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~
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~
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