Question: How to validate a ss and rs for SNPs?
1
gravatar for MichaelTrev
6 months ago by
MichaelTrev10
MichaelTrev10 wrote:

Hello, I have a many of SNP from SNPchimp base, and for example, in two files I have the same rs number, with the same position and same chromosome, but another ss.

Example: (chip_name, rs,ss,allels,orient, allels1, allels2, chromosome, positionOnChromosome)

Bov_IDBv2   rs17871566  ss28451907  A/G     forward     A/G     A/G     1   138583183

and:

Bov_IlluHD  rs17871566  ss251326633     A/G     forward     A/G     A/G     1   138583183

I have to be sure that rs are the same, and this is not just a mistake. So I would like to check if both "ss" refer to the same "rs". Where can I check it? dbSNP worked before but now it's only for human snps (?) in my case its cow SNPs, but now it does not search for "ss". Can anyone help?

snp • 242 views
ADD COMMENTlink modified 5 months ago by Kevin Blighe50k • written 6 months ago by MichaelTrev10
0
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe50k
Kevin Blighe50k wrote:

Each variant that is submitted to dbSNP is assigned a unique 'ss' number. In some cases, 2 or more submissions (and, thus, two or more ss numbers) will actually relate to the same variant. So, in such cases, we will have a single rs ID with multiple ss IDs.

Kevin

ADD COMMENTlink written 5 months ago by Kevin Blighe50k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2391 users visited in the last hour