the result assembled mito genome have more than one contigs

[jiangzy26]

Hi,
I found the result 'my_species.megahit.mitogenome.fa' has more than one contig, which one should I use? Thank you!
"
k141_84035_FivePCGs 4615 37 4615 4616
k141_321078_FivePCGs 5007 4691 5007 5008
k141_98991 18980 9727 18980 18981
k141_6742_FivePCGs 16774 28744 16774 16775
k141_398225_FivePCGs 16868 45557 16868 16869

"

[jiangzy26]

I downloaded the re-sequencing data from NCBI, it is only one species, why there are FivePCGs of other species? what are the implications? The best close species of these five contigs is not the species itself, I am not sure whether there are problems, could you share your help? Thank you very much

[linzhi2013]

In the MitoZ paper,

In addition, Sequences, regardless of gene conflicts, containing ≥ 5 PCGs (complete or not) will be retained to confirm identities, e.g. parasites.

Therefore, the users should further check what the "_FivePCGs" sequences belong to. The first and easy step, is to do a NT blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)

[linzhi2013]

See also https://github.com/linzhi2013/MitoZ/wiki/Tutorial#7-what-now

[jiangzy26]

Thank you very much for your kind reply, I'll read these carefully.