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
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