PAF.md

PAF: a Pairwise mApping Format

PAF is a text format describing the approximate mapping positions between two set of sequences. PAF is TAB-delimited with each line consisting of the following predefined fields:

Col	Type	Description
1	string	Query sequence name
2	int	Query sequence length
3	int	Query start (0-based; BED-like; closed)
4	int	Query end (0-based; BED-like; open)
5	char	Relative strand: "+" or "-"
6	string	Target sequence name
7	int	Target sequence length
8	int	Target start on original strand (0-based)
9	int	Target end on original strand (0-based)
10	int	Number of residue matches
11	int	Alignment block length
12	int	Mapping quality (0-255; 255 for missing)

If PAF is generated from an alignment, column 10 equals the number of sequence matches, and column 11 equals the total number of sequence matches, mismatches, insertions and deletions in the alignment. If alignment is not available, column 10 and 11 are still required but may be highly inaccurate.

A PAF file may optionally contain SAM-like typed key-value pairs at the end of each line.