Whole Exome Sequencing: genotype format

Question

[fanStar]

Hi All,

We are currently analyzing whole exome sequencing data produced by 'SureSelect Human All Exon v.1 Kit' .

We've found that most of SNPs with the form 'var_chr*_<number>' and the rest of SNPs with the standard form 'rs_<number>'.

The example is given as below:

example.bim

--------------------------------------------------------------------------->>>

1 var_chr1_69270 0 69270 A G

1 rs140739101 0 69428 G T

1 rs142004627 0 69453 A G

1 rs75062661 0 69511 A G

1 rs55874132 0 69552 C G

1 var_chr1_69569 0 69569 C T

1 var_chr1_69761 0 69761 T A

1 var_chr1_69897 0 69897 T C

----------------------------------------------------------------------------<<<

Could you maybe give any hint about this? What does 'var_chr*_<number>' mean? Many thanks for your information!

Answer 1

[NB]

This just means that there is no rs id associated with that particular variant. 'var_chr_<number> just implies the variant with its chromosome number and genomic coordinate position.

[fanStar]

@NB, thanks for your answer, but it's self-explanatory. Does it mean that 'rs_<number>' is the SNP that belongs to the exome region?

[NB]

The rs number is an accession number, it stands for Reference SNP cluster ID. Please have a look at dbSNP