Why the sequences are completely different with the same position in 1000 genome bam file

Question

[nonaddldy]

I am processing with the bam file whose Biosample name is SAMN00797154 and DNA-ID is NA07051 from 1000 genome project. And I filtered out the reads aligned to the chromosome Y, however, I found their sequences are totally different, even though they were aligned to the same position, so how can I select the read sequences if I try to assembly them.

A00132:45:HCFCVDSXX:4:1340:13810:3020   99      chrY    2781477 60      13S137M =       2781668 342     GATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGATTGGCGGATCACGAGGTCAGGAGATCGAGACCATCTTGGCTAACACCGCGAAACCCCGTCTCTACTAAAAATACAAAAAAAT  ??????????????????????????5????????????????+??????5??55???????????+??5????+??+?????+??????????????????????????????????????+??5???????????????????????+  MC:Z:94M1D56M   PG:Z:MarkDuplicates     MQ:i:60 AS:i:132        XS:i:102        MD:Z:0N0N0N53G80        NM:i:4  RG:Z:NA07051_CCAAGTCT-AAGGATGA_HCFCVDSXX_L004
A00217:59:HCFNWDSXX:1:1622:18756:6449   99      chrY    2781477 42      40S110M =       2781841 514     ATGCTCAGGACTCAGACCTTAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGATGGGCGGATCACGAGGTCAGGAGATCGAGACCATCTTGGCTAACACCGCGAAACC  ??????????????????5???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????  SA:Z:chrY,12476915,-,107S40M3S,0,0;     XA:Z:chr18,-70930457,107M43S,3; MC:Z:150M       PG:Z:MarkDuplicates     MQ:i:60 AS:i:110        XS:i:93 MD:Z:0N0N0N107  NM:i:3  RG:Z:NA07051_CCAAGTCT-AAGGATGA_HCFNWDSXX_L001
A00217:59:HCFNWDSXX:3:1605:10366:13401  163     chrY    2781477 60      22S128M =       2781693 367     TTAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGATGGGCGGATCACGAGGTCAGGAGATCGAGACCATCTTGGCTAACACCGCGAAACCCCGTCTCTACTAAAAATA  ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????+??????????????????  XA:Z:chr18,-70930439,125M25S,3; MC:Z:68M1D82M   PG:Z:MarkDuplicates     MQ:i:60 AS:i:128        XS:i:110        MD:Z:0N0N0N125  NM:i:3  RG:Z:NA07051_CCAAGTCT-AAGGATGA_HCFNWDSXX_L003

[microfuge]

I guess, the reads are soft clipped so the clipped sequences are in the read sequence. You can cut out first 13 bases of read1, first 40 bases of read2 and first 22 bases of read3 in your example.

[nonaddldy]

Thanks for your advice, so I am puzzed about how long are the clipped sequences now. Can I get the related information from the file instead of processing alignment again.

[WouterDeCoster]

It's in the CIGAR string. 13S, 40S and 22S.

[nonaddldy]

Thanks a lot.