Regarding Sam output

Question

[DL]

Hello,

Can someone explain me this output of sam file:

H1:1:H5GCLBCXY:1:2207:12808:60271       163     Chr01   12      0       48M103S =       1031    1164    TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACTTCTGTAGACCAAAAATCTTTCATATGATATCGGAATTTAGCGTGCCACATGTCTAGAAACTCGTATCTACATGCTCTTCGACACTCATTAAGAATATGTTCAA      DDDDDIIIIIIIIIIIIIIIIIIIIIHIIIHIHIIIIGHFEECHHIG?1C111<<<11DGEEH?11111<?F11<11111/<C111@11/<00<C?<111<<1<1@C@1<<<EE@11<<G111<C@?DE0<.<<@GC11<111@C1<D1<C      SA:Z:Chr01,801,+,55S96M,0,12;   MD:Z:48 PG:Z:MarkDuplicates     RG:Z:DC NM:i:0  AS:i:48 XS:i:48
H1:1:H5G72BCXY:2:2111:11610:91258       2129    Chr01   146     0       37H30M84H       Chr07   931     0       AAACCCTAACCCCTAAACCCTAACCCCTAA  000<110/</C1110111111/0/111111  SA:Z:Chr03,5064978,+,76M75S,5,3;     XA:Z:Chr05,-221,38S29M84S,0;Chr05,+85885405,84S30M37S,1;Chr05,+85885543,84S30M37S,1;Chr07,-1869,37S30M84S,1;    MD:Z:30 PG:Z:MarkDuplicates     RG:Z:DC      NM:i:0  AS:i:30 XS:i:29
H1:1:H5G72BCXY:1:2202:19457:37002       2211    Chr01   250     0       7H28M7D48M68H   Chr07   2937    0       GCCCTTCCATAATCCGGAGGTCTAGAACACCCCTAAACCCTAACCCCCAAACTTTTGTAGACCAAAACTCCTCCAT IHIIIIIHIIIIIIIIIHHI<GFHHHIIIIIIIIIIIIIIIIIIIIHIHIIIFGHGHHFHIIIIIIIIHHG?GEEH    SA:Z:Chr07,2077,+,105S46M,2,2;  XA:Z:Chr01,+499,7S28M7D48M68S,13;Chr01,+1423,7S28M7I77M32S,19;Chr01,+748,7S28M7I85M24S,21;Chr05,-85885426,101S43M7S,3;       MD:Z:23T4^AAGCTTA15T8C7G3C5T5   PG:Z:MarkDuplicates     RG:Z:DC NM:i:13 AS:i:33 XS:i:33
H1:1:H5GFFBCXY:1:2105:17384:57407       2209    Chr01   250     0       68H28M7D48M7H   Chr07   2718    0       GCCCTTCCATAATCCGGAGGTCTAGAACACCCCTAAACCCTAACCCCCAAACTTTTGTAGACCAAAACTCCTCCAT E@EEHEEHHHHHIHGH=EHHHGHEHIIIFEHD<<FG??=@GHHC?CHIDEHHCEFHGHHEHCGCHHHHICFH?CH    SA:Z:Chr05,24166413,+,54M97S,5,2;       XA:Z:Chr01,+499,68S28M7D48M7S,13;Chr01,+1423,68S28M7I19M29S,8;Chr05,-85885426,40S43M68S,3;Chr06,+3699,96S42M13S,3;Chr07,+2138,96S42M13S,3;   MD:Z:23T4^AAGCTTA15T8C7G3C5T5   PG:Z:MarkDuplicates     RG:Z:DC NM:i:13 AS:i:33 XS:i:33
H1:1:H5GFFBCXY:2:1210:7749:52073        2113    Chr01   250     0       68H28M7D48M7H   Chr04   59001326        0       GCCCTTCCATAATCCGGAGGTCTAGAACACCCCTAAACCCTAACCCCCAAACTTTTGTAGACCAAAACTCCTCCAT EHHIIIHIIIIIIHFHHIHIIIEHHIIIHIGI<EGHHEHHHHIIIIDHGEHHIHIIIG@EHCHFHHHIHIHHCHH    SA:Z:Chr05,24166413,+,54M97S,5,2;       XA:Z:Chr01,+499,68S28M7D48M7S,13;Chr01,+1423,68S28M7I19M29S,8;Chr05,-85885426,40S43M68S,3;Chr06,+3699,96S42M13S,3;Chr07,+2138,96S42M13S,3;   MD:Z:23T4^AAGCTTA15T8C7G3C5T5   PG:Z:MarkDuplicates     RG:Z:DC NM:i:13 AS:i:33 XS:i:33

I will be grateful and thanks in advance.

[WouterDeCoster]

Have you read the sam format specifications? What do you not understand?

[yhoogstrate]

The file you refer to has been split up over two files somewhere in the last one or two years. Tags are now desribed in here: https://samtools.github.io/hts-specs/SAMtags.pdf

[DL]

Yes, i have read it. Actually i extract supplementary alignment using SA tag. if you see these reads mapped to more than one position. can you just explain how they were mapped ??

[Devon Ryan]

I think I've fixed the formatting, but I may have accidentally merged a couple columns.