3 reads with the same ID in sam file

Question

[Wang Cong]

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

[benformatics]

could they just be multimapping?

Answer 1

[Pierre Lindenbaum]

second read has flag 2163 : it's a SUPPLEMENTARY alignment . https://broadinstitute.github.io/picard/explain-flags.html

[Wang Cong]

Thanks! Could you explain the meaning of supplementary alignment since the website does not have a clear explanation.

[Pierre Lindenbaum]

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