5 | char | ‘+’ if query/target on the same strand; ‘-’ if opposite
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 matching bases in the mapping
11 | int | Number bases, including gaps, in the mapping
12 | int | Mapping quality (0-255; 255 for missing)
Column 11 gives the total number of sequence matches, mismatches and gaps in the alignment; column 10 divided by column 11 gives the BLAST-like alignment identity.
PAF may optionally have additional fields in the SAM-like typed key-value format. Minimap2 may output the following tags:
Description of the format is available [here](http://www.bx.psu.edu/~dcking/man/maf.xhtml).
## Index file
Index files used in D-Genies are built as follow.
First line contains the name of the sample. Next lines describes contigs of the sample. They are composed of two columns, tab separated. First it the name of the contig, second it's size in bases.
Example:
Homo sapiens
chr1 248956422
chr2 242193529
chr3 198295559
## Backup file
Backup file is a TAR archive. It contains three files:
* The alignment file, in paf format, named `map.paf`.
* The target index, named `target.idx`.
* The query index, named `query.idx`.
Names of files must be kept. Otherwise, the backup file will not be accepted by the run form.