABHet=0.628;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"1 ABHet=0.644;AC=4;AF=0.500;AN=8;BaseQRankSum=-5... GT:AD:DP:GQ:PL \n",
"2 ABHet=0.846;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"3 ABHet=0.359;ABHom=1.00;AC=5;AF=0.625;AN=8;Base... GT:AD:DP:GQ:PL \n",
"4 ABHet=0.735;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"5 ABHet=0.705;ABHom=1.00;AC=2;AF=0.333;AN=6;Base... GT:AD:DP:GQ:PL \n",
"6 AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F... GT:AD:DP:GQ:PL \n",
"7 ABHom=0.982;AC=8;AF=1.00;AN=8;BaseQRankSum=2.0... GT:AD:DP:GQ:PL \n",
"8 ABHet=0.636;ABHom=0.929;AC=1;AF=0.167;AN=6;Bas... GT:AD:DP:GQ:PL \n",
"9 ABHet=0.750;ABHom=0.841;AC=3;AF=0.500;AN=6;Bas... GT:AD:DP:GQ:PL \n",
"10 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... GT:AD:DP:GQ:PL \n",
"11 ABHet=0.702;ABHom=0.938;AC=3;AF=0.375;AN=8;Bas... GT:AD:DP:GQ:PL \n",
"12 AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64... GT:AD:DP:GQ:PL \n",
"13 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00... GT:AD:DP:GQ:PL \n",
"14 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00... GT:AD:DP:GQ:PL \n",
"15 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=31;Dels=0.0... GT:AD:DP:GQ:PL \n",
"16 ABHom=0.952;AC=6;AF=1.00;AN=6;DB;DP=15;Dels=0.... GT:AD:DP:GQ:PL \n",
"17 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"18 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"19 ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0.... GT:AD:DP:GQ:PL \n",
"20 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=222;Dels=0.... GT:AD:DP:GQ:PL \n",
"21 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=234;Dels=0.... GT:AD:DP:GQ:PL \n",
"22 ABHet=0.800;ABHom=0.936;AC=2;AF=0.250;AN=8;Bas... GT:AD:DP:GQ:PL \n",
"23 ABHet=0.865;ABHom=0.932;AC=1;AF=0.125;AN=8;Bas... GT:AD:DP:GQ:PL \n",
"24 ABHet=0.864;ABHom=0.950;AC=1;AF=0.125;AN=8;Bas... GT:AD:DP:GQ:PL \n",
"25 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... GT:AD:DP:GQ:PL \n",
"26 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... GT:AD:DP:GQ:PL \n",
"27 ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3... GT:AD:DP:GQ:PL \n",
"28 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"29 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"... ... ... \n",
"300006 ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS... GT:AD:DP:GQ:PL \n",
"300007 ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS... GT:AD:DP:GQ:PL \n",
"300008 ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... GT:AD:DP:GQ:PL \n",
"300009 ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS... GT:AD:DP:GQ:PL \n",
"300010 ABHet=0.594;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300011 ABHet=0.648;ABHom=0.800;AC=5;AF=0.625;AN=8;Bas... GT:AD:DP:GQ:PL \n",
"300012 ABHet=0.527;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300013 ABHet=0.442;ABHom=1.00;AC=4;AF=0.667;AN=6;Base... GT:AD:DP:GQ:PL \n",
"300014 ABHet=0.378;ABHom=1.00;AC=5;AF=0.625;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300015 ABHet=0.429;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300016 ABHet=0.662;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300017 ABHet=0.460;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300018 ABHet=0.663;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300019 ABHet=0.450;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300020 ABHet=0.460;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300021 ABHet=0.451;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300022 AC=4;AF=0.500;AN=8;BaseQRankSum=-3.358;DP=66;F... GT:AD:DP:GQ:PL \n",
"300023 ABHet=0.625;ABHom=1.00;AC=6;AF=0.750;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300024 ABHom=1.00;AC=4;AF=1.00;AN=4;DP=7;Dels=0.00;FS... GT:AD:DP:GQ:PL \n",
"300025 ABHet=0.498;AC=4;AF=0.500;AN=8;BaseQRankSum=0.... GT:AD:DP:GQ:PL \n",
"300026 ABHet=0.492;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300027 ABHom=0.500;AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;... GT:AD:DP:GQ:PL \n",
"300028 ABHom=0.857;AC=8;AF=1.00;AN=8;DP=111;Dels=0.00... GT:AD:DP:GQ:PL \n",
"300029 AC=3;AF=0.375;AN=8;BaseQRankSum=-0.058;DP=33;F... GT:AD:DP:GQ:PL \n",
"300030 ABHet=0.333;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300031 ABHet=0.640;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... GT:AD:DP:GQ:PL \n",
"300032 ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS... GT:AD:DP:GQ:PL \n",
"300033 AC=2;AF=0.250;AN=8;BaseQRankSum=-3.725;DP=62;F... GT:AD:DP:GQ:PL \n",
"300034 ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.7... GT:AD:DP:GQ:PL \n",
"300035 GENE=FGFR2;INHERITANCE=AD;MIM=101600 GT:AD:DP:GQ:PL \n",
"\n",
" ISDBM322015 ISDBM322016 \\\n",
"0 0/0:6,0:6:18:0,18,178 0/1:17,10:27:99:208,0,341 \n",
"1 0/1:6,1:7:7:7,0,150 0/1:16,13:29:99:296,0,378 \n",
"2 0/0:10,0:10:24:0,24,228 0/0:32,0:32:81:0,81,734 \n",
"3 0/1:1,1:2:17:17,0,17 0/1:3,5:8:8:76,0,8 \n",
"4 0/0:2,0:2:6:0,6,80 0/1:10,2:13:51:51,0,138 \n",
"5 ./. 0/1:31,15:46:99:340,0,308 \n",
"6 ./. 1/1:6,2:4:6:116,6,0 \n",
"7 1/1:2,171:173:99:2218,228,0 1/1:0,33:34:60:508,60,0 \n",
"8 ./. 0/0:11,0:11:33:0,33,436 \n",
"9 1/1:1,3:4:9:109,9,0 0/1:3,1:4:20:20,0,107 \n",
"10 1/1:0,2:2:6:49,6,0 ./. \n",
"11 0/1:3,1:4:13:13,0,60 0/0:15,1:16:8:0,8,212 \n",
"12 0/1:4,1:5:32:32,0,185 0/1:17,4:18:99:132,0,623 \n",
"13 ./. 1/1:0,2:2:6:79,6,0 \n",
"14 ./. 1/1:0,2:2:6:80,6,0 \n",
"15 ./. 1/1:0,14:14:24:221,24,0 \n",
"16 ./. 1/1:0,3:3:9:118,9,0 \n",
"17 1/1:0,2:2:6:77,6,0 ./. \n",
"18 1/1:0,1:1:3:40,3,0 ./. \n",
"19 1/1:0,7:7:21:223,21,0 1/1:0,16:16:48:602,48,0 \n",
"20 1/1:0,43:43:96:1199,96,0 1/1:0,62:62:99:1304,102,0 \n",
"21 1/1:0,48:48:99:1318,111,0 1/1:0,61:61:99:1456,114,0 \n",
"22 0/1:35,6:41:36:36,0,520 0/1:44,15:59:99:109,0,657 \n",
"23 0/1:64,10:74:80:80,0,2123 0/0:58,2:60:99:0,121,2171 \n",
"24 0/1:57,9:67:77:77,0,1851 0/0:57,2:60:99:0,115,2057 \n",
"25 1/1:0,3:3:9:95,9,0 1/1:0,5:5:15:175,15,0 \n",
"26 1/1:0,5:5:15:185,15,0 1/1:0,4:4:12:148,12,0 \n",
"27 ./. 1/1:0,2:2:6:75,6,0 \n",
"28 ./. 1/1:0,2:2:6:80,6,0 \n",
"29 1/1:0,2:2:6:77,6,0 ./. \n",
"... ... ... \n",
"300006 ./. 1/1:0,3:3:9:113,9,0 \n",
"300007 ./. 1/1:0,3:3:9:119,9,0 \n",
"300008 ./. ./. \n",
"300009 1/1:0,2:2:6:80,6,0 1/1:0,1:1:3:32,3,0 \n",
"300010 0/1:37,35:72:99:680,0,597 0/1:30,11:41:99:211,0,460 \n",
"300011 0/1:21,12:33:99:143,0,226 0/1:13,12:25:99:223,0,167 \n",
"300012 0/0:3,0:3:6:0,6,55 0/0:7,0:7:12:0,12,111 \n",
"300013 ./. 0/1:2,1:3:19:19,0,66 \n",
"300014 0/1:6,3:9:93:93,0,186 0/1:3,7:10:75:222,0,75 \n",
"300015 0/1:10,7:17:99:146,0,201 0/1:3,7:10:28:166,0,28 \n",
"300016 0/0:24,0:24:45:0,45,511 0/0:12,0:12:27:0,27,328 \n",
"300017 0/0:39,0:39:78:0,78,1000 0/0:24,0:24:45:0,45,579 \n",
"300018 0/0:45,0:45:51:0,51,470 0/0:29,0:29:51:0,51,463 \n",
"300019 0/1:19,19:38:99:492,0,361 0/1:16,15:31:99:394,0,386 \n",
"300020 0/1:3,3:6:65:65,0,65 0/1:10,9:19:99:155,0,125 \n",
"300021 0/0:27,0:27:57:0,57,725 0/0:18,0:18:30:0,30,363 \n",
"300022 1/1:7,18:20:51:677,51,0 0/1:9,6:10:33:204,0,33 \n",
"300023 0/1:2,2:4:52:60,0,52 0/1:3,1:4:25:25,0,105 \n",
"300024 ./. ./. \n",
"300025 0/1:18,23:41:99:291,0,208 0/1:6,12:18:99:253,0,114 \n",
"300026 0/0:46,0:46:99:0,102,941 0/0:19,0:19:33:0,33,304 \n",
"300027 ./. 1/1:2,2:4:6:78,6,0 \n",
"300028 1/1:4,25:29:66:609,66,0 1/1:2,25:27:57:528,57,0 \n",
"300029 0/0:5,0:4:9:0,9,93 0/1:5,4:7:12:107,0,12 \n",
"300030 0/0:2,0:2:3:0,3,39 0/1:3,6:9:93:212,0,93 \n",
"300031 0/1:42,16:58:55:55,0,587 0/0:34,0:34:42:0,42,447 \n",
"300032 ./. 1/1:0,1:1:3:40,3,0 \n",
"300033 0/0:18,0:18:51:0,51,855 0/0:13,0:13:39:0,39,695 \n",
"300034 ./. 0/0:1,0:1:3:0,3,39 \n",
"300035 0/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 \n",
"\n",
" ISDBM322017 ISDBM322018 \n",
"0 0/1:14,9:23:99:176,0,258 0/1:20,11:31:99:174,0,380 \n",
"1 0/1:19,13:32:99:245,0,420 0/1:24,15:39:99:274,0,535 \n",
"2 0/1:28,6:34:79:79,0,549 0/1:41,6:47:8:8,0,850 \n",
"3 1/1:0,1:1:3:23,3,0 0/1:1,4:5:14:36,0,14 \n",
"4 0/0:23,1:24:0:0,0,418 0/1:14,8:22:99:139,0,243 \n",
"5 0/1:25,9:34:99:159,0,394 0/0:52,0:52:90:0,90,830 \n",
"6 0/1:8,4:8:99:128,0,301 0/0:18,2:15:30:0,30,666 \n",
"7 1/1:0,61:63:93:777,93,0 1/1:0,61:61:96:790,96,0 \n",
"8 0/0:6,1:7:18:0,18,240 0/1:7,4:11:70:70,0,229 \n",
"9 ./. 0/0:1,0:1:3:0,3,40 \n",
"10 ./. 1/1:0,1:1:3:28,3,0 \n",
"11 0/1:4,4:8:71:75,0,71 0/1:13,2:15:13:13,0,203 \n",
"12 0/1:9,7:16:99:273,0,395 0/1:16,4:19:99:125,0,661 \n",
"13 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:36,3,0 \n",
"14 1/1:0,4:4:12:159,12,0 1/1:0,1:1:3:40,3,0 \n",
"15 1/1:0,8:8:12:111,12,0 1/1:0,9:9:15:138,15,0 \n",
"16 1/1:0,6:7:9:83,9,0 1/1:0,5:5:9:108,9,0 \n",
"17 ./. ./. \n",
"18 1/1:0,1:1:3:40,3,0 ./. \n",
"19 1/1:0,13:13:36:457,36,0 1/1:0,16:16:48:611,48,0 \n",
"20 1/1:0,58:58:93:1169,93,0 1/1:0,59:59:99:1288,102,0 \n",
"21 1/1:0,63:63:99:1383,111,0 1/1:0,62:62:99:1448,114,0 \n",
"22 0/0:47,5:52:57:0,57,722 0/0:31,0:32:78:0,78,634 \n",
"23 0/0:42,4:46:17:0,17,1486 0/0:54,5:59:29:0,29,1912 \n",
"24 0/0:46,3:49:59:0,59,1686 0/0:53,3:56:74:0,74,1828 \n",
"25 1/1:0,2:2:6:55,6,0 1/1:0,3:3:9:99,9,0 \n",
"26 1/1:0,2:2:6:55,6,0 1/1:0,2:2:6:79,6,0 \n",
"27 ./. 0/0:3,0:3:9:0,9,99 \n",
"28 ./. ./. \n",
"29 ./. ./. \n",
"... ... ... \n",
"300006 ./. ./. \n",
"300007 ./. ./. \n",
"300008 ./. 1/1:0,2:2:6:78,6,0 \n",
"300009 ./. ./. \n",
"300010 0/1:15,13:28:99:285,0,257 0/0:45,0:45:99:0,123,1131 \n",
"300011 0/1:26,7:33:99:127,0,155 1/1:4,16:20:36:328,36,0 \n",
"300012 0/1:5,4:9:13:96,0,13 0/1:5,5:10:19:19,0,46 \n",
"300013 0/1:1,4:5:11:120,0,11 1/1:0,1:1:3:28,3,0 \n",
"300014 0/1:1,5:6:23:133,0,23 1/1:0,3:3:9:90,9,0 \n",
"300015 0/0:7,0:7:18:0,18,166 0/1:2,3:5:43:43,0,43 \n",
"300016 0/1:6,5:12:99:124,0,131 0/1:14,4:18:67:67,0,313 \n",
"300017 0/1:9,11:20:45:310,0,45 0/1:8,9:17:99:172,0,133 \n",
"300018 0/1:20,7:27:87:87,0,281 0/1:17,12:29:99:241,0,209 \n",
"300019 0/0:28,0:28:84:0,84,918 0/1:6,12:18:99:358,0,137 \n",
"300020 0/0:15,0:15:36:0,36,332 0/1:6,11:17:75:184,0,75 \n",
"300021 0/1:11,4:15:48:48,0,280 0/1:1,5:6:21:159,0,21 \n",
"300022 0/1:8,7:10:19:280,0,19 0/0:6,0:6:9:0,9,141 \n",
"300023 1/1:0,2:2:6:78,6,0 1/1:0,1:1:3:37,3,0 \n",
"300024 1/1:0,4:4:12:111,12,0 1/1:0,3:3:9:83,9,0 \n",
"300025 0/1:7,4:11:62:62,0,90 0/1:11,1:12:1:1,0,194 \n",
"300026 0/1:5,6:11:56:139,0,56 0/1:9,8:17:99:126,0,130 \n",
"300027 ./. ./. \n",
"300028 1/1:6,23:29:66:609,66,0 1/1:4,22:26:57:526,57,0 \n",
"300029 0/1:9,2:3:18:53,0,18 0/1:6,1:4:17:17,0,69 \n",
"300030 1/1:0,2:2:6:80,6,0 0/0:5,0:5:15:0,15,181 \n",
"300031 0/1:26,10:36:57:57,0,367 0/1:19,21:40:99:106,0,367 \n",
"300032 1/1:0,1:1:3:39,3,0 1/1:0,2:2:6:77,6,0 \n",
"300033 0/1:5,10:15:99:438,0,228 0/1:13,3:16:99:102,0,647 \n",
"300034 ./. 1/1:0,2:2:6:80,6,0 \n",
"300035 1/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 \n",
"\n",
"[300036 rows x 13 columns]"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df = pd.read_table('Pfeiffer-quartet.vcf', skiprows=134, dtype={'#CHROM': str})\n",
"df"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"A 74449\n",
"T 73785\n",
"G 72981\n",
"C 72857\n",
"TA 509\n",
"CT 493\n",
"AT 479\n",
"GA 424\n",
"CA 395\n",
"GT 359\n",
"AG 256\n",
"TG 233\n",
"GC 219\n",
"TC 157\n",
"AC 152\n",
"CG 63\n",
"A,T 56\n",
"CTT 50\n",
"CAT 45\n",
"TAA 42\n",
"C,CT 41\n",
"A,C 41\n",
"CAA 40\n",
"TAC 37\n",
"A,G 37\n",
"CAG 37\n",
"C,T 36\n",
"C,G 36\n",
"CCT 35\n",
"G,T 35\n",
" ... \n",
"ATTC 1\n",
"C,CGT 1\n",
"CAACA 1\n",
"TAAA,TA 1\n",
"GTGTT 1\n",
"GATAA 1\n",
"CAGAGAG,C 1\n",
"AGGG 1\n",
"GGAGGAA 1\n",
"GCCTT 1\n",
"G,GTT 1\n",
"GGGT 1\n",
"CTCAT 1\n",
"TACTG 1\n",
"CGGT 1\n",
"GGTTT 1\n",
"CACCT 1\n",
"GA,G 1\n",
"GGGGCTGGTACACACAGGTCAGCACGGCCAGGTTCCCACTCCCG 1\n",
"GT,G 1\n",
"G,GAAA 1\n",
"CATAT 1\n",
"TTGTG,T 1\n",
"CTTAT 1\n",
"GACAC,G 1\n",
"ACCAT 1\n",
"CAAA,C 1\n",
"ACTAT 1\n",
"GTAAA 1\n",
"CCTCTCT,C 1\n",
"Name: ALT, dtype: int64"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df['ALT'].value_counts()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.core.frame.DataFrame'>\n",
"RangeIndex: 300036 entries, 0 to 300035\n",
"Data columns (total 13 columns):\n",
"#CHROM 300036 non-null object\n",
"POS 300036 non-null int64\n",
"ID 300036 non-null object\n",
"REF 300036 non-null object\n",
"ALT 300036 non-null object\n",
"QUAL 300036 non-null float64\n",
"FILTER 300036 non-null object\n",
"INFO 300036 non-null object\n",
"FORMAT 300036 non-null object\n",
"ISDBM322015 300036 non-null object\n",
"ISDBM322016 300036 non-null object\n",
"ISDBM322017 300036 non-null object\n",
"ISDBM322018 300036 non-null object\n",
"dtypes: float64(1), int64(1), object(11)\n",
"memory usage: 29.8+ MB\n"
]
}
],
"source": [
"df.info()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"FILTER가 PASS인 레코드만 취합"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'pandas.core.frame.DataFrame'>\n",
"Int64Index: 268101 entries, 6 to 300035\n",
"Data columns (total 13 columns):\n",
"#CHROM 268101 non-null object\n",
"POS 268101 non-null int64\n",
"ID 268101 non-null object\n",
"REF 268101 non-null object\n",
"ALT 268101 non-null object\n",
"QUAL 268101 non-null float64\n",
"FILTER 268101 non-null object\n",
"INFO 268101 non-null object\n",
"FORMAT 268101 non-null object\n",
"ISDBM322015 268101 non-null object\n",
"ISDBM322016 268101 non-null object\n",
"ISDBM322017 268101 non-null object\n",
"ISDBM322018 268101 non-null object\n",
"dtypes: float64(1), int64(1), object(11)\n",
"memory usage: 28.6+ MB\n"
]
}
],
"source": [
"dfc = df[df['FILTER'] == 'PASS']\n",
"dfc.info()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"dfc = dfc.reset_index()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>ISDBM322015 genotype</th>\n",
" <th>ISDBM322016 genotype</th>\n",
" <th>ISDBM322017 genotype</th>\n",
" <th>ISDBM322018 genotype</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>CCTA-C</td>\n",
" <td>CCTA-CCTA</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>C-C</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>G-G</td>\n",
" <td>G-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>C-C</td>\n",
" <td>C-G</td>\n",
" <td>C-G</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>C-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>G-C</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268071</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268072</th>\n",
" <td>GT-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268073</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268074</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268075</th>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268076</th>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>C-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268077</th>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>A-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268078</th>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>A-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268079</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268080</th>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268081</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268082</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268083</th>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268084</th>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268085</th>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268086</th>\n",
" <td>TC-TC</td>\n",
" <td>TC-TC</td>\n",
" <td>TC-TC</td>\n",
" <td>T-TC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268087</th>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268088</th>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268089</th>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268090</th>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268091</th>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268092</th>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268093</th>\n",
" <td>C-C</td>\n",
" <td>CTG-C</td>\n",
" <td>CTG-C</td>\n",
" <td>CTG-CTG</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268094</th>\n",
" <td>C-T</td>\n",
" <td>C-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268095</th>\n",
" <td>C-C</td>\n",
" <td>C-CT</td>\n",
" <td>C-CT</td>\n",
" <td>C-CT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268096</th>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268097</th>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268098</th>\n",
" <td>TA-TA</td>\n",
" <td>TA-TA</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268099</th>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268100</th>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>G-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>268101 rows × 4 columns</p>\n",
"</div>"
],
"text/plain": [
" ISDBM322015 genotype ISDBM322016 genotype ISDBM322017 genotype \\\n",
"0 - C-C CCTA-C \n",
