% of mtDNA reads of the total sequence reads that mapped to the whole mtDNA in MITObim

[AliBasuony2022]

Dear friends,

I have got a question from a reviewers regarding % of mtDNA reads of the total sequence reads that mapped to the whole mtDNA in MITObim. Where I can find this information in MITObim outputs, please. I have checked all the outputs files, but unfortunately didn't find any information related to that.

There is some information in the log file as below:
readpool contains 353396 reads
assembly contains 1 contig(s)
contig length: 18353

Note: The total number of raw reads is 216,237,628 (both nuDNA and mtDNA)

Kind regards,
Ali

[chrishah]

Hi,

The readpool are the reads that were baited based on your putative mt genome so I would consider these the mitochondrial reads, so about 0.16 % of the total, in your case.

cheers,
Christoph

[AliBasuony2022]

Thanks so much, Christoph.

[AliBasuony2022]

Hi Christoph,

Is this read pairs or individual reads? "readpool contains 353396 reads"
see log file below

mitobim_375_trimmed data.log

Thanks,
Ali