samtools flags

I can never remember the order of the columns in samtools, so here they are

  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. INSIZE: Inferred insert size
  10. SEQ: Sequence on the same strand as the reference
  11. QUAL: Query quality (ASCII-33=Phred base quality)

There are lots more details in the samtools manual

You should also use the samtools flag explainer to understand column 2