"1 TA-T TA-T TA-T \n",
"2 - A-A A-A \n",
"3 - G-G G-G \n",
"4 C-C - - \n",
"5 T-T - T-T \n",
"6 A-A A-A A-A \n",
"7 G-G G-G G-G \n",
"8 G-G G-G G-G \n",
"9 - A-A - \n",
"10 - C-C - \n",
"11 G-G - - \n",
"12 G-G G-G - \n",
"13 G-G - - \n",
"14 T-T C-C - \n",
"15 A-A A-A A-A \n",
"16 CCCCT-CCCCT CCCCT-CCCCT C-C \n",
"17 - - G-G \n",
"18 - - T-T \n",
"19 - - C-C \n",
"20 C-C C-C - \n",
"21 - T-T G-G \n",
"22 T-T T-T - \n",
"23 G-G G-G - \n",
"24 C-C C-G C-G \n",
"25 C-T C-C C-C \n",
"26 G-C G-G G-G \n",
"27 A-A A-A A-A \n",
"28 C-C C-C C-C \n",
"29 G-G G-G G-G \n",
"... ... ... ... \n",
"268071 G-G - G-G \n",
"268072 GT-G G-G - \n",
"268073 G-G - - \n",
"268074 G-G - - \n",
"268075 C-C - - \n",
"268076 T-T - T-T \n",
"268077 - - T-T \n",
"268078 - - G-G \n",
"268079 G-G - - \n",
"268080 C-C C-C C-C \n",
"268081 G-G G-G G-G \n",
"268082 G-G - - \n",
"268083 - C-C C-C \n",
"268084 T-T T-T T-T \n",
"268085 G-G G-G - \n",
"268086 TC-TC TC-TC TC-TC \n",
"268087 C-C - - \n",
"268088 G-G - - \n",
"268089 - T-T - \n",
"268090 - G-G - \n",
"268091 - - - \n",
"268092 T-T T-T - \n",
"268093 C-C CTG-C CTG-C \n",
"268094 C-T C-T T-T \n",
"268095 C-C C-CT C-CT \n",
"268096 C-C C-T T-T \n",
"268097 - C-C C-C \n",
"268098 TA-TA TA-TA TA-T \n",
"268099 - A-A - \n",
"268100 T-T T-T G-T \n",
"\n",
" ISDBM322018 genotype \n",
"0 CCTA-CCTA \n",
"1 TA-T \n",
"2 A-A \n",
"3 G-G \n",
"4 - \n",
"5 - \n",
"6 A-A \n",
"7 G-G \n",
"8 G-G \n",
"9 G-G \n",
"10 - \n",
"11 - \n",
"12 - \n",
"13 G-G \n",
"14 - \n",
"15 A-A \n",
"16 CCCCT-CCCCT \n",
"17 G-G \n",
"18 T-T \n",
"19 C-C \n",
"20 C-C \n",
"21 G-T \n",
"22 - \n",
"23 - \n",
"24 C-C \n",
"25 C-T \n",
"26 G-C \n",
"27 A-A \n",
"28 C-C \n",
"29 G-G \n",
"... ... \n",
"268071 G-G \n",
"268072 G-G \n",
"268073 A-G \n",
"268074 A-G \n",
"268075 C-C \n",
"268076 C-T \n",
"268077 A-T \n",
"268078 A-G \n",
"268079 - \n",
"268080 - \n",
"268081 G-G \n",
"268082 - \n",
"268083 - \n",
"268084 T-T \n",
"268085 - \n",
"268086 T-TC \n",
"268087 - \n",
"268088 - \n",
"268089 - \n",
"268090 - \n",
"268091 T-T \n",
"268092 - \n",
"268093 CTG-CTG \n",
"268094 T-T \n",
"268095 C-CT \n",
"268096 C-C \n",
"268097 C-C \n",
"268098 TA-T \n",
"268099 G-G \n",
"268100 T-T \n",
"\n",
"[268101 rows x 4 columns]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample_ids = ['ISDBM322015', 'ISDBM322016', 'ISDBM322017', 'ISDBM322018']\n",
"sample_ids_genotype = ['{} genotype'.format(s) for s in sample_ids]\n",
"\n",
"def call_genotype(row):\n",
" alts = row['ALT'].split(',')\n",
" m = {\n",
" '0': row['REF'],\n",
" '1': alts[0],\n",
" '2': alts[1] if len(alts) == 2 else alts[0],\n",
" '3': alts[2] if len(alts) == 3 else alts[0],\n",
" '.': '',\n",
" }\n",
" return pd.Series(['{}-{}'.format(\n",
" m[row[s][0]], m[row[s][2]]) for s in sample_ids if s], \n",
" index=sample_ids_genotype)\n",
"\n",
"genotypes = dfc.apply(call_genotype, axis=1)\n",
"genotypes"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>index</th>\n",
" <th>#CHROM</th>\n",
" <th>POS</th>\n",
" <th>ID</th>\n",
" <th>REF</th>\n",
" <th>ALT</th>\n",
" <th>QUAL</th>\n",
" <th>FILTER</th>\n",
" <th>INFO</th>\n",
" <th>FORMAT</th>\n",
" <th>ISDBM322015</th>\n",
" <th>ISDBM322016</th>\n",
" <th>ISDBM322017</th>\n",
" <th>ISDBM322018</th>\n",
" <th>ISDBM322015 genotype</th>\n",
" <th>ISDBM322016 genotype</th>\n",
" <th>ISDBM322017 genotype</th>\n",
" <th>ISDBM322018 genotype</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>6</td>\n",
" <td>1</td>\n",
" <td>63735</td>\n",
" <td>.</td>\n",
" <td>CCTA</td>\n",
" <td>C</td>\n",
" <td>193.23</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:6,2:4:6:116,6,0</td>\n",
" <td>0/1:8,4:8:99:128,0,301</td>\n",
" <td>0/0:18,2:15:30:0,30,666</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>CCTA-C</td>\n",
" <td>CCTA-CCTA</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>12</td>\n",
" <td>1</td>\n",
" <td>745370</td>\n",
" <td>rs146246821</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>510.54</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:4,1:5:32:32,0,185</td>\n",
" <td>0/1:17,4:18:99:132,0,623</td>\n",
" <td>0/1:9,7:16:99:273,0,395</td>\n",
" <td>0/1:16,4:19:99:125,0,661</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>13</td>\n",
" <td>1</td>\n",
" <td>752566</td>\n",
" <td>rs3094315</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>118.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>14</td>\n",
" <td>1</td>\n",
" <td>752721</td>\n",
" <td>rs3131972</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>242.70</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,4:4:12:159,12,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>17</td>\n",
" <td>1</td>\n",
" <td>758324</td>\n",
" <td>rs3131955</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>18</td>\n",
" <td>1</td>\n",
" <td>780027</td>\n",
" <td>rs2977613</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>19</td>\n",
" <td>1</td>\n",
" <td>808631</td>\n",
" <td>rs11240779</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>1853.99</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,7:7:21:223,21,0</td>\n",
" <td>1/1:0,16:16:48:602,48,0</td>\n",
" <td>1/1:0,13:13:36:457,36,0</td>\n",
" <td>1/1:0,16:16:48:611,48,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>25</td>\n",
" <td>1</td>\n",
" <td>812267</td>\n",
" <td>rs7541694</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>385.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,3:3:9:95,9,0</td>\n",
" <td>1/1:0,5:5:15:175,15,0</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,3:3:9:99,9,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>26</td>\n",
" <td>1</td>\n",
" <td>812284</td>\n",
" <td>rs7545373</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>428.75</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,5:5:15:185,15,0</td>\n",
" <td>1/1:0,4:4:12:148,12,0</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>27</td>\n",
" <td>1</td>\n",
" <td>823790</td>\n",
" <td>rs143626389</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>38.82</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:75,6,0</td>\n",
" <td>./.</td>\n",
" <td>0/0:3,0:3:9:0,9,99</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>28</td>\n",
" <td>1</td>\n",
" <td>834832</td>\n",
" <td>rs4411087</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>48.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>29</td>\n",
" <td>1</td>\n",
" <td>849998</td>\n",
" <td>rs13303222</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>30</td>\n",
" <td>1</td>\n",
" <td>851757</td>\n",
" <td>rs62677860</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>63.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:69,6,0</td>\n",
" <td>1/1:0,2:2:3:28,3,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>31</td>\n",
" <td>1</td>\n",
" <td>861808</td>\n",
" <td>rs13302982</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>66.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:64,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>32</td>\n",
" <td>1</td>\n",
" <td>862866</td>\n",
" <td>rs3892970</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>31.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:66,6,0</td>\n",
" <td>0/0:1,0:1:3:0,3,40</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>33</td>\n",
" <td>1</td>\n",
" <td>866319</td>\n",
" <td>rs9988021</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>825.39</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=24;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,11:11:33:427,33,0</td>\n",
" <td>1/1:0,7:7:18:228,18,0</td>\n",
" <td>1/1:0,4:4:12:133,12,0</td>\n",
" <td>1/1:0,2:2:6:76,6,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>34</td>\n",
" <td>1</td>\n",
" <td>866511</td>\n",
" <td>rs60722469</td>\n",
" <td>C</td>\n",
" <td>CCCCT</td>\n",
" <td>325.15</td>\n",
" <td>PASS</td>\n",
" <td>AC=6;AF=0.750;AN=8;BaseQRankSum=0.747;DB;DP=15...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:5,5:10:15:278,15,0</td>\n",
" <td>1/1:3,0:3:3:32,3,0</td>\n",
" <td>0/0:1,0:1:3:0,3,65</td>\n",
" <td>1/1:0,1:1:3:67,3,0</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>C-C</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>35</td>\n",
" <td>1</td>\n",
" <td>866920</td>\n",
" <td>rs2341361</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>36</td>\n",
" <td>1</td>\n",
" <td>867584</td>\n",
" <td>rs2341360</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>37</td>\n",
" <td>1</td>\n",
" <td>869323</td>\n",
" <td>rs13303207</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>69.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:73,6,0</td>\n",
" <td>1/1:0,1:1:3:30,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>40</td>\n",
" <td>1</td>\n",
" <td>870903</td>\n",
" <td>rs13303094</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>183.66</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=6;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:62,6,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>41</td>\n",
" <td>1</td>\n",
" <td>871334</td>\n",
" <td>rs4072383</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>74.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:63,6,0</td>\n",
" <td>0/0:3,0:3:9:0,9,120</td>\n",
" <td>0/1:2,2:4:52:52,0,68</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>G-G</td>\n",
" <td>G-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>42</td>\n",
" <td>1</td>\n",
" <td>873558</td>\n",
" <td>rs1110052</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>39.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,1:1:3:33,3,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>43</td>\n",
" <td>1</td>\n",
" <td>876499</td>\n",
" <td>rs4372192</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>200.89</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=6;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,4:4:12:160,12,0</td>\n",
" <td>1/1:0,2:2:6:76,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>44</td>\n",
" <td>1</td>\n",
" <td>878784</td>\n",
" <td>rs142929357</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>125.24</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.583;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:16,0:16:45:0,45,553</td>\n",
" <td>0/1:4,4:8:99:136,0,113</td>\n",
" <td>0/1:2,1:3:30:30,0,57</td>\n",
" <td>0/0:2,0:2:6:0,6,66</td>\n",
" <td>C-C</td>\n",
" <td>C-G</td>\n",
" <td>C-G</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>45</td>\n",
" <td>1</td>\n",
" <td>879317</td>\n",
" <td>rs7523549</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>388.57</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.493;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:15,8:23:99:243,0,369</td>\n",
" <td>0/0:7,0:7:21:0,21,252</td>\n",
" <td>0/0:12,0:12:36:0,36,405</td>\n",
" <td>0/1:3,6:9:64:187,0,64</td>\n",
" <td>C-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>46</td>\n",
" <td>1</td>\n",
" <td>879482</td>\n",
" <td>rs149880798</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>799.55</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.592;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:27,20:47:99:584,0,841</td>\n",
" <td>0/0:33,0:33:93:0,93,1155</td>\n",
" <td>0/0:19,0:19:51:0,51,650</td>\n",
" <td>0/1:14,9:23:99:257,0,389</td>\n",
" <td>G-C</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>47</td>\n",
" <td>1</td>\n",
" <td>879676</td>\n",
" <td>rs6605067</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>432.72</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=12;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:73,6,0</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,4:4:12:158,12,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>48</td>\n",
" <td>1</td>\n",
" <td>879687</td>\n",
" <td>rs2839</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>335.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,3:3:9:114,9,0</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,4:4:12:139,12,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>49</td>\n",
" <td>1</td>\n",
" <td>880238</td>\n",
" <td>rs3748592</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>516.84</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,5:5:15:199,15,0</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,5:5:15:196,15,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268071</th>\n",
" <td>299643</td>\n",
" <td>GL000225.1</td>\n",
" <td>64237</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>152.14</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=5;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:70,6,0</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268072</th>\n",
" <td>299706</td>\n",
" <td>GL000225.1</td>\n",
" <td>67508</td>\n",
" <td>.</td>\n",
" <td>GT</td>\n",
" <td>G</td>\n",
" <td>229.23</td>\n",
" <td>PASS</td>\n",
" <td>AC=5;AF=0.833;AN=6;BaseQRankSum=-0.742;DP=13;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:1,6:4:40:136,0,40</td>\n",
" <td>1/1:1,1:2:3:47,3,0</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,4:2:6:94,6,0</td>\n",
" <td>GT-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268073</th>\n",
" <td>299713</td>\n",
" <td>GL000225.1</td>\n",
" <td>71934</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>62.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:70,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>0/1:1,1:2:28:28,0,33</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268074</th>\n",
" <td>299714</td>\n",
" <td>GL000225.1</td>\n",
" <td>71966</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>138.21</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.333;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,3:3:9:113,9,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>0/1:1,2:3:30:62,0,30</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268075</th>\n",
" <td>299715</td>\n",
" <td>GL000225.1</td>\n",
" <td>72003</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>119.76</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=5;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,4:4:9:114,9,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268076</th>\n",
" <td>299716</td>\n",
" <td>GL000225.1</td>\n",
" <td>72057</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>75.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=5;AF=0.833;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>0/1:1,1:2:26:33,0,26</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>C-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268077</th>\n",
" <td>299717</td>\n",
" <td>GL000225.1</td>\n",
" <td>72073</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>37.25</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>0/1:1,1:2:30:33,0,30</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>A-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268078</th>\n",
" <td>299718</td>\n",
" <td>GL000225.1</td>\n",
" <td>72104</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>74.02</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>0/1:1,1:2:24:33,0,24</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>A-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268079</th>\n",
" <td>299723</td>\n",
" <td>GL000225.1</td>\n",
" <td>72249</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>37.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:69,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268080</th>\n",
" <td>299734</td>\n",
" <td>GL000225.1</td>\n",
" <td>72555</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>123.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268081</th>\n",
" <td>299735</td>\n",
" <td>GL000225.1</td>\n",
" <td>72582</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>202.89</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DP=8;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,4:4:9:111,9,0</td>\n",
" <td>1/1:0,2:2:6:61,6,0</td>\n",
" <td>1/1:0,1:1:3:35,3,0</td>\n",
" <td>1/1:0,1:1:3:33,3,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268082</th>\n",
" <td>299778</td>\n",
" <td>GL000225.1</td>\n",
" <td>78642</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>32.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:64,6,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268083</th>\n",
" <td>299860</td>\n",
" <td>GL000225.1</td>\n",
" <td>89058</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268084</th>\n",
" <td>299876</td>\n",
" <td>GL000225.1</td>\n",
" <td>89930</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>139.54</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DP=5;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,2:2:6:72,6,0</td>\n",
" <td>1/1:0,1:1:3:30,3,0</td>\n",
