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Question: All Possible Substitutions In The Human Reference Genome
0
gravatar for aravind ramesh
6.6 years ago by
aravind ramesh • 530
India
aravind ramesh • 530 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 • 2.3k views
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modified 2.4 years ago by Biostar ♦♦ 20 • written 6.6 years ago by aravind ramesh • 530
5
gravatar for Pierre Lindenbaum
6.6 years ago by
Pierre Lindenbaum ♦ 131k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 131k 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 6.6 years ago • written 6.6 years ago by Pierre Lindenbaum ♦ 131k
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 6.6 years ago by Chris Miller ♦ 21k
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