Table 1.
Mandatory fields in the SAM format
| No. | Name | Description |
|---|---|---|
| 1 | QNAME | Query NAME of the read or the read pair |
| 2 | FLAG | Bitwise FLAG (pairing, strand, mate strand, etc.) |
| 3 | RNAME | Reference sequence NAME |
| 4 | POS | 1-Based leftmost POSition of clipped alignment |
| 5 | MAPQ | MAPping Quality (Phred-scaled) |
| 6 | CIGAR | Extended CIGAR string (operations: MIDNSHP) |
| 7 | MRNM | Mate Reference NaMe (‘=’ if same as RNAME) |
| 8 | MPOS | 1-Based leftmost Mate POSition |
| 9 | ISIZE | Inferred Insert SIZE |
| 10 | SEQ | Query SEQuence on the same strand as the reference |
| 11 | QUAL | Query QUALity (ASCII-33=Phred base quality) |