" <td>1/1:0,1:1:3:35,3,0</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268085</th>\n",
" <td>299909</td>\n",
" <td>GL000225.1</td>\n",
" <td>96661</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>40.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:33,3,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268086</th>\n",
" <td>299927</td>\n",
" <td>GL000225.1</td>\n",
" <td>114739</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>TC</td>\n",
" <td>679.82</td>\n",
" <td>PASS</td>\n",
" <td>AC=7;AF=0.875;AN=8;BaseQRankSum=3.317;DP=23;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,5:5:15:209,15,0</td>\n",
" <td>1/1:0,6:6:18:260,18,0</td>\n",
" <td>1/1:0,4:4:12:158,12,0</td>\n",
" <td>0/1:5,3:8:99:106,0,182</td>\n",
" <td>TC-TC</td>\n",
" <td>TC-TC</td>\n",
" <td>TC-TC</td>\n",
" <td>T-TC</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268087</th>\n",
" <td>299992</td>\n",
" <td>GL000225.1</td>\n",
" <td>143836</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>117.52</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,4:4:12:150,12,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268088</th>\n",
" <td>299993</td>\n",
" <td>GL000225.1</td>\n",
" <td>143849</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>117.52</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,4:4:12:150,12,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268089</th>\n",
" <td>300006</td>\n",
" <td>GL000225.1</td>\n",
" <td>198637</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>80.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,3:3:9:113,9,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268090</th>\n",
" <td>300007</td>\n",
" <td>GL000225.1</td>\n",
" <td>198643</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>86.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,3:3:9:119,9,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268091</th>\n",
" <td>300008</td>\n",
" <td>GL000225.1</td>\n",
" <td>202533</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>46.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268092</th>\n",
" <td>300009</td>\n",
" <td>GL000225.1</td>\n",
" <td>203673</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>78.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,1:1:3:32,3,0</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268093</th>\n",
" <td>300022</td>\n",
" <td>GL000192.1</td>\n",
" <td>139953</td>\n",
" <td>.</td>\n",
" <td>CTG</td>\n",
" <td>C</td>\n",
" <td>1104.53</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=-3.358;DP=66;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>1/1:7,18:20:51:677,51,0</td>\n",
" <td>0/1:9,6:10:33:204,0,33</td>\n",
" <td>0/1:8,7:10:19:280,0,19</td>\n",
" <td>0/0:6,0:6:9:0,9,141</td>\n",
" <td>C-C</td>\n",
" <td>CTG-C</td>\n",
" <td>CTG-C</td>\n",
" <td>CTG-CTG</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268094</th>\n",
" <td>300023</td>\n",
" <td>GL000192.1</td>\n",
" <td>160087</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>157.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.625;ABHom=1.00;AC=6;AF=0.750;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/1:2,2:4:52:60,0,52</td>\n",
" <td>0/1:3,1:4:25:25,0,105</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>1/1:0,1:1:3:37,3,0</td>\n",
" <td>C-T</td>\n",
" <td>C-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268095</th>\n",
" <td>300029</td>\n",
" <td>GL000192.1</td>\n",
" <td>272061</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>CT</td>\n",
" <td>125.59</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.375;AN=8;BaseQRankSum=-0.058;DP=33;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:5,0:4:9:0,9,93</td>\n",
" <td>0/1:5,4:7:12:107,0,12</td>\n",
" <td>0/1:9,2:3:18:53,0,18</td>\n",
" <td>0/1:6,1:4:17:17,0,69</td>\n",
" <td>C-C</td>\n",
" <td>C-CT</td>\n",
" <td>C-CT</td>\n",
" <td>C-CT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268096</th>\n",
" <td>300030</td>\n",
" <td>GL000192.1</td>\n",
" <td>311575</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>248.50</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.333;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:2,0:2:3:0,3,39</td>\n",
" <td>0/1:3,6:9:93:212,0,93</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>0/0:5,0:5:15:0,15,181</td>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268097</th>\n",
" <td>300032</td>\n",
" <td>GL000192.1</td>\n",
" <td>313701</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>120.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268098</th>\n",
" <td>300033</td>\n",
" <td>GL000192.1</td>\n",
" <td>337826</td>\n",
" <td>.</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>489.51</td>\n",
" <td>PASS</td>\n",
" <td>AC=2;AF=0.250;AN=8;BaseQRankSum=-3.725;DP=62;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:18,0:18:51:0,51,855</td>\n",
" <td>0/0:13,0:13:39:0,39,695</td>\n",
" <td>0/1:5,10:15:99:438,0,228</td>\n",
" <td>0/1:13,3:16:99:102,0,647</td>\n",
" <td>TA-TA</td>\n",
" <td>TA-TA</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268099</th>\n",
" <td>300034</td>\n",
" <td>GL000192.1</td>\n",
" <td>394140</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.7...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>./.</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268100</th>\n",
" <td>300035</td>\n",
" <td>10</td>\n",
" <td>123256215</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>G</td>\n",
" <td>100.00</td>\n",
" <td>PASS</td>\n",
" <td>GENE=FGFR2;INHERITANCE=AD;MIM=101600</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>1/0:1,0:1:3:0,3,39</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>G-T</td>\n",
" <td>T-T</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>268101 rows × 18 columns</p>\n",
"</div>"
],
"text/plain": [
" index #CHROM POS ID REF ALT QUAL \\\n",
"0 6 1 63735 . CCTA C 193.23 \n",
"1 12 1 745370 rs146246821 TA T 510.54 \n",
"2 13 1 752566 rs3094315 G A 118.67 \n",
"3 14 1 752721 rs3131972 A G 242.70 \n",
"4 17 1 758324 rs3131955 T C 45.77 \n",
"5 18 1 780027 rs2977613 G T 47.01 \n",
"6 19 1 808631 rs11240779 G A 1853.99 \n",
"7 25 1 812267 rs7541694 A G 385.67 \n",
"8 26 1 812284 rs7545373 C G 428.75 \n",
"9 27 1 823790 rs143626389 G A 38.82 \n",
"10 28 1 834832 rs4411087 G C 48.77 \n",
"11 29 1 849998 rs13303222 A G 45.77 \n",
"12 30 1 851757 rs62677860 A G 63.22 \n",
"13 31 1 861808 rs13302982 A G 66.22 \n",
"14 32 1 862866 rs3892970 C T 31.26 \n",
"15 33 1 866319 rs9988021 G A 825.39 \n",
"16 34 1 866511 rs60722469 C CCCCT 325.15 \n",
"17 35 1 866920 rs2341361 A G 47.01 \n",
"18 36 1 867584 rs2341360 A T 47.01 \n",
"19 37 1 869323 rs13303207 T C 69.22 \n",
"20 40 1 870903 rs13303094 T C 183.66 \n",
"21 41 1 871334 rs4072383 G T 74.01 \n",
"22 42 1 873558 rs1110052 G T 39.01 \n",
"23 43 1 876499 rs4372192 A G 200.89 \n",
"24 44 1 878784 rs142929357 C G 125.24 \n",
"25 45 1 879317 rs7523549 C T 388.57 \n",
"26 46 1 879482 rs149880798 G C 799.55 \n",
"27 47 1 879676 rs6605067 G A 432.72 \n",
"28 48 1 879687 rs2839 T C 335.22 \n",
"29 49 1 880238 rs3748592 A G 516.84 \n",
"... ... ... ... ... ... ... ... \n",
"268071 299643 GL000225.1 64237 . A G 152.14 \n",
"268072 299706 GL000225.1 67508 . GT G 229.23 \n",
"268073 299713 GL000225.1 71934 . A G 62.01 \n",
"268074 299714 GL000225.1 71966 . A G 138.21 \n",
"268075 299715 GL000225.1 72003 . T C 119.76 \n",
"268076 299716 GL000225.1 72057 . C T 75.26 \n",
"268077 299717 GL000225.1 72073 . A T 37.25 \n",
"268078 299718 GL000225.1 72104 . A G 74.02 \n",
"268079 299723 GL000225.1 72249 . A G 37.77 \n",
"268080 299734 GL000225.1 72555 . T C 123.67 \n",
"268081 299735 GL000225.1 72582 . A G 202.89 \n",
"268082 299778 GL000225.1 78642 . A G 32.77 \n",
"268083 299860 GL000225.1 89058 . T C 47.01 \n",
"268084 299876 GL000225.1 89930 . A T 139.54 \n",
"268085 299909 GL000225.1 96661 . A G 40.01 \n",
"268086 299927 GL000225.1 114739 . T TC 679.82 \n",
"268087 299992 GL000225.1 143836 . T C 117.52 \n",
"268088 299993 GL000225.1 143849 . A G 117.52 \n",
"268089 300006 GL000225.1 198637 . C T 80.98 \n",
"268090 300007 GL000225.1 198643 . A G 86.98 \n",
"268091 300008 GL000225.1 202533 . C T 46.77 \n",
"268092 300009 GL000225.1 203673 . C T 78.22 \n",
"268093 300022 GL000192.1 139953 . CTG C 1104.53 \n",
"268094 300023 GL000192.1 160087 . C T 157.22 \n",
"268095 300029 GL000192.1 272061 . C CT 125.59 \n",
"268096 300030 GL000192.1 311575 . C T 248.50 \n",
"268097 300032 GL000192.1 313701 . T C 120.67 \n",
"268098 300033 GL000192.1 337826 . TA T 489.51 \n",
"268099 300034 GL000192.1 394140 . A G 45.26 \n",
"268100 300035 10 123256215 . T G 100.00 \n",
"\n",
" FILTER INFO \\\n",
"0 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F... \n",
"1 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64... \n",
"2 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00... \n",
"3 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00... \n",
"4 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... \n",
"5 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"6 PASS ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0.... \n",
"7 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... \n",
"8 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... \n",
"9 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3... \n",
"10 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... \n",
"11 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... \n",
"12 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00... \n",
"13 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... \n",
"14 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0.... \n",
"15 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=24;Dels=0.0... \n",
"16 PASS AC=6;AF=0.750;AN=8;BaseQRankSum=0.747;DB;DP=15... \n",
"17 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"18 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"19 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... \n",
"20 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=6;Dels=0.00... \n",
"21 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;Base... \n",
"22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"23 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=6;Dels=0.00... \n",
"24 PASS ABHet=0.583;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... \n",
"25 PASS ABHet=0.493;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... \n",
"26 PASS ABHet=0.592;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... \n",
"27 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=12;Dels=0.0... \n",
"28 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0... \n",
"29 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.0... \n",
"... ... ... \n",
"268071 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DP=5;Dels=0.00;FS... \n",
"268072 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-0.742;DP=13;F... \n",
"268073 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268074 PASS ABHet=0.333;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268075 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=5;Dels=0.00;FS... \n",
"268076 PASS ABHet=0.500;ABHom=1.00;AC=5;AF=0.833;AN=6;Base... \n",
"268077 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268078 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268079 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... \n",
"268080 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS... \n",
"268081 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DP=8;Dels=0.00;FS... \n",
"268082 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... \n",
"268083 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS... \n",
"268084 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DP=5;Dels=0.00;FS... \n",
"268085 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS... \n",
"268086 PASS AC=7;AF=0.875;AN=8;BaseQRankSum=3.317;DP=23;FS... \n",
"268087 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS... \n",
"268088 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS... \n",
"268089 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS... \n",
"268090 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS... \n",
"268091 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... \n",
"268092 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS... \n",
"268093 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-3.358;DP=66;F... \n",
"268094 PASS ABHet=0.625;ABHom=1.00;AC=6;AF=0.750;AN=8;Base... \n",
"268095 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-0.058;DP=33;F... \n",
"268096 PASS ABHet=0.333;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... \n",
"268097 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS... \n",
"268098 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=-3.725;DP=62;F... \n",
"268099 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.7... \n",
"268100 PASS GENE=FGFR2;INHERITANCE=AD;MIM=101600 \n",
"\n",
" FORMAT ISDBM322015 ISDBM322016 \\\n",
"0 GT:AD:DP:GQ:PL ./. 1/1:6,2:4:6:116,6,0 \n",
"1 GT:AD:DP:GQ:PL 0/1:4,1:5:32:32,0,185 0/1:17,4:18:99:132,0,623 \n",
"2 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:79,6,0 \n",
"3 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:80,6,0 \n",
"4 GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 ./. \n",
"5 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 ./. \n",
"6 GT:AD:DP:GQ:PL 1/1:0,7:7:21:223,21,0 1/1:0,16:16:48:602,48,0 \n",
"7 GT:AD:DP:GQ:PL 1/1:0,3:3:9:95,9,0 1/1:0,5:5:15:175,15,0 \n",
"8 GT:AD:DP:GQ:PL 1/1:0,5:5:15:185,15,0 1/1:0,4:4:12:148,12,0 \n",
"9 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:75,6,0 \n",
"10 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:80,6,0 \n",
"11 GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 ./. \n",
"12 GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 1/1:0,2:2:3:28,3,0 \n",
"13 GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 ./. \n",
"14 GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 0/0:1,0:1:3:0,3,40 \n",
"15 GT:AD:DP:GQ:PL 1/1:0,11:11:33:427,33,0 1/1:0,7:7:18:228,18,0 \n",
"16 GT:AD:DP:GQ:PL 1/1:5,5:10:15:278,15,0 1/1:3,0:3:3:32,3,0 \n",
"17 GT:AD:DP:GQ:PL ./. ./. \n",
"18 GT:AD:DP:GQ:PL ./. ./. \n",
"19 GT:AD:DP:GQ:PL ./. ./. \n",
"20 GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 1/1:0,2:2:6:79,6,0 \n",
"21 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:63,6,0 \n",
"22 GT:AD:DP:GQ:PL 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:33,3,0 \n",
"23 GT:AD:DP:GQ:PL 1/1:0,4:4:12:160,12,0 1/1:0,2:2:6:76,6,0 \n",
"24 GT:AD:DP:GQ:PL 0/0:16,0:16:45:0,45,553 0/1:4,4:8:99:136,0,113 \n",
"25 GT:AD:DP:GQ:PL 0/1:15,8:23:99:243,0,369 0/0:7,0:7:21:0,21,252 \n",
"26 GT:AD:DP:GQ:PL 0/1:27,20:47:99:584,0,841 0/0:33,0:33:93:0,93,1155 \n",
"27 GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 1/1:0,3:3:9:120,9,0 \n",
"28 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,3:3:9:114,9,0 \n",
"29 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,5:5:15:199,15,0 \n",
"... ... ... ... \n",
"268071 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. \n",
"268072 GT:AD:DP:GQ:PL 0/1:1,6:4:40:136,0,40 1/1:1,1:2:3:47,3,0 \n",
"268073 GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. \n",
"268074 GT:AD:DP:GQ:PL 1/1:0,3:3:9:113,9,0 ./. \n",
"268075 GT:AD:DP:GQ:PL 1/1:0,4:4:9:114,9,0 ./. \n",
"268076 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 ./. \n",
"268077 GT:AD:DP:GQ:PL ./. ./. \n",
"268078 GT:AD:DP:GQ:PL ./. ./. \n",
"268079 GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. \n",
"268080 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:79,6,0 \n",
"268081 GT:AD:DP:GQ:PL 1/1:0,4:4:9:111,9,0 1/1:0,2:2:6:61,6,0 \n",
"268082 GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 ./. \n",
"268083 GT:AD:DP:GQ:PL ./. 1/1:0,2:2:3:40,3,0 \n",
"268084 GT:AD:DP:GQ:PL 1/1:0,1:1:3:39,3,0 1/1:0,2:2:6:72,6,0 \n",
"268085 GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:33,3,0 \n",
"268086 GT:AD:DP:GQ:PL 1/1:0,5:5:15:209,15,0 1/1:0,6:6:18:260,18,0 \n",
"268087 GT:AD:DP:GQ:PL 1/1:0,4:4:12:150,12,0 ./. \n",
"268088 GT:AD:DP:GQ:PL 1/1:0,4:4:12:150,12,0 ./. \n",
"268089 GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:113,9,0 \n",
"268090 GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:119,9,0 \n",
"268091 GT:AD:DP:GQ:PL ./. ./. \n",
"268092 GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 1/1:0,1:1:3:32,3,0 \n",
"268093 GT:AD:DP:GQ:PL 1/1:7,18:20:51:677,51,0 0/1:9,6:10:33:204,0,33 \n",
"268094 GT:AD:DP:GQ:PL 0/1:2,2:4:52:60,0,52 0/1:3,1:4:25:25,0,105 \n",
"268095 GT:AD:DP:GQ:PL 0/0:5,0:4:9:0,9,93 0/1:5,4:7:12:107,0,12 \n",
"268096 GT:AD:DP:GQ:PL 0/0:2,0:2:3:0,3,39 0/1:3,6:9:93:212,0,93 \n",
"268097 GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:40,3,0 \n",
