minigraph --call output

[panosioannidis]

I'm running minigraph -cxasm --call out.gfa sample.fa > sample.bed to find the coverage of sample in the bubbles of the graph. The output is not hard to understand, but I am a bit confused with the coordinates.

For one particular bubble I get the following 3 different types of output (for 3 different samples):

Sample Th_026

CHM13#1#chr1	3690	3752	>s1	>s3	>s2:62:+:Th_026#1#ptg000057l:2751:2893

Sample Th_009

CHM13#1#chr1	3690	3752	>s1	>s3	.

Sample Th_137

CHM13#1#chr1	3690	3752	>s1	>s3	*:0:+:Th_137#1#ptg000037l:5644:5724

My interpretation is this:
For Th_026, there's an insertion. The insertion is on contig ptg000057l of Th_026, from position 2751 to 2893.

For Th_009, there's nothing (no insertion, no deletion); it contains the reference sequence.

For Th_137, there's a deletion (denoted by the *). The deletion is on contig ptg0000037l, but I don't understand what the coordinates mean; how can it be that the deletion goes from 5644 to 5724 on that contig of Th_137? In contrast, I would understand it if it had a range on the CHM13 genome (i.e. the reference used for building the graph). It would mean that this sequence from CHM13 is missing from sample Th_137...

What am I missing?

[panosioannidis]

Does anyone have any idea about the above? Thanks!