Is there any documented information on how many of the ESP/1000 genomes samples were included in the ExAC data release? I was under the impression that all samples were included but when I'm trying to annotate a few SNPs I can see some discordance in the allele frequencies.
For example I see this Exonic SNP with 0.119 allele frequency in 1000 genomes Phase 3 dataset but this cannot be found in ExAC data
5 131705587 rs13180043 C T 100 PASS AF=0.11901
Another example, present in both ESP & 1000 genomes but not in ExAC
1 156108976 rs7339 G C . PASS DBSNP=dbSNP_52;EA_AC=246,2936;AA_AC=561,823;TAC=807,3759; 1 156108976 rs7339 G C 100 PASS AF=0.185304;
I'd like to know preferably what kind of overlap exists between these 3 population sets and if possible what kind of capture regions were used for ExAC data.