"268098 GT:AD:DP:GQ:PL 0/0:18,0:18:51:0,51,855 0/0:13,0:13:39:0,39,695 \n",
"268099 GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,39 \n",
"268100 GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 \n",
"\n",
" ISDBM322017 ISDBM322018 \\\n",
"0 0/1:8,4:8:99:128,0,301 0/0:18,2:15:30:0,30,666 \n",
"1 0/1:9,7:16:99:273,0,395 0/1:16,4:19:99:125,0,661 \n",
"2 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:36,3,0 \n",
"3 1/1:0,4:4:12:159,12,0 1/1:0,1:1:3:40,3,0 \n",
"4 ./. ./. \n",
"5 1/1:0,1:1:3:40,3,0 ./. \n",
"6 1/1:0,13:13:36:457,36,0 1/1:0,16:16:48:611,48,0 \n",
"7 1/1:0,2:2:6:55,6,0 1/1:0,3:3:9:99,9,0 \n",
"8 1/1:0,2:2:6:55,6,0 1/1:0,2:2:6:79,6,0 \n",
"9 ./. 0/0:3,0:3:9:0,9,99 \n",
"10 ./. ./. \n",
"11 ./. ./. \n",
"12 ./. ./. \n",
"13 ./. 1/1:0,1:1:3:36,3,0 \n",
"14 ./. ./. \n",
"15 1/1:0,4:4:12:133,12,0 1/1:0,2:2:6:76,6,0 \n",
"16 0/0:1,0:1:3:0,3,65 1/1:0,1:1:3:67,3,0 \n",
"17 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 \n",
"18 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 \n",
"19 1/1:0,2:2:6:73,6,0 1/1:0,1:1:3:30,3,0 \n",
"20 ./. 1/1:0,2:2:6:79,6,0 \n",
"21 0/0:3,0:3:9:0,9,120 0/1:2,2:4:52:52,0,68 \n",
"22 ./. ./. \n",
"23 ./. ./. \n",
"24 0/1:2,1:3:30:30,0,57 0/0:2,0:2:6:0,6,66 \n",
"25 0/0:12,0:12:36:0,36,405 0/1:3,6:9:64:187,0,64 \n",
"26 0/0:19,0:19:51:0,51,650 0/1:14,9:23:99:257,0,389 \n",
"27 1/1:0,3:3:9:120,9,0 1/1:0,4:4:12:158,12,0 \n",
"28 1/1:0,2:2:6:80,6,0 1/1:0,4:4:12:139,12,0 \n",
"29 1/1:0,3:3:9:120,9,0 1/1:0,5:5:15:196,15,0 \n",
"... ... ... \n",
"268071 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:78,6,0 \n",
"268072 ./. 1/1:0,4:2:6:94,6,0 \n",
"268073 ./. 0/1:1,1:2:28:28,0,33 \n",
"268074 ./. 0/1:1,2:3:30:62,0,30 \n",
"268075 ./. 1/1:0,1:1:3:40,3,0 \n",
"268076 1/1:0,1:1:3:40,3,0 0/1:1,1:2:26:33,0,26 \n",
"268077 1/1:0,1:1:3:39,3,0 0/1:1,1:2:30:33,0,30 \n",
"268078 1/1:0,2:2:6:77,6,0 0/1:1,1:2:24:33,0,24 \n",
"268079 ./. ./. \n",
"268080 1/1:0,1:1:3:40,3,0 ./. \n",
"268081 1/1:0,1:1:3:35,3,0 1/1:0,1:1:3:33,3,0 \n",
"268082 ./. ./. \n",
"268083 1/1:0,1:1:3:40,3,0 ./. \n",
"268084 1/1:0,1:1:3:30,3,0 1/1:0,1:1:3:35,3,0 \n",
"268085 ./. ./. \n",
"268086 1/1:0,4:4:12:158,12,0 0/1:5,3:8:99:106,0,182 \n",
"268087 ./. ./. \n",
"268088 ./. ./. \n",
"268089 ./. ./. \n",
"268090 ./. ./. \n",
"268091 ./. 1/1:0,2:2:6:78,6,0 \n",
"268092 ./. ./. \n",
"268093 0/1:8,7:10:19:280,0,19 0/0:6,0:6:9:0,9,141 \n",
"268094 1/1:0,2:2:6:78,6,0 1/1:0,1:1:3:37,3,0 \n",
"268095 0/1:9,2:3:18:53,0,18 0/1:6,1:4:17:17,0,69 \n",
"268096 1/1:0,2:2:6:80,6,0 0/0:5,0:5:15:0,15,181 \n",
"268097 1/1:0,1:1:3:39,3,0 1/1:0,2:2:6:77,6,0 \n",
"268098 0/1:5,10:15:99:438,0,228 0/1:13,3:16:99:102,0,647 \n",
"268099 ./. 1/1:0,2:2:6:80,6,0 \n",
"268100 1/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 \n",
"\n",
" ISDBM322015 genotype ISDBM322016 genotype ISDBM322017 genotype \\\n",
"0 - C-C CCTA-C \n",
"1 TA-T TA-T TA-T \n",
"2 - A-A A-A \n",
"3 - G-G G-G \n",
"4 C-C - - \n",
"5 T-T - T-T \n",
"6 A-A A-A A-A \n",
"7 G-G G-G G-G \n",
"8 G-G G-G G-G \n",
"9 - A-A - \n",
"10 - C-C - \n",
"11 G-G - - \n",
"12 G-G G-G - \n",
"13 G-G - - \n",
"14 T-T C-C - \n",
"15 A-A A-A A-A \n",
"16 CCCCT-CCCCT CCCCT-CCCCT C-C \n",
"17 - - G-G \n",
"18 - - T-T \n",
"19 - - C-C \n",
"20 C-C C-C - \n",
"21 - T-T G-G \n",
"22 T-T T-T - \n",
"23 G-G G-G - \n",
"24 C-C C-G C-G \n",
"25 C-T C-C C-C \n",
"26 G-C G-G G-G \n",
"27 A-A A-A A-A \n",
"28 C-C C-C C-C \n",
"29 G-G G-G G-G \n",
"... ... ... ... \n",
"268071 G-G - G-G \n",
"268072 GT-G G-G - \n",
"268073 G-G - - \n",
"268074 G-G - - \n",
"268075 C-C - - \n",
"268076 T-T - T-T \n",
"268077 - - T-T \n",
"268078 - - G-G \n",
"268079 G-G - - \n",
"268080 C-C C-C C-C \n",
"268081 G-G G-G G-G \n",
"268082 G-G - - \n",
"268083 - C-C C-C \n",
"268084 T-T T-T T-T \n",
"268085 G-G G-G - \n",
"268086 TC-TC TC-TC TC-TC \n",
"268087 C-C - - \n",
"268088 G-G - - \n",
"268089 - T-T - \n",
"268090 - G-G - \n",
"268091 - - - \n",
"268092 T-T T-T - \n",
"268093 C-C CTG-C CTG-C \n",
"268094 C-T C-T T-T \n",
"268095 C-C C-CT C-CT \n",
"268096 C-C C-T T-T \n",
"268097 - C-C C-C \n",
"268098 TA-TA TA-TA TA-T \n",
"268099 - A-A - \n",
"268100 T-T T-T G-T \n",
"\n",
" ISDBM322018 genotype \n",
"0 CCTA-CCTA \n",
"1 TA-T \n",
"2 A-A \n",
"3 G-G \n",
"4 - \n",
"5 - \n",
"6 A-A \n",
"7 G-G \n",
"8 G-G \n",
"9 G-G \n",
"10 - \n",
"11 - \n",
"12 - \n",
"13 G-G \n",
"14 - \n",
"15 A-A \n",
"16 CCCCT-CCCCT \n",
"17 G-G \n",
"18 T-T \n",
"19 C-C \n",
"20 C-C \n",
"21 G-T \n",
"22 - \n",
"23 - \n",
"24 C-C \n",
"25 C-T \n",
"26 G-C \n",
"27 A-A \n",
"28 C-C \n",
"29 G-G \n",
"... ... \n",
"268071 G-G \n",
"268072 G-G \n",
"268073 A-G \n",
"268074 A-G \n",
"268075 C-C \n",
"268076 C-T \n",
"268077 A-T \n",
"268078 A-G \n",
"268079 - \n",
"268080 - \n",
"268081 G-G \n",
"268082 - \n",
"268083 - \n",
"268084 T-T \n",
"268085 - \n",
"268086 T-TC \n",
"268087 - \n",
"268088 - \n",
"268089 - \n",
"268090 - \n",
"268091 T-T \n",
"268092 - \n",
"268093 CTG-CTG \n",
"268094 T-T \n",
"268095 C-CT \n",
"268096 C-C \n",
"268097 C-C \n",
"268098 TA-T \n",
"268099 G-G \n",
"268100 T-T \n",
"\n",
"[268101 rows x 18 columns]"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dfc[sample_ids_genotype] = genotypes\n",
"dfc"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 유전자형을 숫자로 추가하기 (AA: 0, AB: 1, BB:2)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>index</th>\n",
" <th>#CHROM</th>\n",
" <th>POS</th>\n",
" <th>ID</th>\n",
" <th>REF</th>\n",
" <th>ALT</th>\n",
" <th>QUAL</th>\n",
" <th>FILTER</th>\n",
" <th>INFO</th>\n",
" <th>FORMAT</th>\n",
" <th>...</th>\n",
" <th>ISDBM322017</th>\n",
" <th>ISDBM322018</th>\n",
" <th>ISDBM322015 genotype</th>\n",
" <th>ISDBM322016 genotype</th>\n",
" <th>ISDBM322017 genotype</th>\n",
" <th>ISDBM322018 genotype</th>\n",
" <th>ISDBM322015 num</th>\n",
" <th>ISDBM322016 num</th>\n",
" <th>ISDBM322017 num</th>\n",
" <th>ISDBM322018 num</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>6</td>\n",
" <td>1</td>\n",
" <td>63735</td>\n",
" <td>.</td>\n",
" <td>CCTA</td>\n",
" <td>C</td>\n",
" <td>193.23</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:8,4:8:99:128,0,301</td>\n",
" <td>0/0:18,2:15:30:0,30,666</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>CCTA-C</td>\n",
" <td>CCTA-CCTA</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>12</td>\n",
" <td>1</td>\n",
" <td>745370</td>\n",
" <td>rs146246821</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>510.54</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:9,7:16:99:273,0,395</td>\n",
" <td>0/1:16,4:19:99:125,0,661</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>13</td>\n",
" <td>1</td>\n",
" <td>752566</td>\n",
" <td>rs3094315</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>118.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>14</td>\n",
" <td>1</td>\n",
" <td>752721</td>\n",
" <td>rs3131972</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>242.70</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,4:4:12:159,12,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>17</td>\n",
" <td>1</td>\n",
" <td>758324</td>\n",
" <td>rs3131955</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>18</td>\n",
" <td>1</td>\n",
" <td>780027</td>\n",
" <td>rs2977613</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>19</td>\n",
" <td>1</td>\n",
" <td>808631</td>\n",
" <td>rs11240779</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>1853.99</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,13:13:36:457,36,0</td>\n",
" <td>1/1:0,16:16:48:611,48,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>25</td>\n",
" <td>1</td>\n",
" <td>812267</td>\n",
" <td>rs7541694</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>385.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,3:3:9:99,9,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>26</td>\n",
" <td>1</td>\n",
" <td>812284</td>\n",
" <td>rs7545373</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>428.75</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>27</td>\n",
" <td>1</td>\n",
" <td>823790</td>\n",
" <td>rs143626389</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>38.82</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>0/0:3,0:3:9:0,9,99</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>28</td>\n",
" <td>1</td>\n",
" <td>834832</td>\n",
" <td>rs4411087</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>48.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>29</td>\n",
" <td>1</td>\n",
" <td>849998</td>\n",
" <td>rs13303222</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>30</td>\n",
" <td>1</td>\n",
" <td>851757</td>\n",
" <td>rs62677860</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>63.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>31</td>\n",
" <td>1</td>\n",
" <td>861808</td>\n",
" <td>rs13302982</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>66.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>32</td>\n",
" <td>1</td>\n",
" <td>862866</td>\n",
" <td>rs3892970</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>31.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>33</td>\n",
" <td>1</td>\n",
" <td>866319</td>\n",
" <td>rs9988021</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>825.39</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=24;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,4:4:12:133,12,0</td>\n",
" <td>1/1:0,2:2:6:76,6,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>34</td>\n",
" <td>1</td>\n",
" <td>866511</td>\n",
" <td>rs60722469</td>\n",
" <td>C</td>\n",
" <td>CCCCT</td>\n",
" <td>325.15</td>\n",
" <td>PASS</td>\n",
" <td>AC=6;AF=0.750;AN=8;BaseQRankSum=0.747;DB;DP=15...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:1,0:1:3:0,3,65</td>\n",
" <td>1/1:0,1:1:3:67,3,0</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>C-C</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>35</td>\n",
" <td>1</td>\n",
" <td>866920</td>\n",
" <td>rs2341361</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>36</td>\n",
" <td>1</td>\n",
" <td>867584</td>\n",
" <td>rs2341360</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>37</td>\n",
" <td>1</td>\n",
" <td>869323</td>\n",
" <td>rs13303207</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>69.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:73,6,0</td>\n",
" <td>1/1:0,1:1:3:30,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>40</td>\n",
" <td>1</td>\n",
" <td>870903</td>\n",
" <td>rs13303094</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>183.66</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=6;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>41</td>\n",
" <td>1</td>\n",
" <td>871334</td>\n",
" <td>rs4072383</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>74.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:3,0:3:9:0,9,120</td>\n",
" <td>0/1:2,2:4:52:52,0,68</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>G-G</td>\n",
" <td>G-T</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>42</td>\n",
" <td>1</td>\n",
" <td>873558</td>\n",
" <td>rs1110052</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>39.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>43</td>\n",
" <td>1</td>\n",
" <td>876499</td>\n",
" <td>rs4372192</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>200.89</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=6;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>44</td>\n",
" <td>1</td>\n",
" <td>878784</td>\n",
" <td>rs142929357</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>125.24</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.583;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:2,1:3:30:30,0,57</td>\n",
" <td>0/0:2,0:2:6:0,6,66</td>\n",
" <td>C-C</td>\n",
" <td>C-G</td>\n",
" <td>C-G</td>\n",
" <td>C-C</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>45</td>\n",
" <td>1</td>\n",
" <td>879317</td>\n",
" <td>rs7523549</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>388.57</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.493;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:12,0:12:36:0,36,405</td>\n",
" <td>0/1:3,6:9:64:187,0,64</td>\n",
" <td>C-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>46</td>\n",
" <td>1</td>\n",
" <td>879482</td>\n",
" <td>rs149880798</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>799.55</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.592;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:19,0:19:51:0,51,650</td>\n",
" <td>0/1:14,9:23:99:257,0,389</td>\n",
" <td>G-C</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-C</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>47</td>\n",
" <td>1</td>\n",
" <td>879676</td>\n",
" <td>rs6605067</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>432.72</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=12;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,4:4:12:158,12,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>48</td>\n",
" <td>1</td>\n",
" <td>879687</td>\n",
" <td>rs2839</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>335.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,4:4:12:139,12,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>49</td>\n",
" <td>1</td>\n",
" <td>880238</td>\n",
" <td>rs3748592</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>516.84</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,5:5:15:196,15,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268071</th>\n",
" <td>299643</td>\n",
" <td>GL000225.1</td>\n",
" <td>64237</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>152.14</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=5;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268072</th>\n",
" <td>299706</td>\n",
" <td>GL000225.1</td>\n",
" <td>67508</td>\n",
" <td>.</td>\n",
" <td>GT</td>\n",
" <td>G</td>\n",
" <td>229.23</td>\n",
" <td>PASS</td>\n",
" <td>AC=5;AF=0.833;AN=6;BaseQRankSum=-0.742;DP=13;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,4:2:6:94,6,0</td>\n",
" <td>GT-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>1.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268073</th>\n",
" <td>299713</td>\n",
" <td>GL000225.1</td>\n",
" <td>71934</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>62.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>0/1:1,1:2:28:28,0,33</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-G</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268074</th>\n",
" <td>299714</td>\n",
" <td>GL000225.1</td>\n",
" <td>71966</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>138.21</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.333;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>0/1:1,2:3:30:62,0,30</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-G</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268075</th>\n",
" <td>299715</td>\n",
" <td>GL000225.1</td>\n",
" <td>72003</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>119.76</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=5;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268076</th>\n",
" <td>299716</td>\n",
" <td>GL000225.1</td>\n",
" <td>72057</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>75.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=5;AF=0.833;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>0/1:1,1:2:26:33,0,26</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>C-T</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268077</th>\n",
" <td>299717</td>\n",
" <td>GL000225.1</td>\n",
" <td>72073</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>37.25</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>0/1:1,1:2:30:33,0,30</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>A-T</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268078</th>\n",
" <td>299718</td>\n",
" <td>GL000225.1</td>\n",
" <td>72104</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>74.02</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>0/1:1,1:2:24:33,0,24</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>A-G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268079</th>\n",
" <td>299723</td>\n",
" <td>GL000225.1</td>\n",
" <td>72249</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>37.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268080</th>\n",
" <td>299734</td>\n",
" <td>GL000225.1</td>\n",
" <td>72555</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>123.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268081</th>\n",
" <td>299735</td>\n",
" <td>GL000225.1</td>\n",
" <td>72582</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>202.89</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DP=8;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:35,3,0</td>\n",
" <td>1/1:0,1:1:3:33,3,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268082</th>\n",
