Zeroes In Bim File Instead Of Allele Codes

Question

[Click downvote]

I have many plink bim files that contain lines like these:

1       200262  0       20994217        C       T
1       rs1000233       0       13153104        0       0
1       rs10271981      0       83862170        0       0
1       rs10399793      0       49298   0       0

Or like this:

1       chr1:11890189   0       11967602        0       A

Has 0 ever had any meaning in plink bim files, or is this an error, plain and simple?

Answer 1

[zx8754]

My guess is, when it is "0 0" then all individuals failed for this SNP, when "0 A" then all individuals are "AA".

Check these SNPs on NCBI for population specific frequency, they might be monomorphic. Also, checked your SNPs on UCSC Table browser, and weight is either 2 or 3. Meaning:

The quality of the alignment: 1 = unique mapping, 2 = non-unique, 3 = many matches

Answer 2

[dani.mag.fernandes]

I have found out that when converting from non-binary ped/map to binary bed/bim/fam, all my SNPs are losing one allele. Very rarely I have two alleles as "0 0", as in the above example. My ped file is however is homozygous for all SNPs, and is missing a couple of them, so "0 0", corresponding to the bim "0 0" cases. Could the homozygosity be the cause for the lost of one of the reference allele information? And does it influence in any way the results once this sample is merged into a larger dataset? Thanks.

Map file:

1  Affx-13943225     0.020130       752566 G A
1  Affx-15485777     0.024457       903426 C T
1  Affx-15871758     0.025727       949654 A G
1  Affx-3942202     0.026288      1018704 A G
1  Affx-3979904     0.026674      1048955 A G
1  Affx-3995844     0.026711      1061166 T C
1  Affx-4055225     0.028311      1108637 G A
1  Affx-4572154     0.029335      1156131 T C
1  Affx-4575207     0.029356      1157547 T C
1  Affx-4576587     0.029367      1158277 G A
1  Affx-4584321     0.029391      1161780 C T
1  Affx-4604366     0.029450      1170587 C T
1  Affx-4690339     0.029735      1205155 A C
1  Affx-50009264     0.030225      1287562 G A
1  Affx-50010124     0.030503      1340241 T C

Ped file:

PL N17_merged 0 0 1 1 G G C C G G G G A A T T G G T T T T G G C C C C A A G G 0 0

PLINK-converted bim file:

1   Affx-13943225   0.02013 752566  0   G
1   Affx-15485777   0.024457    903426  0   C
1   Affx-15871758   0.025727    949654  0   G
1   Affx-3942202    0.026288    1018704 0   G
1   Affx-3979904    0.026674    1048955 0   A
1   Affx-3995844    0.026711    1061166 0   T
1   Affx-4055225    0.028311    1108637 0   G
1   Affx-4572154    0.029335    1156131 0   T
1   Affx-4575207    0.029356    1157547 0   T
1   Affx-4576587    0.029367    1158277 0   G
1   Affx-4584321    0.029391    1161780 0   C
1   Affx-4604366    0.02945 1170587 0   C
1   Affx-4690339    0.029735    1205155 0   A
1   Affx-50009264   0.030225    1287562 0   G
1   Affx-50010124   0.030503    1340241 0   0

Any help would be welcome!