The .map file

The file S3/BY_RM_gxcomp.map gives an overview of the organization of the final sequence alignments. For each reference sequence, you have something like that:

>chrX [24352 - 729989]
chrX 24352 197492 cis + supercontig_1.8 1 29024 202068 99.14 0.23 0.24
chrX 204115 354637 cis + supercontig_1.8 1 202521 353040 99.59 0.20 0.21
chrX 354638 354832 cis + supercontig_1.8 1 353377 353570 97.07 0.00 0.00
chrX 355170 400123 cis + supercontig_1.8 1 353571 398451 99.17 0.06 0.06
chrX 400124 472455 cis + supercontig_1.8 1 398731 471082 99.31 0.10 0.10
chrX 483971 538095 cis + supercontig_1.8 1 471083 525249 99.36 0.07 0.07
chrX 538433 541087 cis + supercontig_1.8 1 525250 527879 97.71 0.00 0.00
chrX 541426 543597 cis + supercontig_1.8 1 527880 530052 99.08 0.00 0.00
chrX 543695 620997 cis + supercontig_1.8 1 530053 607313 99.42 0.10 0.11
chrX 621007 628798 cis + supercontig_1.8 1 607448 615241 99.12 0.01 0.01
chrX 628799 713797 cis + supercontig_1.8 1 615525 700524 99.68 0.11 0.12
chrX 715484 729989 cis + supercontig_1.8 1 702196 716707 99.47 0.02 0.02
*chrX - - - - supercontig_1.8 - - - - 0.92 0.95

where >chrX [24352 - 729989] indicates that the following section (until reaching a new > sign, like for a fasta file) deals with the alignments starting from position 24,352 (bp) to position 729,989 (bp) on reference sequence called chrX. Then comes a table into which each row stands for a full-length alignment (including moderate gaps). The column meaning is:

1. the name of the reference sequence,
2. the starting position of the alignment of the reference sequence,
3. the ending position of the alignment of the reference sequence,
4. the nature of the alignment,
5. the name of the query sequence involved in the alignment,
6. the strand of the alignment (1 is normal and -1 is reverse),
7. the starting position of the alignment of the query sequence,
8. the ending position of the alignment of the query sequence,
9. the percentage of identity,
10. the percentage of insertion (in the reference, or deletion in query),
11. the percentage of deletion (in the reference, or insertion in query).