" <td>299778</td>\n",
" <td>GL000225.1</td>\n",
" <td>78642</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>32.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268083</th>\n",
" <td>299860</td>\n",
" <td>GL000225.1</td>\n",
" <td>89058</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268084</th>\n",
" <td>299876</td>\n",
" <td>GL000225.1</td>\n",
" <td>89930</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>139.54</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DP=5;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:30,3,0</td>\n",
" <td>1/1:0,1:1:3:35,3,0</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268085</th>\n",
" <td>299909</td>\n",
" <td>GL000225.1</td>\n",
" <td>96661</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>40.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268086</th>\n",
" <td>299927</td>\n",
" <td>GL000225.1</td>\n",
" <td>114739</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>TC</td>\n",
" <td>679.82</td>\n",
" <td>PASS</td>\n",
" <td>AC=7;AF=0.875;AN=8;BaseQRankSum=3.317;DP=23;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,4:4:12:158,12,0</td>\n",
" <td>0/1:5,3:8:99:106,0,182</td>\n",
" <td>TC-TC</td>\n",
" <td>TC-TC</td>\n",
" <td>TC-TC</td>\n",
" <td>T-TC</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268087</th>\n",
" <td>299992</td>\n",
" <td>GL000225.1</td>\n",
" <td>143836</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>117.52</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268088</th>\n",
" <td>299993</td>\n",
" <td>GL000225.1</td>\n",
" <td>143849</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>117.52</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268089</th>\n",
" <td>300006</td>\n",
" <td>GL000225.1</td>\n",
" <td>198637</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>80.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268090</th>\n",
" <td>300007</td>\n",
" <td>GL000225.1</td>\n",
" <td>198643</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>86.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268091</th>\n",
" <td>300008</td>\n",
" <td>GL000225.1</td>\n",
" <td>202533</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>46.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268092</th>\n",
" <td>300009</td>\n",
" <td>GL000225.1</td>\n",
" <td>203673</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>78.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268093</th>\n",
" <td>300022</td>\n",
" <td>GL000192.1</td>\n",
" <td>139953</td>\n",
" <td>.</td>\n",
" <td>CTG</td>\n",
" <td>C</td>\n",
" <td>1104.53</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=-3.358;DP=66;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:8,7:10:19:280,0,19</td>\n",
" <td>0/0:6,0:6:9:0,9,141</td>\n",
" <td>C-C</td>\n",
" <td>CTG-C</td>\n",
" <td>CTG-C</td>\n",
" <td>CTG-CTG</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268094</th>\n",
" <td>300023</td>\n",
" <td>GL000192.1</td>\n",
" <td>160087</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>157.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.625;ABHom=1.00;AC=6;AF=0.750;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:78,6,0</td>\n",
" <td>1/1:0,1:1:3:37,3,0</td>\n",
" <td>C-T</td>\n",
" <td>C-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268095</th>\n",
" <td>300029</td>\n",
" <td>GL000192.1</td>\n",
" <td>272061</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>CT</td>\n",
" <td>125.59</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.375;AN=8;BaseQRankSum=-0.058;DP=33;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:9,2:3:18:53,0,18</td>\n",
" <td>0/1:6,1:4:17:17,0,69</td>\n",
" <td>C-C</td>\n",
" <td>C-CT</td>\n",
" <td>C-CT</td>\n",
" <td>C-CT</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268096</th>\n",
" <td>300030</td>\n",
" <td>GL000192.1</td>\n",
" <td>311575</td>\n",
" <td>.</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>248.50</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.333;ABHom=1.00;AC=3;AF=0.375;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>0/0:5,0:5:15:0,15,181</td>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268097</th>\n",
" <td>300032</td>\n",
" <td>GL000192.1</td>\n",
" <td>313701</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>120.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268098</th>\n",
" <td>300033</td>\n",
" <td>GL000192.1</td>\n",
" <td>337826</td>\n",
" <td>.</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>489.51</td>\n",
" <td>PASS</td>\n",
" <td>AC=2;AF=0.250;AN=8;BaseQRankSum=-3.725;DP=62;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:5,10:15:99:438,0,228</td>\n",
" <td>0/1:13,3:16:99:102,0,647</td>\n",
" <td>TA-TA</td>\n",
" <td>TA-TA</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268099</th>\n",
" <td>300034</td>\n",
" <td>GL000192.1</td>\n",
" <td>394140</td>\n",
" <td>.</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.7...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268100</th>\n",
" <td>300035</td>\n",
" <td>10</td>\n",
" <td>123256215</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>G</td>\n",
" <td>100.00</td>\n",
" <td>PASS</td>\n",
" <td>GENE=FGFR2;INHERITANCE=AD;MIM=101600</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/0:1,0:1:3:0,3,39</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>G-T</td>\n",
" <td>T-T</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>268101 rows × 22 columns</p>\n",
"</div>"
],
"text/plain": [
" index #CHROM POS ID REF ALT QUAL \\\n",
"0 6 1 63735 . CCTA C 193.23 \n",
"1 12 1 745370 rs146246821 TA T 510.54 \n",
"2 13 1 752566 rs3094315 G A 118.67 \n",
"3 14 1 752721 rs3131972 A G 242.70 \n",
"4 17 1 758324 rs3131955 T C 45.77 \n",
"5 18 1 780027 rs2977613 G T 47.01 \n",
"6 19 1 808631 rs11240779 G A 1853.99 \n",
"7 25 1 812267 rs7541694 A G 385.67 \n",
"8 26 1 812284 rs7545373 C G 428.75 \n",
"9 27 1 823790 rs143626389 G A 38.82 \n",
"10 28 1 834832 rs4411087 G C 48.77 \n",
"11 29 1 849998 rs13303222 A G 45.77 \n",
"12 30 1 851757 rs62677860 A G 63.22 \n",
"13 31 1 861808 rs13302982 A G 66.22 \n",
"14 32 1 862866 rs3892970 C T 31.26 \n",
"15 33 1 866319 rs9988021 G A 825.39 \n",
"16 34 1 866511 rs60722469 C CCCCT 325.15 \n",
"17 35 1 866920 rs2341361 A G 47.01 \n",
"18 36 1 867584 rs2341360 A T 47.01 \n",
"19 37 1 869323 rs13303207 T C 69.22 \n",
"20 40 1 870903 rs13303094 T C 183.66 \n",
"21 41 1 871334 rs4072383 G T 74.01 \n",
"22 42 1 873558 rs1110052 G T 39.01 \n",
"23 43 1 876499 rs4372192 A G 200.89 \n",
"24 44 1 878784 rs142929357 C G 125.24 \n",
"25 45 1 879317 rs7523549 C T 388.57 \n",
"26 46 1 879482 rs149880798 G C 799.55 \n",
"27 47 1 879676 rs6605067 G A 432.72 \n",
"28 48 1 879687 rs2839 T C 335.22 \n",
"29 49 1 880238 rs3748592 A G 516.84 \n",
"... ... ... ... ... ... ... ... \n",
"268071 299643 GL000225.1 64237 . A G 152.14 \n",
"268072 299706 GL000225.1 67508 . GT G 229.23 \n",
"268073 299713 GL000225.1 71934 . A G 62.01 \n",
"268074 299714 GL000225.1 71966 . A G 138.21 \n",
"268075 299715 GL000225.1 72003 . T C 119.76 \n",
"268076 299716 GL000225.1 72057 . C T 75.26 \n",
"268077 299717 GL000225.1 72073 . A T 37.25 \n",
"268078 299718 GL000225.1 72104 . A G 74.02 \n",
"268079 299723 GL000225.1 72249 . A G 37.77 \n",
"268080 299734 GL000225.1 72555 . T C 123.67 \n",
"268081 299735 GL000225.1 72582 . A G 202.89 \n",
"268082 299778 GL000225.1 78642 . A G 32.77 \n",
"268083 299860 GL000225.1 89058 . T C 47.01 \n",
"268084 299876 GL000225.1 89930 . A T 139.54 \n",
"268085 299909 GL000225.1 96661 . A G 40.01 \n",
"268086 299927 GL000225.1 114739 . T TC 679.82 \n",
"268087 299992 GL000225.1 143836 . T C 117.52 \n",
"268088 299993 GL000225.1 143849 . A G 117.52 \n",
"268089 300006 GL000225.1 198637 . C T 80.98 \n",
"268090 300007 GL000225.1 198643 . A G 86.98 \n",
"268091 300008 GL000225.1 202533 . C T 46.77 \n",
"268092 300009 GL000225.1 203673 . C T 78.22 \n",
"268093 300022 GL000192.1 139953 . CTG C 1104.53 \n",
"268094 300023 GL000192.1 160087 . C T 157.22 \n",
"268095 300029 GL000192.1 272061 . C CT 125.59 \n",
"268096 300030 GL000192.1 311575 . C T 248.50 \n",
"268097 300032 GL000192.1 313701 . T C 120.67 \n",
"268098 300033 GL000192.1 337826 . TA T 489.51 \n",
"268099 300034 GL000192.1 394140 . A G 45.26 \n",
"268100 300035 10 123256215 . T G 100.00 \n",
"\n",
" FILTER INFO \\\n",
"0 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F... \n",
"1 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64... \n",
"2 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00... \n",
"3 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00... \n",
"4 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... \n",
"5 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"6 PASS ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0.... \n",
"7 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... \n",
"8 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... \n",
"9 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3... \n",
"10 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... \n",
"11 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... \n",
"12 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00... \n",
"13 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... \n",
"14 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0.... \n",
"15 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=24;Dels=0.0... \n",
"16 PASS AC=6;AF=0.750;AN=8;BaseQRankSum=0.747;DB;DP=15... \n",
"17 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"18 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"19 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... \n",
"20 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=6;Dels=0.00... \n",
"21 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;Base... \n",
"22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... \n",
"23 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=6;Dels=0.00... \n",
"24 PASS ABHet=0.583;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... \n",
"25 PASS ABHet=0.493;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... \n",
"26 PASS ABHet=0.592;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... \n",
"27 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=12;Dels=0.0... \n",
"28 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0... \n",
"29 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.0... \n",
"... ... ... \n",
"268071 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DP=5;Dels=0.00;FS... \n",
"268072 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-0.742;DP=13;F... \n",
"268073 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268074 PASS ABHet=0.333;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268075 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=5;Dels=0.00;FS... \n",
"268076 PASS ABHet=0.500;ABHom=1.00;AC=5;AF=0.833;AN=6;Base... \n",
"268077 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268078 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;Base... \n",
"268079 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... \n",
"268080 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS... \n",
"268081 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DP=8;Dels=0.00;FS... \n",
"268082 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... \n",
"268083 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS... \n",
"268084 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DP=5;Dels=0.00;FS... \n",
"268085 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS... \n",
"268086 PASS AC=7;AF=0.875;AN=8;BaseQRankSum=3.317;DP=23;FS... \n",
"268087 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS... \n",
"268088 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS... \n",
"268089 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS... \n",
"268090 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS... \n",
"268091 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS... \n",
"268092 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DP=3;Dels=0.00;FS... \n",
"268093 PASS AC=4;AF=0.500;AN=8;BaseQRankSum=-3.358;DP=66;F... \n",
"268094 PASS ABHet=0.625;ABHom=1.00;AC=6;AF=0.750;AN=8;Base... \n",
"268095 PASS AC=3;AF=0.375;AN=8;BaseQRankSum=-0.058;DP=33;F... \n",
"268096 PASS ABHet=0.333;ABHom=1.00;AC=3;AF=0.375;AN=8;Base... \n",
"268097 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DP=4;Dels=0.00;FS... \n",
"268098 PASS AC=2;AF=0.250;AN=8;BaseQRankSum=-3.725;DP=62;F... \n",
"268099 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.7... \n",
"268100 PASS GENE=FGFR2;INHERITANCE=AD;MIM=101600 \n",
"\n",
" FORMAT ... ISDBM322017 \\\n",
"0 GT:AD:DP:GQ:PL ... 0/1:8,4:8:99:128,0,301 \n",
"1 GT:AD:DP:GQ:PL ... 0/1:9,7:16:99:273,0,395 \n",
"2 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:39,3,0 \n",
"3 GT:AD:DP:GQ:PL ... 1/1:0,4:4:12:159,12,0 \n",
"4 GT:AD:DP:GQ:PL ... ./. \n",
"5 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"6 GT:AD:DP:GQ:PL ... 1/1:0,13:13:36:457,36,0 \n",
"7 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:55,6,0 \n",
"8 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:55,6,0 \n",
"9 GT:AD:DP:GQ:PL ... ./. \n",
"10 GT:AD:DP:GQ:PL ... ./. \n",
"11 GT:AD:DP:GQ:PL ... ./. \n",
"12 GT:AD:DP:GQ:PL ... ./. \n",
"13 GT:AD:DP:GQ:PL ... ./. \n",
"14 GT:AD:DP:GQ:PL ... ./. \n",
"15 GT:AD:DP:GQ:PL ... 1/1:0,4:4:12:133,12,0 \n",
"16 GT:AD:DP:GQ:PL ... 0/0:1,0:1:3:0,3,65 \n",
"17 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"18 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"19 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:73,6,0 \n",
"20 GT:AD:DP:GQ:PL ... ./. \n",
"21 GT:AD:DP:GQ:PL ... 0/0:3,0:3:9:0,9,120 \n",
"22 GT:AD:DP:GQ:PL ... ./. \n",
"23 GT:AD:DP:GQ:PL ... ./. \n",
"24 GT:AD:DP:GQ:PL ... 0/1:2,1:3:30:30,0,57 \n",
"25 GT:AD:DP:GQ:PL ... 0/0:12,0:12:36:0,36,405 \n",
"26 GT:AD:DP:GQ:PL ... 0/0:19,0:19:51:0,51,650 \n",
"27 GT:AD:DP:GQ:PL ... 1/1:0,3:3:9:120,9,0 \n",
"28 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:80,6,0 \n",
"29 GT:AD:DP:GQ:PL ... 1/1:0,3:3:9:120,9,0 \n",
"... ... ... ... \n",
"268071 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"268072 GT:AD:DP:GQ:PL ... ./. \n",
"268073 GT:AD:DP:GQ:PL ... ./. \n",
"268074 GT:AD:DP:GQ:PL ... ./. \n",
"268075 GT:AD:DP:GQ:PL ... ./. \n",
"268076 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"268077 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:39,3,0 \n",
"268078 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:77,6,0 \n",
"268079 GT:AD:DP:GQ:PL ... ./. \n",
"268080 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"268081 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:35,3,0 \n",
"268082 GT:AD:DP:GQ:PL ... ./. \n",
"268083 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:40,3,0 \n",
"268084 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:30,3,0 \n",
"268085 GT:AD:DP:GQ:PL ... ./. \n",
"268086 GT:AD:DP:GQ:PL ... 1/1:0,4:4:12:158,12,0 \n",
"268087 GT:AD:DP:GQ:PL ... ./. \n",
"268088 GT:AD:DP:GQ:PL ... ./. \n",
"268089 GT:AD:DP:GQ:PL ... ./. \n",
"268090 GT:AD:DP:GQ:PL ... ./. \n",
"268091 GT:AD:DP:GQ:PL ... ./. \n",
"268092 GT:AD:DP:GQ:PL ... ./. \n",
"268093 GT:AD:DP:GQ:PL ... 0/1:8,7:10:19:280,0,19 \n",
"268094 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:78,6,0 \n",
"268095 GT:AD:DP:GQ:PL ... 0/1:9,2:3:18:53,0,18 \n",
"268096 GT:AD:DP:GQ:PL ... 1/1:0,2:2:6:80,6,0 \n",
"268097 GT:AD:DP:GQ:PL ... 1/1:0,1:1:3:39,3,0 \n",
"268098 GT:AD:DP:GQ:PL ... 0/1:5,10:15:99:438,0,228 \n",
"268099 GT:AD:DP:GQ:PL ... ./. \n",
"268100 GT:AD:DP:GQ:PL ... 1/0:1,0:1:3:0,3,39 \n",
"\n",
" ISDBM322018 ISDBM322015 genotype ISDBM322016 genotype \\\n",
"0 0/0:18,2:15:30:0,30,666 - C-C \n",
"1 0/1:16,4:19:99:125,0,661 TA-T TA-T \n",
"2 1/1:0,1:1:3:36,3,0 - A-A \n",
"3 1/1:0,1:1:3:40,3,0 - G-G \n",
"4 ./. C-C - \n",
"5 ./. T-T - \n",
"6 1/1:0,16:16:48:611,48,0 A-A A-A \n",
"7 1/1:0,3:3:9:99,9,0 G-G G-G \n",
"8 1/1:0,2:2:6:79,6,0 G-G G-G \n",
"9 0/0:3,0:3:9:0,9,99 - A-A \n",
"10 ./. - C-C \n",
"11 ./. G-G - \n",
"12 ./. G-G G-G \n",
"13 1/1:0,1:1:3:36,3,0 G-G - \n",
"14 ./. T-T C-C \n",
"15 1/1:0,2:2:6:76,6,0 A-A A-A \n",
"16 1/1:0,1:1:3:67,3,0 CCCCT-CCCCT CCCCT-CCCCT \n",
"17 1/1:0,1:1:3:40,3,0 - - \n",
"18 1/1:0,1:1:3:40,3,0 - - \n",
"19 1/1:0,1:1:3:30,3,0 - - \n",
"20 1/1:0,2:2:6:79,6,0 C-C C-C \n",
"21 0/1:2,2:4:52:52,0,68 - T-T \n",
"22 ./. T-T T-T \n",
"23 ./. G-G G-G \n",
"24 0/0:2,0:2:6:0,6,66 C-C C-G \n",
"25 0/1:3,6:9:64:187,0,64 C-T C-C \n",
"26 0/1:14,9:23:99:257,0,389 G-C G-G \n",
"27 1/1:0,4:4:12:158,12,0 A-A A-A \n",
"28 1/1:0,4:4:12:139,12,0 C-C C-C \n",
"29 1/1:0,5:5:15:196,15,0 G-G G-G \n",
"... ... ... ... \n",
"268071 1/1:0,2:2:6:78,6,0 G-G - \n",
"268072 1/1:0,4:2:6:94,6,0 GT-G G-G \n",
