Mapping short reads with a ~50bp INDEL

0.00README.md

This is a small experiment on the alignment of ~50bp INDELs. The query sequences are shown in 0.01.fq below, where seq_ori is a 204bp sequence extracted from the human reference genome, seq_del54 contains a 54bp deletion in the middle, seq_del84 contains a 84bp deletion in a 120bp read, and seq_ins40 contains a 40bp insertion in a 140bp read. These four short sequences were mapped to the human reference genome with Bowtie2, BWA-MEM, LAST, Novoalign, SNAP and Stampy with default settings. Non-default scoring functions were also tested for Bowtie2 (--rdg 5,1 --rfg 5,1), BWA-MEM (-A2 -E1) and LAST (-r2 -q4). The output by various mappers/settings can be found in this gist. The following table gives my summary:

Mapper	Setting	-84bp	-54bp	+40bp
BBMAP	default	Yes	Yes	Yes
Bowtie2	default	No	No	No
Bowtie2	--rdg 5,1 --rfg 5,1	as insertion	as insertion	Yes
BWA-MEM	default	as split	Yes	Yes
BWA-MEM	-A2 -E1	Yes	Yes	Yes
LAST	default	as split	as split	as split
LAST	-r2 -q4	as split	as split	as split
Novoalign	default	No	Yes	Yes
SNAP	default	No	No	No
Stampy	default	No	No	Yes

SNAP finds hits within an edit-distance threshold (14 by default). It is practically unable to find ~50bp INDELs. I believe Bowtie2, LAST and Stampy should all be able to find the deletions in theory. I guess they don't because they have not used long enough reference subsequence in Smith-Waterman.

Disclaimer: I developed BWA-MEM and have evaluated it against similar examples (not this one) in development.

0.01.fq

@seq_ori
GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@seq_del54
GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@seq_del84
GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@seq_ins40
GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCtacgatataagcgcatcagtcatgctagtagctcaaattCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

0.bbmap

seq_ori	0	3	10646018	45	204=	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	AM:i:45
seq_del54	0	3	10646018	41	75=54D75=	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:54	AM:i:41
seq_del84	0	3	10646018	39	58=84D62=	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:84	AM:i:39
seq_ins40	0	3	10646122	18	49=40I51=	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:40	AM:i:18

0.bowtie2

seq_ori	0	3	10646018	42	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:204	YT:Z:UU
seq_del54	4	*	0	0	*	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
seq_del84	4	*	0	0	*	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
seq_ins40	4	*	0	0	*	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU

0.bowtie2-5,1

seq_ori	0	3	10646018	42	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:204	YT:Z:UU
seq_del54	0	3	10646142	2	5M70I75M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-81	XS:i:-86	XN:i:0	XM:i:1	XO:i:1	XG:i:70	NM:i:71	MD:Z:1T78	YT:Z:UU
seq_del84	0	3	10646153	2	4M52I2M1D62M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-63	XS:i:-69	XN:i:0	XM:i:0	XO:i:2	XG:i:53	NM:i:53	MD:Z:6^G62	YT:Z:UU
seq_ins40	0	3	10646122	8	49M40I51M	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:40	NM:i:40	MD:Z:100	YT:Z:UU

0.bwamem

seq_ori	0	3	10646018	60	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	MD:Z:204	AS:i:204	XS:i:20
seq_del54	0	3	10646018	60	75M54D75M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:54	MD:Z:75^GGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCT75	AS:i:90	XS:i:21
seq_del84	0	3	10646018	60	62M58S	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	MD:Z:62	AS:i:62	XS:i:19	SA:Z:3,10646160,+,58S62M,60,0;
seq_del84	2048	3	10646160	60	58H62M	*	0	0	GTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	MD:Z:62	AS:i:62	XS:i:0	SA:Z:3,10646018,+,62M58S,60,0;
seq_ins40	0	3	10646122	46	49M40I51M	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:40	MD:Z:100	AS:i:54	XS:i:19

0.bwamem-A2-E1

seq_ori	0	3	10646018	60	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	MD:Z:204	AS:i:408	XS:i:40
seq_del54	0	3	10646018	60	75M54D75M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:54	MD:Z:75^GGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCT75	AS:i:234	XS:i:42
seq_del84	0	3	10646018	58	58M84D62M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:84	MD:Z:58^GTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAG62	AS:i:144	XS:i:38
seq_ins40	0	3	10646122	60	49M40I51M	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:40	MD:Z:100	AS:i:148	XS:i:38

