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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.

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