---
name: "sam"
section: "5"
platform: "linux"
package: "libhts3t64"
version: "1.21+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sam/5"
---

# sam(5)

Sequence Alignment/Map file format

## NAME

sam - Sequence Alignment/Map file format

## DESCRIPTION

Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started with the \`@' symbol, each alignment line consists of:

| | | |
| --- | --- | --- |
| 1 | **QNAME** | Query template/pair NAME |
| 2 | **FLAG** | bitwise FLAG |
| 3 | **RNAME** | Reference sequence NAME |
| 4 | **POS** | 1-based leftmost POSition/coordinate of clipped sequence |
| 5 | **MAPQ** | MAPping Quality (Phred-scaled) |
| 6 | **CIGAR** | extended CIGAR string |
| 7 | **MRNM** | Mate Reference sequence NaMe (\`=' if same as RNAME) |
| 8 | **MPOS** | 1-based Mate POSition |
| 9 | **TLEN** | inferred Template LENgth (insert size) |
| 10 | **SEQ** | query SEQuence on the same strand as the reference |
| 11 | **QUAL** | query QUALity (ASCII-33 gives the Phred base quality) |
| 12+ | **OPT** | variable OPTional fields in the format TAG:VTYPE:VALUE |

Each bit in the FLAG field is defined as:

| | | |
| --- | --- | --- |
| 0x0001 | **p** | the read is paired in sequencing |
| 0x0002 | **P** | the read is mapped in a proper pair |
| 0x0004 | **u** | the query sequence itself is unmapped |
| 0x0008 | **U** | the mate is unmapped |
| 0x0010 | **r** | strand of the query (1 for reverse) |
| 0x0020 | **R** | strand of the mate |
| 0x0040 | **1** | the read is the first read in a pair |
| 0x0080 | **2** | the read is the second read in a pair |
| 0x0100 | **s** | the alignment is not primary |
| 0x0200 | **f** | the read fails platform/vendor quality checks |
| 0x0400 | **d** | the read is either a PCR or an optical duplicate |
| 0x0800 | **S** | the alignment is supplementary |

where the second column gives the string representation of the FLAG field.

## SEE ALSO

- https://github.com/samtools/hts-specs

  The full SAM/BAM file format specification