SAM file format

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

Tab-delimited read alignment information lines

readID43GYAX15:7:1:1202:19894/1 256 contig43 613960 1 65M * 0 0 CCAGCGCGAACGAAATCCGCATGCGTCTGGTCGTTGCACGGAACGGCGGCGGTGTGATGCACGGC 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 GCCGGACGTCACACGGCCGCCGGGCCGGTCTACGACCAGACGCATGCGGATTTCGTTAGAGCCGG #??@?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 CCTGCACGAACGAAATCCGCATGCGTCTGGTCGTTGTACGGAACGGCGGTTGTGTGACGAACGGC 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

• 1. Read Name

  2. SAM flag --> decode

  3. contig name or * for unmapped

  4. mapped position of base 1 of a read on the reference sequence

  5. MAPQ mapping quality

  6. CIGAR string describing insertions and deletions

  7. Name of mate

  8. Position of mate

  9. Template length

  10. Read Sequence

  11. Read Quality

  12. Additional information in TAG:TYPE:VALUE format

Read also

SAM Format Specification (PDF)

→ How to filter reads using the SAM flags? (How to count the number of reads?)