Quality control analysis of novel A/J SNPs. A sample of novel SNPs was genotyped using the Sequenom platform. (a) Plot shows the proportion of calls confirmed by genotyping for differing qualities of SNP. (b) Quality controlling SNPs on basis of mapping depth as well as quality. Confirmation data were used to calculate a score for each SNP based on quality and depth. Plot shows estimated sensitivity and false discovery rate (FDR) based on using different thresholds of p-score. (c) SNPs missed by MAQ. A sample of SNPs present in dbSNP but absent from the MAQ was were genotyped. The reason for the absence of each SNP is shown. 'Filtered' SNPs were called by MAQ but filtered out as being of low quality. 'dbSNP errors' are SNPs where our genotyping agrees with the MAQ call but not dbSNP. 'No base call SNPs' are SNPs for which MAQ did not make a base call (generally due to zero depth). MAQ errors are bases where our genotyping agreed with the dbSNP call.