Flag=4 in SAM

[Rachelly]

Hi all,

As I understood from the SAM-BAM specification if the flag has a value of 4 it is an unmapped read.
In my SAM file I see lines that contain a flag with a 4 value, but also a mapping to a specific location in a scaffold (see below).

What am I missing here? Are these reads aligned or not?

Thanks!
Rachelly.

HWUSI-EAS1701:5:43:18320:19669#0 4 scaffold_1 2409915 37 26M1I11M * 0 0 ATTTTATAATAATTATTATAATTTTTAAATATTATATA ggggcgggfgggggagggdgggggcgff_ggggggggg XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i
:2 XO:i:1 XG:i:1 MD:Z:27T8T0
HWUSI-EAS1701:5:50:10811:4208#0 4 scaffold_1 2409937 37 4M1D34M * 0 0 ATATTTATTATATTAATAAATTAATAAATAATTATAAT hhhhhhhhhchfhgaddhhhfghhhhhhghghghhhhg XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i
:1 MD:Z:0T1T1^A34
HWUSI-EAS1701:5:71:15668:16046#0 4 scaffold_1 2409937 37 4M1D34M * 0 0 ATATTTATTATATTAATAAATTAATAAATAATTATAAT cgggdgfgggggdg_fffffgggggggggfgggggggg XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i
:1 XG:i:1 MD:Z:0T1T1^A34

[drio]

From the bwa FAQ:


Q. I see a read stands out the end of a chromosome and is flagged as unmapped (flag 0x4). What is happening here?

A. Internally BWA concatenates all reference sequences into one long sequence. A read may be mapped to the junction of two adjacent reference sequences. In this case, BWA will flag the read as unmapped, but you will see position, CIGAR and all the tags. A better solution would be to choose an alternative position or trim the alignment out of the end, but this is quite complicated in programming and is not implemented at the moment.

[Rachelly]

Thanks very much drio!