Question: GC content and average fold coverage of contigs
1
gravatar for BAGeno
2.4 years ago by
BAGeno140
BAGeno140 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 2.4 years ago by BAGeno140

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

Best

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Titus900

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

ADD REPLYlink written 2.4 years ago by BAGeno140

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

ADD REPLYlink written 2.4 years ago by Titus900

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 2.4 years ago by BAGeno140

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 2.4 years ago by Titus900
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