bamcov
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Nice tool, but bugs with short contigs and long reads?
This contig has 0 reads, but paradoxically coverage is listed. Seen for quite a few contigs. Having said that, this is not classic aligned data, but rather long reads ONT data from the Megalodon pipeline (you can't call SNPs on this data weirdly) so it might be my weird stuff. Just a note for other users.
contig96 (291.7Kbp)
> 90.00% │ ████████████████ │ Number of reads: 0
> 80.00% │ ▄████████████████▄ │
> 70.00% │ ██████████████████ │ Covered bases: 103.4Kbp
> 60.00% │ ██████████████████ │ Percent covered: 35.44%
> 50.00% │ ██████████████████ │ Mean coverage: 0.354x
> 40.00% │ ██████████████████ │ Mean baseQ: 255
> 30.00% │ ██████████████████ │ Mean mapQ: -nan
> 20.00% │ ██████████████████ │
> 10.00% │ ██████████████████ │ Histo bin width: 5.8Kbp
> 0.00% │ ██████████████████ │ Histo max bin: 100%
1 58.3K 116.7K 175.0K 233.4K 291.7K