Hi Bastien, first of all thanks for the answer!I supposed CnNoCov meant that but I wasn't sure... Anyway, I would like to show you the results as in the four contigs obtained I've got values for CnNoCov. I'm almost sure this is a bug but I wanted to show it just in case it's useful for someone.
I also wanted to point out something strange for me. In the contigs 2, 3 and 4 I've got than the number of reads of each of those contigs is 1, that the mx. cov is also 1 and that the av. cov is "inf". I suppose I must also ignore this but I wanted to be sure. Could you please tell what this could mean?
# name length av.qual #-reads mx.cov. av.cov GC% CnIUPAC CnFunny CnN CnX CnGap CnNoCov contig00001 2834715 59 83314 315 16.07 59.82 13579 0 2 0 9417 1220315 contig00002 3626 30 1 1 inf 64.81 0 0 0 0 0 3626 contig00003 10073 30 1 1 inf 62.18 0 0 0 0 0 10073 contig00004 3661 30 1 1 inf 66.18 0 0 0 0 0 3661
Regards Marina Bastien Chevreux escribió:
On Donnerstag 04 März 2010 Marina Manrique wrote:I've run an assembly using the version V3.0.0 and I'd like to know what the fields of info_contigstats.txt are. I've got these fields # name length av.qual #-reads mx.cov. av.cov GC% CnIUPAC CnFunny CnN CnX CnGap CnNoCov According to the main manual (http://mira-assembler.sourceforge.net/docs/mira.html) these fields should be like this "This file contains statistics about the contigs themselves, their length, average consensus quality, number of reads, maximum and average coverage, average read length, number of A, C, G, T, N, X and gaps in consensus." I'd need to know what CnFunny and CnNoCov mean.CoNsensus Funny: non-IUPAC characters in the consenus, which would point at a bug. You may safely ignore that column, it should always be 0 anyway (if not I've got a problem)CoNsensus No Coverage: parts with a contig where no coverage is present. Should also never happen and would be a sign of a bug. ignore :-)Regards, Bastien
