The 'S' in CIGAR of sam file (bwa)

[qixiaofei]

the S means "soft clipping (clipped sequences present in SEQ)".
but I saw an example of CIGAR which is "72M28S" (4mismatch),and actually, there is only one mismatch in the 28S! I doubt why the result of aln is not 100M (5mismatch)? I saw Many similar situation ? who can help me ? thank U~

[nilshomer]

Can you show is the read and alignment?

[qixiaofei]

Can you show is the read and alignment?

B80FGAABXX:6:23:6777:40030#0 83 chr10 42383349 10 28S72M = 42383248 -173 AATCAGATGGAATCATCGAATGGACTTGAATGGAATCGTTGAATGGACTCGAATGGAATCATTATTGAATGGAATTGAATAGAATCATCGAATGGTCTCG ??A??ED=E:ECD=?EDD:AEEEEEDFDGEDGFGEDFGEGEEGDGGBGGEDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGG XT:A:M NM:i:5 SM:i:10 AM:i:10 XM:i:5 XO:i:0 XG:i:0 MD:Z:9A2A39G5T2C10
B80FGAABXX:6:25:6662:82018#0 147 chr10 42383349 10 30S70M = 42383248 -171 GGAATCAGATGGAATCATCGAATGGACTGGAATGGAATCATTGAATGGACTCGAAAGGGATCATTATTGAATGGAATTGAATGGAAGCATCGAATGGTCT DEFEAGFEGFFEF?BGGG?GDFFGEEGDFFGEGFDGGGGGGGGFGGGGFGGGEGGGGGGFEGGGGGGFGGGGGGGFEGGGGGGGGGGGGGGGGGGGGGFG XT:A:M NM:i:6 SM:i:10 AM:i:10 XM:i:6 XO:i:0 XG:i:0 MD:Z:12A12T2A27T1T2C8

I give two lines , and the ref before the pos 42383349 is ggaatcagatggaatcatcgaatggacttt(30bp) only the last 2 bp is mismatch with the second read given.

[nilshomer]

I agree, looking at BLAT it seems as though this read is quite repetitive too, and is not annotated as such. It would be great to post to the bwa mailing list to file a bug.

What is your mismatch tolerance (show the command line)? BWA (short) will try to align a prefix of the read, and it may be hitting its mismatch/indel tolerance limit.

[qixiaofei]

I agree, looking at BLAT it seems as though this read is quite repetitive too, and is not annotated as such. It would be great to post to the bwa mailing list to file a bug.

What is your mismatch tolerance (show the command line)? BWA (short) will try to align a prefix of the read, and it may be hitting its mismatch/indel tolerance limit.

I only have the results, and don't know the command line. but there is "XM:i:22" on other line of the sam . the example I gave before only "XM:i:5"and "XM:i:6",respectively. I am a beginner, don't know the principle of bwa. why it happens?

[nilshomer]

You will have to play with it yourself and read the paper. Unfortunately, it is beyond the scope of this forum for me to try to debug and explain it to you. Can you get the command line?

[qixiaofei]

You will have to play with it yourself and read the paper. Unfortunately, it is beyond the scope of this forum for me to try to debug and explain it to you. Can you get the command line?

I'm sorry for replying so late .
the command line as follows
bwa aln -n 3 -o 1 -e 15 -i 5 -l 32 -t 4