vg stats meaning: difference between Total alignments and Total alignments
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
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