Interpreting "Mapping quality across reference" in qualimap

[Barbara Binney]

Using shovil I created a draft genome for  some ~4MBp bacteria. Then I mapped each draft genome to itself. When I look at the results in qualimap there is good coverage of the whole genome. However in some cases when I look at the  "Mapping quality across reference" analysis, it shows the quality drops very low for a section of the genome. These same genomes when I look at them in checkm show results that suggest contamination. Is it possible the sections with poor quality are contigs that may be contaminated and hence the drop in quality compared to the rest?

[Konstantin Okonechnikov]

Hi,

Indeed mapping quality reflects possible unclear mapping due to sequence segment similarity, but there could be some other issues. Qualimap only integrates already computed values as provided in BAM file. Here probably checking the read alignments in these segments would be useful. Also I would suggest checking how mapping quality is provided by the alignment tool that was applied to have a clear explanation. Maybe this could be useful: http://www.acgt.me/blog/2014/12/16/understanding-mapq-scores-in-sam-files-does-37-42 

Best regards,

   Konstantin

On Fri, Jan 7, 2022 at 3:23 AM Barbara Binney <5apt...@gmail.com> wrote:

Using shovil I created a draft genome for  some ~4MBp bacteria. Then I mapped each draft genome to itself. When I look at the results in qualimap there is good coverage of the whole genome. However in some cases when I look at the  "Mapping quality across reference" analysis, it shows the quality drops very low for a section of the genome. These same genomes when I look at them in checkm show results that suggest contamination. Is it possible the sections with poor quality are contigs that may be contaminated and hence the drop in quality compared to the rest?

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