0.last

seq_ori	0	3	10646018	255	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:204
seq_del54	0	3	10646018	255	75M75H	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCC	*	NM:i:0	AS:i:75
seq_del54	0	3	10646147	255	75H75M	*	0	0	TCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:75
seq_del84	0	3	10646018	255	62M58H	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCT	*	NM:i:0	AS:i:62
seq_del84	0	3	10646160	255	58H62M	*	0	0	GTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:62
seq_ins40	0	3	10646171	255	89H51M	*	0	0	CAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:51
seq_ins40	0	3	10646122	255	50M90H	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCC	*	NM:i:0	AS:i:50

0.last-r2-q4

seq_ori	0	3	10646018	255	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:408
seq_del54	0	3	10646018	255	75M75H	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCC	*	NM:i:0	AS:i:150
seq_del54	0	3	10646147	255	75H75M	*	0	0	TCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:150
seq_del84	0	3	10646018	255	62M58H	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCT	*	NM:i:0	AS:i:124
seq_del84	0	3	10646160	255	58H62M	*	0	0	GTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:124
seq_ins40	0	3	10646171	255	89H51M	*	0	0	CAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	NM:i:0	AS:i:102
seq_ins40	0	3	10646122	255	50M90H	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCC	*	NM:i:0	AS:i:100
seq_ori	0	1	153945575	255	126H27M51H	*	0	0	GCTTCTTGTGGGCCAGGTCTTGGCCCC	*	NM:i:2	AS:i:42
seq_ins40	0	1	153945575	255	22H27M91H	*	0	0	GCTTCTTGTGGGCCAGGTCTTGGCCCC	*	NM:i:2	AS:i:42
seq_ori	16	11	119608589	255	107H29M68H	*	0	0	TTAGGGAGTTTGGACTTCATCCGGAAGGT	*	NM:i:3	AS:i:40
seq_ori	16	12	424106	255	106H23M75H	*	0	0	GTTAGGGAGTTTGGACTTCATCC	*	NM:i:1	AS:i:40

0.novoalign

seq_ori	0	3	10646018	70	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	PG:Z:novoalign	AS:i:0	UQ:i:0	NM:i:0	MD:Z:204
seq_del54	0	3	10646018	70	75M54D75M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	PG:Z:novoalign	AS:i:364	UQ:i:364	NM:i:54	MD:Z:75^GGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCT75
seq_del84	0	3	10646160	6	58S62M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	PG:Z:novoalign	AS:i:382	UQ:i:382	NM:i:0	MD:Z:62
seq_ins40	0	3	10646122	70	49M40I51M	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCtacgatataagcgcatcagtcatgctagtagctcaaattCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	*	PG:Z:novoalign	AS:i:280	UQ:i:280	NM:i:40	MD:Z:100

0.snap

seq_ori	0	3	10646018	70	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	PG:Z:SNAP	NM:i:0	RG:Z:FASTQ	PL:Z:Illumina	PU:Z:pu	LB:Z:lb	SM:Z:sm
seq_del54	4	*	0	0	*	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	PG:Z:SNAP	NM:i:-1	RG:Z:FASTQ	PL:Z:Illumina	PU:Z:pu	LB:Z:lb	SM:Z:sm
seq_del84	4	*	0	0	*	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	PG:Z:SNAP	NM:i:-1	RG:Z:FASTQ	PL:Z:Illumina	PU:Z:pu	LB:Z:lb	SM:Z:sm
seq_ins40	4	*	0	0	*	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	PG:Z:SNAP	NM:i:-1	RG:Z:FASTQ	PL:Z:Illumina	PU:Z:pu	LB:Z:lb	SM:Z:sm

0.stampy

seq_ori	0	3	10646018	96	204M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCGGATGAAGTCCAAACTCCCTAACTCCTCTGCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	UQ:i:0	NM:i:0
seq_del54	0	3	10646088	70	21I5M18D1M6I12M12I2M20D1M15I75M	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTCCCCTAACCTTCCTCTTGTGGGCCAGGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	UQ:i:858	NM:i:94
seq_del84	0	3	10646018	32	62M4I4M11D1M17I2M21D8M22I	*	0	0	GGGCTAAAGTCATACAACACACTTCCCATTGTTTCACTTCTCTGCCCCAAACCTCACAGTCTTGGCCCCCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	UQ:i:680	NM:i:76
seq_ins40	0	3	10646122	14	50M40I50M	*	0	0	GCAGACCAAGTATTGATTGGGTGCTTCTTGTGGGCCAGGTCTTGGCCCCCTACGATATAAGCGCATCAGTCATGCTAGTAGCTCAAATTCAGCTATCAGACACAAGCCTGTCTGCACAGAGTCTGGAATCCATAGCTTCT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	UQ:i:362	NM:i:40