Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: All Possible Substitutions In The Human Reference Genome
0
gravatar for aravind ramesh
6.0 years ago by
aravind ramesh • 520
India
aravind ramesh • 520 wrote:

I was recently reading the CADD paper, they say that "all 8.6 billion possible substitutions in the human reference genome (GRCh37)". I thought possible substituiions should be more than that because of the genome size is arround 3 billion bases. Why is it different ?
human • 2.2k views
ADD COMMENT • link •
modified 22 months ago by Biostar ♦♦ 20 • written 6.0 years ago by aravind ramesh • 520
5
gravatar for Pierre Lindenbaum
6.0 years ago by
Pierre Lindenbaum ♦ 127k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 127k wrote:

count all ATGC bases in the genome:

$ cat human_g1k_v37.fasta | grep -v ">" | tr -d -c "[ATGCatgc]" | wc -c
2864785220

2864785220*3 = 8,594,355,660 ~ "8.6 billion possible substitutions"
ADD COMMENT • link modified 6.0 years ago • written 6.0 years ago by Pierre Lindenbaum ♦ 127k
3

To expand on what Pierre shows here, there are large stretches of the genome where the sequence has not been resolved and is represented by "N". These are especially common near the centromeres and telomeres.

ADD REPLY • link written 6.0 years ago by Chris Miller ♦ 21k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2055 users visited in the last hour