"268073 0/1:1,1:2:28:28,0,33 G-G - \n",
"268074 0/1:1,2:3:30:62,0,30 G-G - \n",
"268075 1/1:0,1:1:3:40,3,0 C-C - \n",
"268076 0/1:1,1:2:26:33,0,26 T-T - \n",
"268077 0/1:1,1:2:30:33,0,30 - - \n",
"268078 0/1:1,1:2:24:33,0,24 - - \n",
"268079 ./. G-G - \n",
"268080 ./. C-C C-C \n",
"268081 1/1:0,1:1:3:33,3,0 G-G G-G \n",
"268082 ./. G-G - \n",
"268083 ./. - C-C \n",
"268084 1/1:0,1:1:3:35,3,0 T-T T-T \n",
"268085 ./. G-G G-G \n",
"268086 0/1:5,3:8:99:106,0,182 TC-TC TC-TC \n",
"268087 ./. C-C - \n",
"268088 ./. G-G - \n",
"268089 ./. - T-T \n",
"268090 ./. - G-G \n",
"268091 1/1:0,2:2:6:78,6,0 - - \n",
"268092 ./. T-T T-T \n",
"268093 0/0:6,0:6:9:0,9,141 C-C CTG-C \n",
"268094 1/1:0,1:1:3:37,3,0 C-T C-T \n",
"268095 0/1:6,1:4:17:17,0,69 C-C C-CT \n",
"268096 0/0:5,0:5:15:0,15,181 C-C C-T \n",
"268097 1/1:0,2:2:6:77,6,0 - C-C \n",
"268098 0/1:13,3:16:99:102,0,647 TA-TA TA-TA \n",
"268099 1/1:0,2:2:6:80,6,0 - A-A \n",
"268100 0/0:1,0:1:3:0,3,39 T-T T-T \n",
"\n",
" ISDBM322017 genotype ISDBM322018 genotype ISDBM322015 num \\\n",
"0 CCTA-C CCTA-CCTA NaN \n",
"1 TA-T TA-T 1.0 \n",
"2 A-A A-A NaN \n",
"3 G-G G-G NaN \n",
"4 - - 2.0 \n",
"5 T-T - 2.0 \n",
"6 A-A A-A 2.0 \n",
"7 G-G G-G 2.0 \n",
"8 G-G G-G 2.0 \n",
"9 - G-G NaN \n",
"10 - - NaN \n",
"11 - - 2.0 \n",
"12 - - 2.0 \n",
"13 - G-G 2.0 \n",
"14 - - 2.0 \n",
"15 A-A A-A 2.0 \n",
"16 C-C CCCCT-CCCCT 2.0 \n",
"17 G-G G-G NaN \n",
"18 T-T T-T NaN \n",
"19 C-C C-C NaN \n",
"20 - C-C 2.0 \n",
"21 G-G G-T NaN \n",
"22 - - 2.0 \n",
"23 - - 2.0 \n",
"24 C-G C-C 0.0 \n",
"25 C-C C-T 1.0 \n",
"26 G-G G-C 1.0 \n",
"27 A-A A-A 2.0 \n",
"28 C-C C-C 2.0 \n",
"29 G-G G-G 2.0 \n",
"... ... ... ... \n",
"268071 G-G G-G 2.0 \n",
"268072 - G-G 1.0 \n",
"268073 - A-G 2.0 \n",
"268074 - A-G 2.0 \n",
"268075 - C-C 2.0 \n",
"268076 T-T C-T 2.0 \n",
"268077 T-T A-T NaN \n",
"268078 G-G A-G NaN \n",
"268079 - - 2.0 \n",
"268080 C-C - 2.0 \n",
"268081 G-G G-G 2.0 \n",
"268082 - - 2.0 \n",
"268083 C-C - NaN \n",
"268084 T-T T-T 2.0 \n",
"268085 - - 2.0 \n",
"268086 TC-TC T-TC 2.0 \n",
"268087 - - 2.0 \n",
"268088 - - 2.0 \n",
"268089 - - NaN \n",
"268090 - - NaN \n",
"268091 - T-T NaN \n",
"268092 - - 2.0 \n",
"268093 CTG-C CTG-CTG 2.0 \n",
"268094 T-T T-T 1.0 \n",
"268095 C-CT C-CT 0.0 \n",
"268096 T-T C-C 0.0 \n",
"268097 C-C C-C NaN \n",
"268098 TA-T TA-T 0.0 \n",
"268099 - G-G NaN \n",
"268100 G-T T-T 0.0 \n",
"\n",
" ISDBM322016 num ISDBM322017 num ISDBM322018 num \n",
"0 2.0 1.0 0.0 \n",
"1 1.0 1.0 1.0 \n",
"2 2.0 2.0 2.0 \n",
"3 2.0 2.0 2.0 \n",
"4 NaN NaN NaN \n",
"5 NaN 2.0 NaN \n",
"6 2.0 2.0 2.0 \n",
"7 2.0 2.0 2.0 \n",
"8 2.0 2.0 2.0 \n",
"9 2.0 NaN 0.0 \n",
"10 2.0 NaN NaN \n",
"11 NaN NaN NaN \n",
"12 2.0 NaN NaN \n",
"13 NaN NaN 2.0 \n",
"14 0.0 NaN NaN \n",
"15 2.0 2.0 2.0 \n",
"16 2.0 0.0 2.0 \n",
"17 NaN 2.0 2.0 \n",
"18 NaN 2.0 2.0 \n",
"19 NaN 2.0 2.0 \n",
"20 2.0 NaN 2.0 \n",
"21 2.0 0.0 1.0 \n",
"22 2.0 NaN NaN \n",
"23 2.0 NaN NaN \n",
"24 1.0 1.0 0.0 \n",
"25 0.0 0.0 1.0 \n",
"26 0.0 0.0 1.0 \n",
"27 2.0 2.0 2.0 \n",
"28 2.0 2.0 2.0 \n",
"29 2.0 2.0 2.0 \n",
"... ... ... ... \n",
"268071 NaN 2.0 2.0 \n",
"268072 2.0 NaN 2.0 \n",
"268073 NaN NaN 1.0 \n",
"268074 NaN NaN 1.0 \n",
"268075 NaN NaN 2.0 \n",
"268076 NaN 2.0 1.0 \n",
"268077 NaN 2.0 1.0 \n",
"268078 NaN 2.0 1.0 \n",
"268079 NaN NaN NaN \n",
"268080 2.0 2.0 NaN \n",
"268081 2.0 2.0 2.0 \n",
"268082 NaN NaN NaN \n",
"268083 2.0 2.0 NaN \n",
"268084 2.0 2.0 2.0 \n",
"268085 2.0 NaN NaN \n",
"268086 2.0 2.0 1.0 \n",
"268087 NaN NaN NaN \n",
"268088 NaN NaN NaN \n",
"268089 2.0 NaN NaN \n",
"268090 2.0 NaN NaN \n",
"268091 NaN NaN 2.0 \n",
"268092 2.0 NaN NaN \n",
"268093 1.0 1.0 0.0 \n",
"268094 1.0 2.0 2.0 \n",
"268095 1.0 1.0 1.0 \n",
"268096 1.0 2.0 0.0 \n",
"268097 2.0 2.0 2.0 \n",
"268098 0.0 1.0 1.0 \n",
"268099 0.0 NaN 2.0 \n",
"268100 0.0 1.0 0.0 \n",
"\n",
"[268101 rows x 22 columns]"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample_ids_number = ['{} num'.format(s) for s in sample_ids]\n",
"\n",
"def get_number(ref, alt):\n",
" if ',' in alt or '.' in ref or '.' in alt:\n",
" return np.nan\n",
" return sum(map(int, [ref, alt]))\n",
"\n",
"def call_genotype_number(row):\n",
" return pd.Series(\n",
" [get_number(row[s][0], row[s][2]) for s in sample_ids if s], \n",
" index=sample_ids_number)\n",
"\n",
"dfc[sample_ids_number] = dfc.apply(call_genotype_number, axis=1)\n",
"dfc"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>index</th>\n",
" <th>#CHROM</th>\n",
" <th>POS</th>\n",
" <th>ID</th>\n",
" <th>REF</th>\n",
" <th>ALT</th>\n",
" <th>QUAL</th>\n",
" <th>FILTER</th>\n",
" <th>INFO</th>\n",
" <th>FORMAT</th>\n",
" <th>...</th>\n",
" <th>ISDBM322017</th>\n",
" <th>ISDBM322018</th>\n",
" <th>ISDBM322015 genotype</th>\n",
" <th>ISDBM322016 genotype</th>\n",
" <th>ISDBM322017 genotype</th>\n",
" <th>ISDBM322018 genotype</th>\n",
" <th>ISDBM322015 num</th>\n",
" <th>ISDBM322016 num</th>\n",
" <th>ISDBM322017 num</th>\n",
" <th>ISDBM322018 num</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>6</td>\n",
" <td>1</td>\n",
" <td>63735</td>\n",
" <td>.</td>\n",
" <td>CCTA</td>\n",
" <td>C</td>\n",
" <td>193.23</td>\n",
" <td>PASS</td>\n",
" <td>AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:8,4:8:99:128,0,301</td>\n",
" <td>0/0:18,2:15:30:0,30,666</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>CCTA-C</td>\n",
" <td>CCTA-CCTA</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>12</td>\n",
" <td>1</td>\n",
" <td>745370</td>\n",
" <td>rs146246821</td>\n",
" <td>TA</td>\n",
" <td>T</td>\n",
" <td>510.54</td>\n",
" <td>PASS</td>\n",
" <td>AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:9,7:16:99:273,0,395</td>\n",
" <td>0/1:16,4:19:99:125,0,661</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>TA-T</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>13</td>\n",
" <td>1</td>\n",
" <td>752566</td>\n",
" <td>rs3094315</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>118.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>14</td>\n",
" <td>1</td>\n",
" <td>752721</td>\n",
" <td>rs3131972</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>242.70</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,4:4:12:159,12,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>17</td>\n",
" <td>1</td>\n",
" <td>758324</td>\n",
" <td>rs3131955</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>18</td>\n",
" <td>1</td>\n",
" <td>780027</td>\n",
" <td>rs2977613</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>19</td>\n",
" <td>1</td>\n",
" <td>808631</td>\n",
" <td>rs11240779</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>1853.99</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,13:13:36:457,36,0</td>\n",
" <td>1/1:0,16:16:48:611,48,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>25</td>\n",
" <td>1</td>\n",
" <td>812267</td>\n",
" <td>rs7541694</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>385.67</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,3:3:9:99,9,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>26</td>\n",
" <td>1</td>\n",
" <td>812284</td>\n",
" <td>rs7545373</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>428.75</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:55,6,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>27</td>\n",
" <td>1</td>\n",
" <td>823790</td>\n",
" <td>rs143626389</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>38.82</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>0/0:3,0:3:9:0,9,99</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>28</td>\n",
" <td>1</td>\n",
" <td>834832</td>\n",
" <td>rs4411087</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>48.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>29</td>\n",
" <td>1</td>\n",
" <td>849998</td>\n",
" <td>rs13303222</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>45.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>30</td>\n",
" <td>1</td>\n",
" <td>851757</td>\n",
" <td>rs62677860</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>63.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>31</td>\n",
" <td>1</td>\n",
" <td>861808</td>\n",
" <td>rs13302982</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>66.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:36,3,0</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>32</td>\n",
" <td>1</td>\n",
" <td>862866</td>\n",
" <td>rs3892970</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>31.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>33</td>\n",
" <td>1</td>\n",
" <td>866319</td>\n",
" <td>rs9988021</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>825.39</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=24;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,4:4:12:133,12,0</td>\n",
" <td>1/1:0,2:2:6:76,6,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>34</td>\n",
" <td>1</td>\n",
" <td>866511</td>\n",
" <td>rs60722469</td>\n",
" <td>C</td>\n",
" <td>CCCCT</td>\n",
" <td>325.15</td>\n",
" <td>PASS</td>\n",
" <td>AC=6;AF=0.750;AN=8;BaseQRankSum=0.747;DB;DP=15...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:1,0:1:3:0,3,65</td>\n",
" <td>1/1:0,1:1:3:67,3,0</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>C-C</td>\n",
" <td>CCCCT-CCCCT</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>35</td>\n",
" <td>1</td>\n",
" <td>866920</td>\n",
" <td>rs2341361</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>36</td>\n",
" <td>1</td>\n",
" <td>867584</td>\n",
" <td>rs2341360</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>47.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>37</td>\n",
" <td>1</td>\n",
" <td>869323</td>\n",
" <td>rs13303207</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>69.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:73,6,0</td>\n",
" <td>1/1:0,1:1:3:30,3,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>40</td>\n",
" <td>1</td>\n",
" <td>870903</td>\n",
" <td>rs13303094</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>183.66</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=6;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>41</td>\n",
" <td>1</td>\n",
" <td>871334</td>\n",
" <td>rs4072383</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>74.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:3,0:3:9:0,9,120</td>\n",
" <td>0/1:2,2:4:52:52,0,68</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>G-G</td>\n",
" <td>G-T</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>42</td>\n",
" <td>1</td>\n",
" <td>873558</td>\n",
" <td>rs1110052</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>39.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>43</td>\n",
" <td>1</td>\n",
" <td>876499</td>\n",
" <td>rs4372192</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>200.89</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=6;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>44</td>\n",
" <td>1</td>\n",
" <td>878784</td>\n",
" <td>rs142929357</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>125.24</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.583;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/1:2,1:3:30:30,0,57</td>\n",
" <td>0/0:2,0:2:6:0,6,66</td>\n",
" <td>C-C</td>\n",
" <td>C-G</td>\n",
" <td>C-G</td>\n",
" <td>C-C</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>45</td>\n",
" <td>1</td>\n",
" <td>879317</td>\n",
" <td>rs7523549</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>388.57</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.493;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:12,0:12:36:0,36,405</td>\n",
" <td>0/1:3,6:9:64:187,0,64</td>\n",
" <td>C-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-T</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>46</td>\n",
" <td>1</td>\n",
" <td>879482</td>\n",
" <td>rs149880798</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>799.55</td>\n",
" <td>PASS</td>\n",
" <td>ABHet=0.592;ABHom=1.00;AC=2;AF=0.250;AN=8;Base...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:19,0:19:51:0,51,650</td>\n",
" <td>0/1:14,9:23:99:257,0,389</td>\n",
" <td>G-C</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-C</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>47</td>\n",
" <td>1</td>\n",
" <td>879676</td>\n",
" <td>rs6605067</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>432.72</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=12;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,4:4:12:158,12,0</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>48</td>\n",
" <td>1</td>\n",
" <td>879687</td>\n",
" <td>rs2839</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>335.22</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,4:4:12:139,12,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>49</td>\n",
" <td>1</td>\n",
" <td>880238</td>\n",
" <td>rs3748592</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>516.84</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,3:3:9:120,9,0</td>\n",
" <td>1/1:0,5:5:15:196,15,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267146</th>\n",
" <td>296313</td>\n",
" <td>Y</td>\n",
" <td>59026513</td>\n",
" <td>rs1826575</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>42.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:74,6,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267147</th>\n",
" <td>296320</td>\n",
" <td>Y</td>\n",
" <td>59033110</td>\n",
" <td>rs28628009</td>\n",
" <td>A</td>\n",
" <td>T</td>\n",
" <td>36.01</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267148</th>\n",
" <td>296321</td>\n",
" <td>Y</td>\n",
" <td>59033139</td>\n",
" <td>rs55686319</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>37.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:69,6,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267149</th>\n",
" <td>296322</td>\n",
" <td>MT</td>\n",
" <td>73</td>\n",
" <td>rs3087742</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>327.99</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,3:3:9:94,9,0</td>\n",
" <td>1/1:0,2:2:6:79,6,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267150</th>\n",
" <td>296323</td>\n",
" <td>MT</td>\n",
" <td>195</td>\n",
" <td>rs2857291</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>47.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>./.</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267151</th>\n",
" <td>296324</td>\n",
" <td>MT</td>\n",
" <td>263</td>\n",
" <td>rs2853515</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>229.77</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=8;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:35,3,0</td>\n",
" <td>1/1:0,1:1:3:32,3,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267152</th>\n",
" <td>296325</td>\n",
" <td>MT</td>\n",
" <td>709</td>\n",
" <td>rs2853517</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>346.40</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=1.4...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,5:5:15:193,15,0</td>\n",
" <td>A-A</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267153</th>\n",
" <td>296326</td>\n",
" <td>MT</td>\n",
" <td>750</td>\n",
" <td>rs2853518</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>476.08</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=15;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,7:7:21:273,21,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267154</th>\n",
" <td>296327</td>\n",
" <td>MT</td>\n",
" <td>1243</td>\n",
" <td>rs28358572</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>422.79</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=0.6...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,5:5:9:119,9,0</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267155</th>\n",
" <td>296329</td>\n",
" <td>MT</td>\n",
" <td>1719</td>\n",
" <td>rs3928305</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>35.00</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:1,0:1:3:0,3,32</td>\n",
" <td>0/0:4,0:4:12:0,12,159</td>\n",
" <td>G-G</td>\n",
" <td>A-A</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267156</th>\n",
" <td>296330</td>\n",
" <td>MT</td>\n",
" <td>2706</td>\n",
" <td>rs2854128</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>300.19</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=0.899;AC=6;AF=1.00;AN=6;DB;DP=10;Dels=0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:3:6:73,6,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267157</th>\n",
" <td>296331</td>\n",
" <td>MT</td>\n",
" <td>3505</td>\n",
" <td>rs28358585</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>219.20</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=1.6...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:40,3,0</td>\n",
" <td>1/1:0,2:2:6:67,6,0</td>\n",
" <td>G-G</td>\n",
