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Table 1 The Graphical mApping Format (GAF)

From: The design and construction of reference pangenome graphs with minigraph

Col

Type

Description

1

string

Query sequence name

2

int

Query sequence length

3

int

Query start coordinate (0-based; closed)

4

int

Query end coordinate (0-based; open)

5

char

Strand relative to col. 6

6

string

Graph path matching regular expression

  

/([><][^\s><]+(:\d+-\d+)?)+|([^\s><]+)/

7

int

Path sequence length

8

int

Path start coordinate

9

int

Path end coordinate

10

int

Number of matching bases in the mapping

11

int

Number of bases, including gaps, in the mapping

12

int

Mapping quality (0–255 with 255 for missing)