I have sam files for the chimeric reads, which come from two different parts of the genome (For example, the first half of the read from part of Chromosome 1 and the second half of the read from part of Chromosome 3). I found 3 reads with the same ID in the sam files. Could anyone explain this? Thanks!
L180:234:HTHGMADXX:1:1101:1137:6179 99 V 10092485 60 29S33M = 10092488 63 ACATGTGCGAAAAAAAAACTTTGAGTATTTTGTGCGTTGATGATGTTGGGGGAATGAGTGTG BBBFFFFFFFFFFIIIIIFFFIFIFFFIFBFFFFIIBFFIIFIIIBFFFFFFBFFFFFBB<B NM:i:0 MD:Z:33 MC:Z:60M AS:i:33 XS:i:0 SA:Z:V,10092453,-,29S33M,60,0;
L180:234:HTHGMADXX:1:1101:1137:6179 2163 V 10092453 60 29H33M = 10092488 63 ACAAAATACTCAAAGTTTTTTTTTCGCACATGT FFFBFIFFFIFIFFFIIIIIFFFFFFFFFFBBB NM:i:0 MD:Z:33 MC:Z:60M AS:i:33XS:i:0 SA:Z:V,10092485,+,29S33M,60,0;
L180:234:HTHGMADXX:1:1101:1137:6179 147 V 10092488 60 60M = 10092485 -63 TGCGTTGATGATGTTGGGGGAATGAGTGTGACGAAATTGAAAAACTAAAAGCAGAAGTAG IIFIIIIIIIIFFIIIIIIIIIIIIIIIIFFIIIIIIIIIIIIFIFIFFFFFFFFFFBBB NM:i:0 MD:Z:60 MC:Z:29S33M AS:i:60 XS:i:0
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Wang Cong •
second read has flag 2163 : it's a SUPPLEMENTARY alignment . https://broadinstitute.github.io/picard/explain-flags.html
Thanks! Could you explain the meaning of supplementary alignment since the website does not have a clear explanation.
https://www.slideshare.net/lindenb/ngsformats
slide 44: a part of the read that maps elsewhere. The first 29 base of the read are hard-clipped. see SA:Z flag. A part of the read also maps at V:10092485
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could they just be multimapping?