Question: GC content and average fold coverage of contigs
1
gravatar for BAGeno
12 months ago by
BAGeno70
BAGeno70 wrote:

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?

ADD COMMENTlink written 12 months ago by BAGeno70

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

Best

ADD REPLYlink modified 12 months ago • written 12 months ago by Titus610

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

ADD REPLYlink written 12 months ago by BAGeno70

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

ADD REPLYlink written 12 months ago by Titus610

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.Here is its link

ADD REPLYlink written 12 months ago by BAGeno70

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.

ADD REPLYlink written 12 months ago by Titus610
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