Sorry for yet another basic question. I can't get the number of cow SNPs in dnSNP to add up. If i get the total SNPs for bos taurus of type SNP i get 2,210,399 SNPs. If i then get all of the SNPs on chromosomes 1-29 and X and Y I get 1,877,229. If i get the number of unknown SNPs i get 150,853. These last 2 numbers don't add up to the total number of 2,210,399. I tried checking every chromosome in the chromosome option box including unknown and i only got 2028082 SNPs (1,877,229 +150,853), but if i don't make any chromosome selection and just choose cow as the organism I get 2,210,399.
Does anyone know what might be causing this disparity?
Also my eutils query to get only those SNPs on a chromosome doesn't work:
my$query = 'bos taurus[ORG] AND snp[SNP_CLASS] AND (Not Un[CHR]) ';
This returns those SNPs on unknown chromosomes which is the opposite to what I want. It returns the same as this for some reason:
my$query = 'bos taurus[ORG] AND snp[SNP_CLASS] AND Un[CHR] ';