Question: Variant Present In 1000 Genomes Data But Not In Esp
gravatar for Vivek
6.9 years ago by
Vivek2.4k wrote:

Hello all,

I'm finding some variants that are present with a high allele fraction in the 1000 genomes project but not in the ESP project, despite good coverage available in the region.

For example:

11    58207204    rs4938895    A    G    100    PASS    AC=2166;THETA=0.0002;SNPSOURCE=LOWCOV,EXOME;AA=G;AN=2184;RSQ=0.9430;VT=SNP;AVGPOST=0.9991;ERATE=0.0008;LDAF=0.9912;AF=0.99;ASN_AF=1.00;AMR_AF=1.00;AFR_AF=0.97;EUR_AF=1.00

is an exonic variant in 1000 genomes and while the region has high enough coverage in the ESP data, there is no variant call.

Any ideas on why this might be happening?

1000genomes variant • 2.0k views
ADD COMMENTlink modified 6.9 years ago by rbagnall1.5k • written 6.9 years ago by Vivek2.4k
gravatar for rbagnall
6.9 years ago by
rbagnall1.5k wrote:

The human reference sequence contains some rare alleles, and some sequencing errors.

The 1000 Genomes data reports the frequency of alleles that differ from the reference sequence, so in the above example, all of the EUR and AMR individuals differed from the reference, hence an allele frequency of 1.00 (i.e. everybody was different from the reference).

In the ESP, all of the alleles at the above position are the same; there is no variation within the cohort, and no variant is reported.

ADD COMMENTlink written 6.9 years ago by rbagnall1.5k

The ESP project has samples from populations with European ethnicity as well. So, does it not seem a little strange that not one person in the population has an alternate allele at this locus when the 1000 genomes suggests that its pretty much a common variant in the same population?

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by Vivek2.4k

All people in the population have the alternate allele.

ADD REPLYlink written 6.9 years ago by Bert Overduin3.7k
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