what does this "/" in coverage_map mean?

tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

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what does this "/" in coverage_map mean? #118

Closed wn835166087 closed 5 years ago

wn835166087 commented 5 years ago

Hi, I got the coverage map of each contigs but I had no idea what does it mean... I assume "=" means aligned area while "..." means unaligned. But what does the "/" mean? Thank you!

best, nan

tseemann commented 5 years ago

Thank you for sending this, I realise that COVERAGE_MAP is not properly documented at https://github.com/tseemann/abricate#output - I will fix it.

Yes, = is aligned, . is unaligned, and / means the alignment had some gaps in it. These gaps could be "harmless" (a deleted in-frame codon) or could be damaging (frame-shift). It was designed as a quick visual aid, but I would like to do more work to properly illustrate what happened to the protein.

Also see #10