" <td>A-A</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267158</th>\n",
" <td>296333</td>\n",
" <td>MT</td>\n",
" <td>5460</td>\n",
" <td>rs3021088</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>515.25</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=0.1...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,4:4:12:144,12,0</td>\n",
" <td>1/1:0,12:12:33:380,33,0</td>\n",
" <td>A-A</td>\n",
" <td>G-G</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267159</th>\n",
" <td>296335</td>\n",
" <td>MT</td>\n",
" <td>6371</td>\n",
" <td>rs41366755</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>116.32</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=0.5...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:1,0:1:3:0,3,40</td>\n",
" <td>0/0:8,0:8:24:0,24,297</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267160</th>\n",
" <td>296336</td>\n",
" <td>MT</td>\n",
" <td>8697</td>\n",
" <td>rs28358886</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>280.28</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=8;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,7:7:21:275,21,0</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>A-A</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267161</th>\n",
" <td>296340</td>\n",
" <td>MT</td>\n",
" <td>11947</td>\n",
" <td>rs28359168</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>529.29</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=-1....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,7:7:21:243,21,0</td>\n",
" <td>G-G</td>\n",
" <td>A-A</td>\n",
" <td>-</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267162</th>\n",
" <td>296341</td>\n",
" <td>MT</td>\n",
" <td>12414</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>547.46</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=-0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,10:10:30:392,30,0</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267163</th>\n",
" <td>296342</td>\n",
" <td>MT</td>\n",
" <td>12705</td>\n",
" <td>rs2854122</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>272.26</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=9;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267164</th>\n",
" <td>296343</td>\n",
" <td>MT</td>\n",
" <td>13819</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>77.31</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=1.4...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:4,0:4:12:0,12,159</td>\n",
" <td>0/0:7,0:7:21:0,21,268</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267165</th>\n",
" <td>296344</td>\n",
" <td>MT</td>\n",
" <td>13966</td>\n",
" <td>rs41535848</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>188.02</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=3.3...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:2,0:2:6:0,6,75</td>\n",
" <td>0/0:10,0:10:27:0,27,316</td>\n",
" <td>A-A</td>\n",
" <td>G-G</td>\n",
" <td>A-A</td>\n",
" <td>A-A</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267166</th>\n",
" <td>296345</td>\n",
" <td>MT</td>\n",
" <td>14371</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>634.48</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=2.3...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:29,3,0</td>\n",
" <td>1/1:0,9:9:27:336,27,0</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267167</th>\n",
" <td>296346</td>\n",
" <td>MT</td>\n",
" <td>14470</td>\n",
" <td>rs3135030</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>288.43</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=3.4...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>0/0:7,0:7:21:0,21,243</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267168</th>\n",
" <td>296347</td>\n",
" <td>MT</td>\n",
" <td>14766</td>\n",
" <td>rs3135031</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>526.56</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=15;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:77,6,0</td>\n",
" <td>1/1:0,3:3:9:116,9,0</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267169</th>\n",
" <td>296349</td>\n",
" <td>MT</td>\n",
" <td>15326</td>\n",
" <td>rs2853508</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>557.29</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=16;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:37,3,0</td>\n",
" <td>1/1:0,9:9:27:333,27,0</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>G-G</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267170</th>\n",
" <td>296350</td>\n",
" <td>MT</td>\n",
" <td>15884</td>\n",
" <td>rs28617642</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>83.98</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,3:3:9:116,9,0</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>-</td>\n",
" <td>C-C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267171</th>\n",
" <td>296351</td>\n",
" <td>MT</td>\n",
" <td>16223</td>\n",
" <td>rs2853513</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>396.83</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=11;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>./.</td>\n",
" <td>1/1:0,4:4:12:155,12,0</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>-</td>\n",
" <td>T-T</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267172</th>\n",
" <td>296352</td>\n",
" <td>MT</td>\n",
" <td>16278</td>\n",
" <td>rs41458645</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>109.32</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-2....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>0/0:1,0:1:3:0,3,40</td>\n",
" <td>0/0:5,0:5:15:0,15,180</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267173</th>\n",
" <td>296353</td>\n",
" <td>MT</td>\n",
" <td>16290</td>\n",
" <td>rs34524463</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>583.33</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=-0....</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,1:1:3:39,3,0</td>\n",
" <td>1/1:0,5:5:15:181,15,0</td>\n",
" <td>T-T</td>\n",
" <td>C-C</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>2.0</td>\n",
" <td>0.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267174</th>\n",
" <td>296356</td>\n",
" <td>MT</td>\n",
" <td>16519</td>\n",
" <td>rs3937033</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>455.12</td>\n",
" <td>PASS</td>\n",
" <td>ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0...</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/1:0,2:2:6:80,6,0</td>\n",
" <td>1/1:0,3:3:9:116,9,0</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>C-C</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" <td>2.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268100</th>\n",
" <td>300035</td>\n",
" <td>10</td>\n",
" <td>123256215</td>\n",
" <td>.</td>\n",
" <td>T</td>\n",
" <td>G</td>\n",
" <td>100.00</td>\n",
" <td>PASS</td>\n",
" <td>GENE=FGFR2;INHERITANCE=AD;MIM=101600</td>\n",
" <td>GT:AD:DP:GQ:PL</td>\n",
" <td>...</td>\n",
" <td>1/0:1,0:1:3:0,3,39</td>\n",
" <td>0/0:1,0:1:3:0,3,39</td>\n",
" <td>T-T</td>\n",
" <td>T-T</td>\n",
" <td>G-T</td>\n",
" <td>T-T</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>267176 rows × 22 columns</p>\n",
"</div>"
],
"text/plain": [
" index #CHROM POS ID REF ALT QUAL FILTER \\\n",
"0 6 1 63735 . CCTA C 193.23 PASS \n",
"1 12 1 745370 rs146246821 TA T 510.54 PASS \n",
"2 13 1 752566 rs3094315 G A 118.67 PASS \n",
"3 14 1 752721 rs3131972 A G 242.70 PASS \n",
"4 17 1 758324 rs3131955 T C 45.77 PASS \n",
"5 18 1 780027 rs2977613 G T 47.01 PASS \n",
"6 19 1 808631 rs11240779 G A 1853.99 PASS \n",
"7 25 1 812267 rs7541694 A G 385.67 PASS \n",
"8 26 1 812284 rs7545373 C G 428.75 PASS \n",
"9 27 1 823790 rs143626389 G A 38.82 PASS \n",
"10 28 1 834832 rs4411087 G C 48.77 PASS \n",
"11 29 1 849998 rs13303222 A G 45.77 PASS \n",
"12 30 1 851757 rs62677860 A G 63.22 PASS \n",
"13 31 1 861808 rs13302982 A G 66.22 PASS \n",
"14 32 1 862866 rs3892970 C T 31.26 PASS \n",
"15 33 1 866319 rs9988021 G A 825.39 PASS \n",
"16 34 1 866511 rs60722469 C CCCCT 325.15 PASS \n",
"17 35 1 866920 rs2341361 A G 47.01 PASS \n",
"18 36 1 867584 rs2341360 A T 47.01 PASS \n",
"19 37 1 869323 rs13303207 T C 69.22 PASS \n",
"20 40 1 870903 rs13303094 T C 183.66 PASS \n",
"21 41 1 871334 rs4072383 G T 74.01 PASS \n",
"22 42 1 873558 rs1110052 G T 39.01 PASS \n",
"23 43 1 876499 rs4372192 A G 200.89 PASS \n",
"24 44 1 878784 rs142929357 C G 125.24 PASS \n",
"25 45 1 879317 rs7523549 C T 388.57 PASS \n",
"26 46 1 879482 rs149880798 G C 799.55 PASS \n",
"27 47 1 879676 rs6605067 G A 432.72 PASS \n",
"28 48 1 879687 rs2839 T C 335.22 PASS \n",
"29 49 1 880238 rs3748592 A G 516.84 PASS \n",
"... ... ... ... ... ... ... ... ... \n",
"267146 296313 Y 59026513 rs1826575 A G 42.77 PASS \n",
"267147 296320 Y 59033110 rs28628009 A T 36.01 PASS \n",
"267148 296321 Y 59033139 rs55686319 T C 37.77 PASS \n",
"267149 296322 MT 73 rs3087742 A G 327.99 PASS \n",
"267150 296323 MT 195 rs2857291 T C 47.77 PASS \n",
"267151 296324 MT 263 rs2853515 A G 229.77 PASS \n",
"267152 296325 MT 709 rs2853517 G A 346.40 PASS \n",
"267153 296326 MT 750 rs2853518 A G 476.08 PASS \n",
"267154 296327 MT 1243 rs28358572 T C 422.79 PASS \n",
"267155 296329 MT 1719 rs3928305 G A 35.00 PASS \n",
"267156 296330 MT 2706 rs2854128 A G 300.19 PASS \n",
"267157 296331 MT 3505 rs28358585 A G 219.20 PASS \n",
"267158 296333 MT 5460 rs3021088 G A 515.25 PASS \n",
"267159 296335 MT 6371 rs41366755 C T 116.32 PASS \n",
"267160 296336 MT 8697 rs28358886 G A 280.28 PASS \n",
"267161 296340 MT 11947 rs28359168 A G 529.29 PASS \n",
"267162 296341 MT 12414 . T C 547.46 PASS \n",
"267163 296342 MT 12705 rs2854122 C T 272.26 PASS \n",
"267164 296343 MT 13819 . T C 77.31 PASS \n",
"267165 296344 MT 13966 rs41535848 A G 188.02 PASS \n",
"267166 296345 MT 14371 . T C 634.48 PASS \n",
"267167 296346 MT 14470 rs3135030 T C 288.43 PASS \n",
"267168 296347 MT 14766 rs3135031 C T 526.56 PASS \n",
"267169 296349 MT 15326 rs2853508 A G 557.29 PASS \n",
"267170 296350 MT 15884 rs28617642 G C 83.98 PASS \n",
"267171 296351 MT 16223 rs2853513 C T 396.83 PASS \n",
"267172 296352 MT 16278 rs41458645 C T 109.32 PASS \n",
"267173 296353 MT 16290 rs34524463 C T 583.33 PASS \n",
"267174 296356 MT 16519 rs3937033 T C 455.12 PASS \n",
"268100 300035 10 123256215 . T G 100.00 PASS \n",
"\n",
" INFO FORMAT \\\n",
"0 AC=3;AF=0.500;AN=6;BaseQRankSum=-0.960;DP=42;F... GT:AD:DP:GQ:PL \n",
"1 AC=4;AF=0.500;AN=8;BaseQRankSum=1.905;DB;DP=64... GT:AD:DP:GQ:PL \n",
"2 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00... GT:AD:DP:GQ:PL \n",
"3 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00... GT:AD:DP:GQ:PL \n",
"4 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"5 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"6 ABHom=1.000;AC=8;AF=1.00;AN=8;DB;DP=52;Dels=0.... GT:AD:DP:GQ:PL \n",
"7 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... GT:AD:DP:GQ:PL \n",
"8 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... GT:AD:DP:GQ:PL \n",
"9 ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.3... GT:AD:DP:GQ:PL \n",
"10 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"11 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"12 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00... GT:AD:DP:GQ:PL \n",
"13 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... GT:AD:DP:GQ:PL \n",
"14 ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=-0.... GT:AD:DP:GQ:PL \n",
"15 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=24;Dels=0.0... GT:AD:DP:GQ:PL \n",
"16 AC=6;AF=0.750;AN=8;BaseQRankSum=0.747;DB;DP=15... GT:AD:DP:GQ:PL \n",
"17 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"18 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"19 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00... GT:AD:DP:GQ:PL \n",
"20 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=6;Dels=0.00... GT:AD:DP:GQ:PL \n",
"21 ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;Base... GT:AD:DP:GQ:PL \n",
"22 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"23 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=6;Dels=0.00... GT:AD:DP:GQ:PL \n",
"24 ABHet=0.583;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"25 ABHet=0.493;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"26 ABHet=0.592;ABHom=1.00;AC=2;AF=0.250;AN=8;Base... GT:AD:DP:GQ:PL \n",
"27 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=12;Dels=0.0... GT:AD:DP:GQ:PL \n",
"28 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0... GT:AD:DP:GQ:PL \n",
"29 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.0... GT:AD:DP:GQ:PL \n",
"... ... ... \n",
"267146 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267147 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267148 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267149 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=10;Dels=0.0... GT:AD:DP:GQ:PL \n",
"267150 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267151 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=8;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267152 ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=1.4... GT:AD:DP:GQ:PL \n",
"267153 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=15;Dels=0.0... GT:AD:DP:GQ:PL \n",
"267154 ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=0.6... GT:AD:DP:GQ:PL \n",
"267155 ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-0.... GT:AD:DP:GQ:PL \n",
"267156 ABHom=0.899;AC=6;AF=1.00;AN=6;DB;DP=10;Dels=0.... GT:AD:DP:GQ:PL \n",
"267157 ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=1.6... GT:AD:DP:GQ:PL \n",
"267158 ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=0.1... GT:AD:DP:GQ:PL \n",
"267159 ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=0.5... GT:AD:DP:GQ:PL \n",
"267160 ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=8;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267161 ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=-1.... GT:AD:DP:GQ:PL \n",
"267162 ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=-0.... GT:AD:DP:GQ:PL \n",
"267163 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=9;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267164 ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=1.4... GT:AD:DP:GQ:PL \n",
"267165 ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=3.3... GT:AD:DP:GQ:PL \n",
"267166 ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=2.3... GT:AD:DP:GQ:PL \n",
"267167 ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=3.4... GT:AD:DP:GQ:PL \n",
"267168 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=15;Dels=0.0... GT:AD:DP:GQ:PL \n",
"267169 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=16;Dels=0.0... GT:AD:DP:GQ:PL \n",
"267170 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00... GT:AD:DP:GQ:PL \n",
"267171 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=11;Dels=0.0... GT:AD:DP:GQ:PL \n",
"267172 ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-2.... GT:AD:DP:GQ:PL \n",
"267173 ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=-0.... GT:AD:DP:GQ:PL \n",
"267174 ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=13;Dels=0.0... GT:AD:DP:GQ:PL \n",
"268100 GENE=FGFR2;INHERITANCE=AD;MIM=101600 GT:AD:DP:GQ:PL \n",
"\n",
" ... ISDBM322017 ISDBM322018 \\\n",
"0 ... 0/1:8,4:8:99:128,0,301 0/0:18,2:15:30:0,30,666 \n",
"1 ... 0/1:9,7:16:99:273,0,395 0/1:16,4:19:99:125,0,661 \n",
"2 ... 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:36,3,0 \n",
"3 ... 1/1:0,4:4:12:159,12,0 1/1:0,1:1:3:40,3,0 \n",
"4 ... ./. ./. \n",
"5 ... 1/1:0,1:1:3:40,3,0 ./. \n",
"6 ... 1/1:0,13:13:36:457,36,0 1/1:0,16:16:48:611,48,0 \n",
"7 ... 1/1:0,2:2:6:55,6,0 1/1:0,3:3:9:99,9,0 \n",
"8 ... 1/1:0,2:2:6:55,6,0 1/1:0,2:2:6:79,6,0 \n",
"9 ... ./. 0/0:3,0:3:9:0,9,99 \n",
"10 ... ./. ./. \n",
"11 ... ./. ./. \n",
"12 ... ./. ./. \n",
"13 ... ./. 1/1:0,1:1:3:36,3,0 \n",
"14 ... ./. ./. \n",
"15 ... 1/1:0,4:4:12:133,12,0 1/1:0,2:2:6:76,6,0 \n",
"16 ... 0/0:1,0:1:3:0,3,65 1/1:0,1:1:3:67,3,0 \n",
"17 ... 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 \n",
"18 ... 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 \n",
"19 ... 1/1:0,2:2:6:73,6,0 1/1:0,1:1:3:30,3,0 \n",
"20 ... ./. 1/1:0,2:2:6:79,6,0 \n",
"21 ... 0/0:3,0:3:9:0,9,120 0/1:2,2:4:52:52,0,68 \n",
"22 ... ./. ./. \n",
"23 ... ./. ./. \n",
"24 ... 0/1:2,1:3:30:30,0,57 0/0:2,0:2:6:0,6,66 \n",
"25 ... 0/0:12,0:12:36:0,36,405 0/1:3,6:9:64:187,0,64 \n",
"26 ... 0/0:19,0:19:51:0,51,650 0/1:14,9:23:99:257,0,389 \n",
"27 ... 1/1:0,3:3:9:120,9,0 1/1:0,4:4:12:158,12,0 \n",
"28 ... 1/1:0,2:2:6:80,6,0 1/1:0,4:4:12:139,12,0 \n",
"29 ... 1/1:0,3:3:9:120,9,0 1/1:0,5:5:15:196,15,0 \n",
"... ... ... ... \n",
"267146 ... ./. 1/1:0,2:2:6:74,6,0 \n",
"267147 ... ./. 1/1:0,1:1:3:39,3,0 \n",
