| Key | Definition |
|---|---|
| SAMPLE | Sample name |
| TYPE | Variant Type: SNV Insertion Deletion Complex |
| DP | Total depth |
| End | Chromosome end position |
| VD | Variant depth |
| AF | Allele frequency |
| BIAS | Strand bias info |
| REFBIAS | Reference depth by strand |
| VARBIAS | Variant depth by strand |
| PMEAN | Mean position in reads |
| PSTD | Standard deviation of position in reads |
| QUAL | Mean quality score of reads |
| QSTD | Standard deviation of quality score of reads |
| SBF | Strand bias Fisher p-value |
| ODDRATIO | Strand bias odd ratio |
| MQ | Mean mapping quality |
| SN | Signal to noise |
| HIAF | Allele frequency using only high quality bases |
| ADJAF | Adjusted allele frequency for indels due to local realignment |
| SHIFT3 | Number of bases to be shifted to 3 prime for deletions due to alternative alignment |
| MSI | Microsatellite - greater than 1 indicates MSI |
| MSILEN | Microsatellite unit length in bp |
| NM | Mean mismatches in reads |
| LSEQ | 5' flanking sequence |
| RSEQ | 3' flanking sequence |
| GDAMP | Number of amplicons supporting variant |
| TLAMP | Total of amplicons covering variant |
| NCAMP | Number of amplicons don't work (WTF?) |
| AMPFLAG | Top variant in amplicons don't match |
| HICNT | High quality variant reads |
| HICOV | High quality total reads |
| Key | Definition |
|---|---|
| Q25 | Mean base quality below 25 |
| Q10 | Mean mapping quality below 10 |
| p8 | Mean position in reads less than 8 |
| SN1.5 | Signal to noise ratio less than 1.5 |
| Bias | Strand bias |
| pSTD | Position in reads has a standard deviation of 0 |
| d3 | Total depth < 3 |
| v2 | Variant depth < 2 |
| f0.0 | Allele frequency < 0.0 |
| MSI12 | Variant in MSI region with 12 non-monomer or 13 monomer MSI |
| NM4.25 | Mean mismatches in reads >= 4.25 thus likely false positives |
| InGap | The variant is in the deletion gap, thus likely false positive |
| InIns | The variant is adjacent to an insertion variant |
| Cluster0bp | Two variants are within 0 bp |
| LongMSI | The somatic variant is flanked by a long A/T (>=14) |
| AMPBIAS | Indicates the variant has amplicon bias |
| Key | Definition |
|---|---|
| GT | Genotype |
| DP | Total depth |
| VD | Variant depth |
| AD | Allelic depths for the REF and ALT alleles in the order listed |
| AF | Allele frequency |
| RD | Reference forward, reverse reads |
| ALD | Variant forward, reverse reads |