GC content and average fold coverage of contigs

Question

[BAGeno]

Hi,

I want to know what is the relation between GC content and average fold coverage of contigs? If we have high percentage of GC content but low coverage of contigs what that means?

[Titus]

Hi, That mean you are in low complexity genome zone and probably your assembler/aligner had difficulty merging contigs/reads :)

Best

[BAGeno]

If there is other way around meaning low GC content but high fold coverage?

[Titus]

Not sure to understand your question now :) can you give some details ?

[BAGeno]

I am trying to understand a graph. this graph is plotted between % GC content and average fold coverage. Some point on the graph has low % GC content but high fold coverage and vice versa. I am trying to understand what this means.

[Titus]

Yes but if you are low %GC content you have low complexity sequence too (in an other word you are high %TA), that's also a problems for aligner/assembler. I'm sure to answer to your questions.... In you graph i don't know the normalization they use by species like number of reads per sequencing etc, but it could have an effect on Average Coverage fold.