| field | description |
|---|
| qName | Query template name - name of a read |
| flag | Flags. 0x10 set for reverse complement. See SAM docs for others. |
| rName | Reference sequence name (often a chromosome) |
| pos | 1 based position |
| mapQ | Mapping quality 0-255, 255 is best |
| cigar | CIGAR encoded alignment string. |
| rNext | Ref sequence for next (mate) read. '=' if same as rName, '*' if no mate |
| pNext | Position (1-based) of next (mate) sequence. May be -1 or 0 if no mate |
| tLen | Size of DNA template for mated pairs. -size for one of mate pairs |
| seq | Query template sequence |
| qual | ASCII of Phred-scaled base QUALity+33. Just '*' if no quality scores |
| tagTypeVals | Tab-delimited list of tag:type:value optional extra fields |