"267148 ... ./. 1/1:0,2:2:6:69,6,0 \n",
"267149 ... 1/1:0,3:3:9:94,9,0 1/1:0,2:2:6:79,6,0 \n",
"267150 ... ./. ./. \n",
"267151 ... 1/1:0,1:1:3:35,3,0 1/1:0,1:1:3:32,3,0 \n",
"267152 ... ./. 1/1:0,5:5:15:193,15,0 \n",
"267153 ... ./. 1/1:0,7:7:21:273,21,0 \n",
"267154 ... 1/1:0,1:1:3:40,3,0 1/1:0,5:5:9:119,9,0 \n",
"267155 ... 0/0:1,0:1:3:0,3,32 0/0:4,0:4:12:0,12,159 \n",
"267156 ... ./. 1/1:0,2:3:6:73,6,0 \n",
"267157 ... 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:67,6,0 \n",
"267158 ... 1/1:0,4:4:12:144,12,0 1/1:0,12:12:33:380,33,0 \n",
"267159 ... 0/0:1,0:1:3:0,3,40 0/0:8,0:8:24:0,24,297 \n",
"267160 ... ./. 1/1:0,7:7:21:275,21,0 \n",
"267161 ... ./. 1/1:0,7:7:21:243,21,0 \n",
"267162 ... ./. 1/1:0,10:10:30:392,30,0 \n",
"267163 ... ./. 1/1:0,2:2:6:80,6,0 \n",
"267164 ... 0/0:4,0:4:12:0,12,159 0/0:7,0:7:21:0,21,268 \n",
"267165 ... 0/0:2,0:2:6:0,6,75 0/0:10,0:10:27:0,27,316 \n",
"267166 ... 1/1:0,1:1:3:29,3,0 1/1:0,9:9:27:336,27,0 \n",
"267167 ... ./. 0/0:7,0:7:21:0,21,243 \n",
"267168 ... 1/1:0,2:2:6:77,6,0 1/1:0,3:3:9:116,9,0 \n",
"267169 ... 1/1:0,1:1:3:37,3,0 1/1:0,9:9:27:333,27,0 \n",
"267170 ... ./. 1/1:0,3:3:9:116,9,0 \n",
"267171 ... ./. 1/1:0,4:4:12:155,12,0 \n",
"267172 ... 0/0:1,0:1:3:0,3,40 0/0:5,0:5:15:0,15,180 \n",
"267173 ... 1/1:0,1:1:3:39,3,0 1/1:0,5:5:15:181,15,0 \n",
"267174 ... 1/1:0,2:2:6:80,6,0 1/1:0,3:3:9:116,9,0 \n",
"268100 ... 1/0:1,0:1:3:0,3,39 0/0:1,0:1:3:0,3,39 \n",
"\n",
" ISDBM322015 genotype ISDBM322016 genotype ISDBM322017 genotype \\\n",
"0 - C-C CCTA-C \n",
"1 TA-T TA-T TA-T \n",
"2 - A-A A-A \n",
"3 - G-G G-G \n",
"4 C-C - - \n",
"5 T-T - T-T \n",
"6 A-A A-A A-A \n",
"7 G-G G-G G-G \n",
"8 G-G G-G G-G \n",
"9 - A-A - \n",
"10 - C-C - \n",
"11 G-G - - \n",
"12 G-G G-G - \n",
"13 G-G - - \n",
"14 T-T C-C - \n",
"15 A-A A-A A-A \n",
"16 CCCCT-CCCCT CCCCT-CCCCT C-C \n",
"17 - - G-G \n",
"18 - - T-T \n",
"19 - - C-C \n",
"20 C-C C-C - \n",
"21 - T-T G-G \n",
"22 T-T T-T - \n",
"23 G-G G-G - \n",
"24 C-C C-G C-G \n",
"25 C-T C-C C-C \n",
"26 G-C G-G G-G \n",
"27 A-A A-A A-A \n",
"28 C-C C-C C-C \n",
"29 G-G G-G G-G \n",
"... ... ... ... \n",
"267146 - - - \n",
"267147 - T-T - \n",
"267148 - - - \n",
"267149 G-G G-G G-G \n",
"267150 - C-C - \n",
"267151 G-G G-G G-G \n",
"267152 A-A G-G - \n",
"267153 G-G G-G - \n",
"267154 C-C T-T C-C \n",
"267155 G-G A-A G-G \n",
"267156 G-G G-G - \n",
"267157 G-G A-A G-G \n",
"267158 A-A G-G A-A \n",
"267159 C-C T-T C-C \n",
"267160 A-A - - \n",
"267161 G-G A-A - \n",
"267162 C-C T-T - \n",
"267163 T-T T-T - \n",
"267164 T-T C-C T-T \n",
"267165 A-A G-G A-A \n",
"267166 C-C T-T C-C \n",
"267167 T-T C-C - \n",
"267168 T-T T-T T-T \n",
"267169 G-G G-G G-G \n",
"267170 - - - \n",
"267171 T-T T-T - \n",
"267172 C-C T-T C-C \n",
"267173 T-T C-C T-T \n",
"267174 C-C C-C C-C \n",
"268100 T-T T-T G-T \n",
"\n",
" ISDBM322018 genotype ISDBM322015 num ISDBM322016 num ISDBM322017 num \\\n",
"0 CCTA-CCTA NaN 2.0 1.0 \n",
"1 TA-T 1.0 1.0 1.0 \n",
"2 A-A NaN 2.0 2.0 \n",
"3 G-G NaN 2.0 2.0 \n",
"4 - 2.0 NaN NaN \n",
"5 - 2.0 NaN 2.0 \n",
"6 A-A 2.0 2.0 2.0 \n",
"7 G-G 2.0 2.0 2.0 \n",
"8 G-G 2.0 2.0 2.0 \n",
"9 G-G NaN 2.0 NaN \n",
"10 - NaN 2.0 NaN \n",
"11 - 2.0 NaN NaN \n",
"12 - 2.0 2.0 NaN \n",
"13 G-G 2.0 NaN NaN \n",
"14 - 2.0 0.0 NaN \n",
"15 A-A 2.0 2.0 2.0 \n",
"16 CCCCT-CCCCT 2.0 2.0 0.0 \n",
"17 G-G NaN NaN 2.0 \n",
"18 T-T NaN NaN 2.0 \n",
"19 C-C NaN NaN 2.0 \n",
"20 C-C 2.0 2.0 NaN \n",
"21 G-T NaN 2.0 0.0 \n",
"22 - 2.0 2.0 NaN \n",
"23 - 2.0 2.0 NaN \n",
"24 C-C 0.0 1.0 1.0 \n",
"25 C-T 1.0 0.0 0.0 \n",
"26 G-C 1.0 0.0 0.0 \n",
"27 A-A 2.0 2.0 2.0 \n",
"28 C-C 2.0 2.0 2.0 \n",
"29 G-G 2.0 2.0 2.0 \n",
"... ... ... ... ... \n",
"267146 G-G NaN NaN NaN \n",
"267147 T-T NaN 2.0 NaN \n",
"267148 C-C NaN NaN NaN \n",
"267149 G-G 2.0 2.0 2.0 \n",
"267150 - NaN 2.0 NaN \n",
"267151 G-G 2.0 2.0 2.0 \n",
"267152 A-A 2.0 0.0 NaN \n",
"267153 G-G 2.0 2.0 NaN \n",
"267154 C-C 2.0 0.0 2.0 \n",
"267155 G-G 0.0 2.0 0.0 \n",
"267156 G-G 2.0 2.0 NaN \n",
"267157 G-G 2.0 0.0 2.0 \n",
"267158 A-A 2.0 0.0 2.0 \n",
"267159 C-C 0.0 2.0 0.0 \n",
"267160 A-A 2.0 NaN NaN \n",
"267161 G-G 2.0 0.0 NaN \n",
"267162 C-C 2.0 0.0 NaN \n",
"267163 T-T 2.0 2.0 NaN \n",
"267164 T-T 0.0 2.0 0.0 \n",
"267165 A-A 0.0 2.0 0.0 \n",
"267166 C-C 2.0 0.0 2.0 \n",
"267167 T-T 0.0 2.0 NaN \n",
"267168 T-T 2.0 2.0 2.0 \n",
"267169 G-G 2.0 2.0 2.0 \n",
"267170 C-C NaN NaN NaN \n",
"267171 T-T 2.0 2.0 NaN \n",
"267172 C-C 0.0 2.0 0.0 \n",
"267173 T-T 2.0 0.0 2.0 \n",
"267174 C-C 2.0 2.0 2.0 \n",
"268100 T-T 0.0 0.0 1.0 \n",
"\n",
" ISDBM322018 num \n",
"0 0.0 \n",
"1 1.0 \n",
"2 2.0 \n",
"3 2.0 \n",
"4 NaN \n",
"5 NaN \n",
"6 2.0 \n",
"7 2.0 \n",
"8 2.0 \n",
"9 0.0 \n",
"10 NaN \n",
"11 NaN \n",
"12 NaN \n",
"13 2.0 \n",
"14 NaN \n",
"15 2.0 \n",
"16 2.0 \n",
"17 2.0 \n",
"18 2.0 \n",
"19 2.0 \n",
"20 2.0 \n",
"21 1.0 \n",
"22 NaN \n",
"23 NaN \n",
"24 0.0 \n",
"25 1.0 \n",
"26 1.0 \n",
"27 2.0 \n",
"28 2.0 \n",
"29 2.0 \n",
"... ... \n",
"267146 2.0 \n",
"267147 2.0 \n",
"267148 2.0 \n",
"267149 2.0 \n",
"267150 NaN \n",
"267151 2.0 \n",
"267152 2.0 \n",
"267153 2.0 \n",
"267154 2.0 \n",
"267155 0.0 \n",
"267156 2.0 \n",
"267157 2.0 \n",
"267158 2.0 \n",
"267159 0.0 \n",
"267160 2.0 \n",
"267161 2.0 \n",
"267162 2.0 \n",
"267163 2.0 \n",
"267164 0.0 \n",
"267165 0.0 \n",
"267166 2.0 \n",
"267167 0.0 \n",
"267168 2.0 \n",
"267169 2.0 \n",
"267170 2.0 \n",
"267171 2.0 \n",
"267172 0.0 \n",
"267173 2.0 \n",
"267174 2.0 \n",
"268100 0.0 \n",
"\n",
"[267176 rows x 22 columns]"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dfc[[not x.startswith('G') for x in dfc['#CHROM']]]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## QUAL, 변이 갯수를 염색체별로"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x11d838198>"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
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S+ySnkkUlB3gdyW5Usqjcd0Bnn4BOFpUcoJNFJQd4HckJkbc8rl271t2czI5A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\nPvEs/lEcAAAAAElFTkSuQmCC\n",
"text/plain": [
"<matplotlib.figure.Figure at 0x10db494e0>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"dfc[[not x.startswith('G') for x in dfc['#CHROM']]].boxplot(\n",
" column='QUAL', by='#CHROM', figsize=(15,5))"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x10891ebe0>"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
"image/png": 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"text/plain": [
"<matplotlib.figure.Figure at 0x10db49fd0>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"dfc[[not x.startswith('G') for x in dfc['#CHROM']]]['#CHROM'].value_counts().plot(kind='bar')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## PLINK PED, MAP 파일 내보내기"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>ISDBM322015 genotype</th>\n",
" <th>ISDBM322016 genotype</th>\n",
" <th>ISDBM322017 genotype</th>\n",
" <th>ISDBM322018 genotype</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>NaN</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>NaN</td>\n",
" <td>A A</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" <td>G G</td>\n",
" <td>G T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>C C</td>\n",
" <td>C G</td>\n",
" <td>C G</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>C T</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" <td>C T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>G C</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267146</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267147</th>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267148</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267149</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267150</th>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267151</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267152</th>\n",
" <td>A A</td>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267153</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267154</th>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267155</th>\n",
" <td>G G</td>\n",
" <td>A A</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267156</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267157</th>\n",
" <td>G G</td>\n",
" <td>A A</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267158</th>\n",
" <td>A A</td>\n",
" <td>G G</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267159</th>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267160</th>\n",
" <td>A A</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267161</th>\n",
" <td>G G</td>\n",
" <td>A A</td>\n",
" <td>NaN</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267162</th>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267163</th>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267164</th>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267165</th>\n",
" <td>A A</td>\n",
" <td>G G</td>\n",
" <td>A A</td>\n",
" <td>A A</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267166</th>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267167</th>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267168</th>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267169</th>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" <td>G G</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267170</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267171</th>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" <td>NaN</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267172</th>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267173</th>\n",
" <td>T T</td>\n",
" <td>C C</td>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" <tr>\n",
" <th>267174</th>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" <td>C C</td>\n",
" </tr>\n",
" <tr>\n",
" <th>268100</th>\n",
" <td>T T</td>\n",
" <td>T T</td>\n",
" <td>G T</td>\n",
" <td>T T</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>267176 rows × 4 columns</p>\n",
"</div>"
],
"text/plain": [
" ISDBM322015 genotype ISDBM322016 genotype ISDBM322017 genotype \\\n",
"0 NaN C C NaN \n",
"1 NaN NaN NaN \n",
"2 NaN A A A A \n",
"3 NaN G G G G \n",
"4 C C NaN NaN \n",
"5 T T NaN T T \n",
"6 A A A A A A \n",
"7 G G G G G G \n",
"8 G G G G G G \n",
"9 NaN A A NaN \n",
"10 NaN C C NaN \n",
"11 G G NaN NaN \n",
"12 G G G G NaN \n",
"13 G G NaN NaN \n",
"14 T T C C NaN \n",
"15 A A A A A A \n",
"16 NaN NaN C C \n",
"17 NaN NaN G G \n",
"18 NaN NaN T T \n",
"19 NaN NaN C C \n",
"20 C C C C NaN \n",
"21 NaN T T G G \n",
"22 T T T T NaN \n",
"23 G G G G NaN \n",
"24 C C C G C G \n",
"25 C T C C C C \n",
"26 G C G G G G \n",
"27 A A A A A A \n",
"28 C C C C C C \n",
"29 G G G G G G \n",
"... ... ... ... \n",
"267146 NaN NaN NaN \n",
"267147 NaN T T NaN \n",
"267148 NaN NaN NaN \n",
"267149 G G G G G G \n",
"267150 NaN C C NaN \n",
"267151 G G G G G G \n",
"267152 A A G G NaN \n",
"267153 G G G G NaN \n",
"267154 C C T T C C \n",
"267155 G G A A G G \n",
"267156 G G G G NaN \n",
"267157 G G A A G G \n",
"267158 A A G G A A \n",
"267159 C C T T C C \n",
"267160 A A NaN NaN \n",
"267161 G G A A NaN \n",
"267162 C C T T NaN \n",
"267163 T T T T NaN \n",
"267164 T T C C T T \n",
"267165 A A G G A A \n",
"267166 C C T T C C \n",
"267167 T T C C NaN \n",
"267168 T T T T T T \n",
"267169 G G G G G G \n",
"267170 NaN NaN NaN \n",
"267171 T T T T NaN \n",
"267172 C C T T C C \n",
"267173 T T C C T T \n",
"267174 C C C C C C \n",
"268100 T T T T G T \n",
"\n",
" ISDBM322018 genotype \n",
"0 NaN \n",
"1 NaN \n",
"2 A A \n",
"3 G G \n",
"4 NaN \n",
"5 NaN \n",
"6 A A \n",
"7 G G \n",
"8 G G \n",
"9 G G \n",
"10 NaN \n",
"11 NaN \n",
"12 NaN \n",
"13 G G \n",
"14 NaN \n",
"15 A A \n",
"16 NaN \n",
"17 G G \n",
"18 T T \n",
"19 C C \n",
"20 C C \n",
"21 G T \n",
"22 NaN \n",
"23 NaN \n",
"24 C C \n",
"25 C T \n",
"26 G C \n",
"27 A A \n",
"28 C C \n",
"29 G G \n",
"... ... \n",
"267146 G G \n",
"267147 T T \n",
"267148 C C \n",
"267149 G G \n",
"267150 NaN \n",
"267151 G G \n",
"267152 A A \n",
"267153 G G \n",
"267154 C C \n",
"267155 G G \n",
"267156 G G \n",
"267157 G G \n",
"267158 A A \n",
"267159 C C \n",
"267160 A A \n",
"267161 G G \n",
"267162 C C \n",
"267163 T T \n",
"267164 T T \n",
"267165 A A \n",
"267166 C C \n",
"267167 T T \n",
"267168 T T \n",
"267169 G G \n",
"267170 C C \n",
"267171 T T \n",
"267172 C C \n",
"267173 T T \n",
"267174 C C \n",
"268100 T T \n",
"\n",
"[267176 rows x 4 columns]"
]
},
"execution_count": 34,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"dfc = dfc[[not x.startswith('G') for x in dfc['#CHROM']]]\n",
"sample_ids_snps = ['{} snp'.format(s) for s in sample_ids]\n",
"\n",
"def _call_snp(row, sample_id):\n",
" if ',' in row['ALT']:\n",
" return np.nan\n",
" m = {\n",
" '0': row['REF'],\n",
" '1': row['ALT'],\n",
" '.': ''\n",
" }\n",
" genotype = '{} {}'.format(m[row[sample_id][0]], m[row[sample_id][2]])\n",
" if len(genotype) != 3:\n",
" return np.nan\n",
" return genotype\n",
"\n",
"def call_snp(row):\n",
" return pd.Series([_call_snp(row, s) for s in sample_ids if s], \n",
" index=sample_ids_genotype)\n",
"\n",
"snps = dfc.apply(call_snp, axis=1)\n",
"snps"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def make_plink_map(df):\n",
" with open('pfeiffer.map', 'w') as mapfile:\n",
" for i, r in df.iterrows():\n",
" id_ = r['ID']\n",
" if id_ == '.':\n",
" id_ = '{}-{}'.format(r['#CHROM'], r['POS'])\n",
" mapfile.write(\n",
" '{} {} 0 {}\\n'.format(r['#CHROM'], r['POS'], id_)\n",
" )\n",
"\n",
"make_plink_map(dfc)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1 63735 0 1-63735\r\n",
"1 745370 0 rs146246821\r\n",
"1 752566 0 rs3094315\r\n",
"1 752721 0 rs3131972\r\n",
"1 758324 0 rs3131955\r\n",
"1 780027 0 rs2977613\r\n",
"1 808631 0 rs11240779\r\n",
"1 812267 0 rs7541694\r\n",
"1 812284 0 rs7545373\r\n",
"1 823790 0 rs143626389\r\n",
"1 834832 0 rs4411087\r\n",
"1 849998 0 rs13303222\r\n",
"1 851757 0 rs62677860\r\n",
"1 861808 0 rs13302982\r\n",
"1 862866 0 rs3892970\r\n",
"1 866319 0 rs9988021\r\n",
"1 866511 0 rs60722469\r\n",
"1 866920 0 rs2341361\r\n",
"1 867584 0 rs2341360\r\n",
"1 869323 0 rs13303207\r\n",
"1 870903 0 rs13303094\r\n",
"1 871334 0 rs4072383\r\n",
"1 873558 0 rs1110052\r\n",
"1 876499 0 rs4372192\r\n",
"1 878784 0 rs142929357\r\n",
"1 879317 0 rs7523549\r\n",
"1 879482 0 rs149880798\r\n",
"1 879676 0 rs6605067\r\n",
"1 879687 0 rs2839\r\n",
"1 880238 0 rs3748592\r\n",
"1 880390 0 rs3748593\r\n",
"1 881627 0 rs2272757\r\n",
"1 883625 0 rs4970378\r\n",
"1 884091 0 rs7522415\r\n",
"1 887560 0 rs3748595\r\n",
"1 887801 0 rs3828047\r\n",
"1 888639 0 rs3748596\r\n",
"1 888659 0 rs3748597\r\n",
"1 889158 0 rs56262069\r\n",
"1 889159 0 rs13302945\r\n",
"1 889638 0 rs13303206\r\n",
"1 892460 0 rs41285802\r\n",
"1 892745 0 rs13303227\r\n",
"1 894573 0 rs13303010\r\n",
"1 895706 0 rs13303327\r\n",
"1 896333 0 rs144174542\r\n",
"1 897325 0 rs4970441\r\n",
"1 897564 0 rs13303229\r\n",
"1 897730 0 rs7549631\r\n",
"1 898323 0 rs6605071\r\n",
"1 900285 0 rs4970435\r\n",
"1 900286 0 rs4970434\r\n",
"1 900505 0 rs28705211\r\n",
"1 902069 0 rs116147894\r\n",
"1 908823 0 rs28687780\r\n",
"1 909073 0 rs3892467\r\n",
"1 909238 0 rs3829740\r\n",
"1 909309 0 rs3829738\r\n",
"1 909555 0 rs2340594\r\n",
"1 909768 0 rs2340593\r\n",
"1 911916 0 rs74045046\r\n",
"1 914876 0 rs13302983\r\n",
"1 916549 0 rs6660139\r\n",
"1 928520 0 rs35002855\r\n",
"1 936848 0 rs149671836\r\n",
"1 941539 0 rs9778087\r\n",
"1 943468 0 rs3121567\r\n",
"1 943687 0 rs2465140\r\n",
"1 948846 0 rs3841266\r\n",
"1 948870 0 rs4615788\r\n",
"1 948921 0 rs15842\r\n",
"1 949235 0 rs2465124\r\n",
"1 949608 0 rs1921\r\n",
"1 949654 0 rs8997\r\n",
"1 949925 0 rs2799070\r\n",
"1 957898 0 rs2799064\r\n",
"1 962210 0 rs3128126\r\n",
"1 963249 0 rs2710870\r\n",
"1 971224 0 rs2799055\r\n",
"1 974662 0 rs2465135\r\n",
"1 977203 0 rs3121552\r\n",
"1 977330 0 rs2799066\r\n",
"1 977570 0 rs2710876\r\n",
"1 980460 0 rs3128097\r\n",
"1 981087 0 rs3128098\r\n",
"1 981931 0 rs2465128\r\n",
"1 982444 0 rs3128099\r\n",
"1 982462 0 rs3128100\r\n",
"1 982513 0 rs3128101\r\n",
"1 982941 0 rs3128102\r\n",
"1 982994 0 rs10267\r\n",
"1 986443 0 rs2710887\r\n",
"1 987200 0 rs9803031\r\n",
"1 988932 0 rs2710871\r\n",
"1 990806 0 rs2799073\r\n",
"1 1001177 0 rs4970401\r\n",
"1 1001178 0 1-1001178\r\n",
"1 1017587 0 rs3766191\r\n",
"1 1019175 0 rs2298215\r\n",
"1 1021346 0 rs10907177\r\n"
]
}
],
"source": [
"!head -n 100 pfeiffer.map"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"def make_plink_ped(snps):\n",
" with open('pfeiffer.ped', 'w') as pedfile:\n",
" for i, r in snps.T.iterrows():\n",
" s = ' '.join(list(r))\n",
" pedfile.write(\n",
" 'FAM1 {} 0 0 0 {}'.format(i.split()[0], s)\n",
" )\n",
"\n",
"make_plink_ped(snps.replace(np.nan, '0 0'))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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