hello, I do not understand the FLAG in SAM. could someone explain it. In paper " The Sequence Alignment/Map format and SAMtools", it says that According to FLAG
163(=1+2+32+ 128), the read mapped to position 7 is the second read in
the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to
37 on the reverse strand (32).
and each bit in the FLAG field is defined as:
Flag Description
0x0001 Paired in sequencing
0x0002 Mapped in proper read pair
0x0004 Query unmapped
0x0008 Mate unmapped
0x0010 Strand of the query (1 for reverse)
0x0020 Strand of the mate (1 for reverse)
0x0040 First read in the pair
0x0080 Second read in the pair
0x0100 Secondary alignment
0x0200 QC failure
0x0400 Optical or PCR duplicates
how to explain it. thanks in advance.
163(=1+2+32+ 128), the read mapped to position 7 is the second read in
the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to
37 on the reverse strand (32).
and each bit in the FLAG field is defined as:
Flag Description
0x0001 Paired in sequencing
0x0002 Mapped in proper read pair
0x0004 Query unmapped
0x0008 Mate unmapped
0x0010 Strand of the query (1 for reverse)
0x0020 Strand of the mate (1 for reverse)
0x0040 First read in the pair
0x0080 Second read in the pair
0x0100 Secondary alignment
0x0200 QC failure
0x0400 Optical or PCR duplicates
how to explain it. thanks in advance.
Comment