vg stats meaning: difference between Total alignments and Total alignments
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15 months ago
xwwang ▴ 20

We used vg stats to generate some statistical information. It works well.

The question is what is the difference between "Total alignments" and "Total alignments" in the output. It is very confusing.

Example of vg stat output:

Total alignments: 9991

Total primary: 9991

Total secondary: 0

Total aligned: 7706

Total perfect: 0

Total gapless (softclips allowed): 157

Insertions: 54887 bp in 54133 read events

Deletions: 54045 bp in 53599 read events

Substitutions: 67714 bp in 67286 read events

Softclips: 23 bp in 22 read events
vg graph stats • 386 views

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