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
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
Comment