BWA : XM tag is sometimes wrong

[Lcontami]

Hi,
I've been using the XM tag to find reads with no mismatches but sometimes this tag doesn't give the right number of mismatches.
Has someone else had this problem ? How did you fix it ?

Here is a few examples :

HWI-ST0787:100:C02F9ACXX:7:2307:2404:186548 163 gi|83578099:1-1090946 95044 60 37M1D2M1D62M = 95049 108 GGGGTTTCGGAAAACAAACTCGCTCGATACAGTAATTGCGTTTTATTTACGGAAATTACCGTTCTCGGTTCCAAGAAGGTTAGAAAAATCGGTTGTCGCTC +1+4+0=D+<CFADB9E@@99:CG:BF)*9?DDDC@D?'-<;@=FHCHDB1?EEBCFEFDDCC;?B=8<35@C9?AA?A:?(:4<8ACBB<995>>158 XT:A:U NM:i:4 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:2 MD:Z:0C1T34^G2^A62

HWI-ST0787:100:C02F9ACXX:7:2307:9817:186685 147 gi|83578099:1-1090946 95060 60 21M1D2M1D78M = 94975 -188 AACTCGCTCGATACAGTAATTGCGTTTTATTTACGGAAATTACCGTTCTCGGTTCCAAGAAGGTTAGAAAAATCGGTTGTCGCTCTTTCTTTCCCCCACTT @9B@DDBBDDEEDDDDDDDDBB<@DCDDDAB<@?:3EDC?<8DDDDBDCA??EBHHHHHHIIIIJIIGGJIHIGIIGJJJIIJIGEIHF;@?1FDDBB?B? XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:21^G2^A78

HWI-ST0787:100:C02F9ACXX:7:2307:17522:186893 83 gi|83578099:1-1090946 999268 60 68M1I31M2D1M = 999191 -179 CCCTGTATAATGAAATTTCAAAAATATTTTCGTGAATAGTGATTTATTTAATTTAAGCACTAAATTATCCTTACGGACTTGGGCTACATTCATGTTTGCAC BCCCCDDCADCCCCCCCCEED?3HEEA;4EAHHEG>FDCB=CIHGIIGGIHFF<DBGIHEGEIGGFF<EGGBCFAFAB?B3HB<BFE9B>DDHD??DA@?1 XT:A:U NM:i:4 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:1 MD:Z:3C95^AG1

HWI-ST0787:100:C02F9ACXX:7:2307:12781:188676 83 gi|50593115:1-813178 389360 60 61M1D3M1D37M = 389271 -192 TTTAACTTATGAATGTACTTTACTGGCCAAGAATCCGTCTGGAACCATTCTACGGTGCTCTTGCTAGCGCTAAAGACAGCTATAGTGGATATTCAGACGGT >DDCCCCC@DDFDCCCBCCCCDBCCAECECDB8HHHIHDA@==)GCGDCFC8GEJIFJFIGHDJGIIGGHIIGGEBJJFHIJIGGHFGGGHHDFDDBF@C@ XT:A:U NM:i:3 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:2 MD:Z:61^C1T1^G37

[mastal]

BWA : XM tag is sometimes wrong

from the CIGAR strings for the reads in your examples, it looks like you have some deletions or insertions, but not mismatches.

[Lcontami]

More details

HWI-ST0787:100:C02F9ACXX:7:2307:2404:186548 163 gi|83578099:1-1090946 95044 60 37M1D2M1D62M = 95049 108 GGGGTTTCGGAAAACAAACTCGCTCGATACAGTAATTGCGTTTTATTTACGGAAATTACCGTTCTCGGTTCCAAGAAGGTTAGAAAAATCGGTTGTCGCTC +1+4+0=D+<CFADB9E@@99:CG:BF)*9?DDDC@D?'-<;@=FHCHDB1?EEBCFEFDDCC;?B=8<35@C9?AA?A:?(:4<8ACBB<995>>158 XT:A:U NM:i:4 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:2 MD:Z:0C1T34^G2^A62

For example in this line, we have 2 deletions and 2 mismatches (see the MD tag). It sums to an edit distance of 4 (in accordance to the NM tag)
However, the XM tag is equal to 3, whereas it should be 2.

[mastal]

BWA : XM tag is sometimes wrong

from the CIGAR strings for the reads in your examples, it looks like you have some deletions or insertions, but not mismatches.

sorry, my error, M in the CIGAR string means match or mismatch.