Average Organelle Coverage – not always in the log file?

[akimmitt]

Hello! We assembled hundreds of mtgenomes using Novoplasty and want to report coverage. I know that log files contain a line "Average organelle coverage" but 219/815 of my files are missing this line. These files, however, do report total reads, aligned reads, and assembled reads.

How is the average organelle coverage calculated and what would cause this data to be missing (e.g. uncertainty of about the length of the organelle genome)?

In some cases, most individuals of one species are missing coverage data. But in other cases, there are just a few individuals that are missing coverage data, while it has been calculated for other individuals of the same species.

Thanks in advance! Abby

PS- I've attached an example of a complete log file and a log file missing the "average organelle coverage" line. log_12302.txt

log_12341.txt

[akimmitt]

Hi Nick! I'm checking in to ask if you have any idea on why this data would be missing?

[ndierckx]

Hi,

Sorry I forgot to reply to you. It only outputs coverage data when the genome was circularized...

[akimmitt]

Hi Nick,

Thanks for getting back to me. I'm curious how the average coverage is calculated? For example, if the program has duplicated the genome (so that there are second gene copies in the final output), how does this affect the average coverage?

Thanks in advance, Abby

[ndierckx]

HI It is calculated based on the the amount of reads that were recruited for the assembly. If you need a accurate figure, maybe better to realign the reads

[akimmitt]

Thank you