Question: how to analyze plot-vcfstats
gravatar for viswanathrana29
2.0 years ago by
viswanathrana2920 wrote:

hi all, I am identified the transition and transversion in plant genome and after that i plotted this data through plot-vcfstats in bcftools. then how can i analyze this grapghs.. thank you![this grapgh show i don't know about the number of sites so please help me to explain this graphs

plot-vcfstats • 1.4k views
ADD COMMENTlink modified 2.0 years ago by William4.2k • written 2.0 years ago by viswanathrana2920
gravatar for William
2.0 years ago by
William4.2k wrote:

For a complete genome or exome you expect a stable Ti/Tv ratio per species / sub species. This because there are biological factors at play that influence this number.

For instance for the human genome the ti/tv ratio is 2.1 for the genome and 2.8 for the exome.

False positive variants have a Ti/Tv ratio of 0.5. This because there a no biological factors at play, just sequencing noise, and there are twice as much possible Tv mutations(sequencing errrors) compared to Ti mutations(sequencing errrors).

So when you see a sharp drop of the Ti/Tv ratio towards 0.5 you start selecting for more false positive SNPs than true positive SNPs.

The plot you show indicates that your species probably has a Ti/Tv of 2.1.

It also shows that of the 55k SNPs sorted by variant quality descending, the last ca 5k SNPscause a large drop of the Ti/Tv. So these probably contain a lot of false positive variants not caused by biology but by sequencing noise.

ADD COMMENTlink written 2.0 years ago by William4.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1382 users visited in the last hour