The Sequence Alignment/Map (SAM) is a file format to save alignment information of short reads mapped against reference sequences. It usually starts with a header section followed by alignment information as tab separated lines for each read. Header section@HD VN:1.3 SO:coordinate @SQ SN:conticA LN:443 @SQ SN:contigB LN:1493 @SQ SN:contigC LN:328 readID43GYAX15:7:1:1202:19894/1 256 contig43 613960 1 65M * 0 0 CCAGCGCGAACGAAATCCGCATGC GTCTGGTCGTTGCACGGAACGGCGGCGGTGTGATGCACGGC EDDEEDEE=EE?DE??DDDBADEBEFFFDBEFFEBCBC=?BEEEE@=:?::?7?:8-6?7?@??# AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:65 YT:Z:UU readID43GYAX15:7:1:1202:19894/1 272 contig32 21001 1 65M * 0 0 GCCGGACGTCACACGGCCGCCGGG CCGGTCTACGACCAGACGCATGCGGATTTCGTTAGAGCCGG #??@?7?6-8:?7?::?:=@EEEEB?=CBCBEFFEBDFFFEBEDABDDD??ED?EE=EEDEEDDE AS:i:-5 XS:i:0 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:42T22 YT:Z:UU readID43GYAX15:7:1:1202:19894/1 256 contig87 540849 1 65M * 0 0 CCTGCACGAACGAAATCCGCATGCGTCTGGTC GTTGTACGGAACGGCGGTTGTGTGACGAACGGC EDDEEDEE=EE?DE??DDDBADEBEFFFDBEFFEBCBC=?BEEEE@=:?::?7?:8-6?7?@??# AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:65 YT:Z:UU Meaning of columns QNAME FLAG RNAME POS MAPQ CIGAR RNEXT PNEXT TLEN SEQ QUAL TAGS
Read alsoSAM Format Specification (PDF)→ How to filter reads using the SAM flags? (How to count the number of reads?) |