How to find the allele A and B in the snpmap file?
0
1
Entering edit mode
9.1 years ago
camilaubraz ▴ 10

I have a file like this:

Index    Name                  Chromosome    Position    GenTrain Score    SNP      ILMN Strand    Customer Strand    NormID
1        ARS-BFGL-BAC-10172    14            6371334     0.9014            [A/G]    TOP            TOP                2
2        ARS-BFGL-BAC-1020     14            7928189     0.9260            [T/C]    BOT            TOP                1
5        ARS-BFGL-BAC-10365    14            27005721    0.9176            [A/C]    TOP            BOT                2
7        ARS-BFGL-BAC-10793    14            29259114    0.9233            [C/G]    TOP            BOT                101
8        ARS-BFGL-BAC-10867    14            34639444    0.9293            [G/C]    BOT            BOT                102

The "TOP/BOT strand" file shows that if I have A/C or A/G (like index 1 and 5) is TOP, so the Allele A is A and the allele B is G or C. So, what is the strand that I should use? ILMN strand?

The file shows that if I have C/T or G/T is BOT, so the Allele A is T and Allele B is C or G. But in my file (index 2), the SNP is T/C BOT. what is the Allele A and B?

And index 7 and 8, what is the allele A and B?

Thank you!!

SNP • 2.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 1768 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6