Identifying The Mismatched Bases And Their Locations On The Chromosome In .Sam File
How do I find the mismatched bases in these two segments:
962_1394_1642 163 chr1 156 1 25M10H = 329 197 CTAACCCTAACCCTAACCCTAACCT IIIIIIIIIIIIII,,IICEI((5/ NH:i:3 RG:Z:20110729204302219 CS:Z:T22301002301002331002303022302003000 CQ:Z:0B=@B.=7BB1=;@B,5?.60;(++%3)'%%)-;% SM:i:0 CM:i:2 NM:i:0 MD:Z:25
1517_881_880 147 chr1 159 22 31M4H = 349 215 ACCCTAACCCTAACCCTAACCTAACAATAAC IIIIIIIIIDIIIH=CIIG@:')G)''&13, NH:i:1 RG:Z:20110729204302219 CS:Z:T31002301002301002301022011033011.20 CQ:Z:?9=6>;3>=-8?;54*:<;-4')355)'&,(%!%( SM:i:4 CM:i:3 NM:i:2 MD:Z:25C0C4
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Pierre Lindenbaum
If you to find out the mismatches against a reference genome then you can pull out the corresponding region 'chr1:156-(156+25)' of the reference genome and then perform a sequence alignment. Do the same thing with the second segment. In case you need to compare these two segments with each other then you can simply take the sequence and do the sequence alignment.
Here is the tool for sequence alignment:
BTW, the first sequence has NH:i:3 (multiple hits) so it may or may not belong to the region mentioned in the bam file.
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Ashutosh Pandey
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duplicate of
position of mismatches per read from a sam/bam file