flag inside sam file

[fanping]

I got a read aligned as below:
HWI-1KL138:2:2105:12847:125331#GCCAATGCCAAT 161 chr1 12036 1 74M = 12645 1188 CTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAGTGGGATGGG hhhhhhhhhhhghhhhhhhhhhhhhhhhhheffffdffffhhhghhehefhhhhhghhfhfffWdbfffbffff NM:i:0 NH:i:3 CC:Z:chr15 CP:i:102519061 HI:i:0

The flag here is 161=128+32+1. 128 means 2nd pair; 32 means mated reverse strand; 1 means paired read. I am wondering why there is no information about the alignment in this flag. The alignment info can be either both aligned, read unmapped, mate unmapped indicated by 0x2, 0x4, 0x8 in sam files. Thanks advance for any answer or comment.

fanping

[swbarnes2]

The lack of 4 and 8 means that both aligned.

The 2 flag means "properly paired", not "both aligned". That means not only did both ends map, but that their orientation and distance is what the software was expecting. Your reads are more than a kb apart. This may be why the software didn't think they were properly paired.

[fanping]

Thanks. It makes sense.

fanping

The lack of 4 and 8 means that both aligned.

The 2 flag means "properly paired", not "both aligned". That means not only did both ends map, but that their orientation and distance is what the software was expecting. Your reads are more than a kb apart. This may be why the software didn't think they were properly paired.