Fawcett et al. BMC Genomics 2011, 12:311 http://www.biomedcentral.com/1471-2164/12/311 Page 4 of 13 Figure 2 Genomic distribution of SNPs. (A) The total number of SNPs identified in each chromosome. (B) The second bar graph shows the relative concentrations of SNPs validated in SNPs/Mb by chromosome. Only chromosome X (**) displays a SNP concentration that deviates more than one standard deviation unit (195.3 SNPs/Mb) from the mean (1057.1 SNPs/Mb). found that only ~10% of all of our validated SNPs are scored as heterozygous in all three animals (note how- ever, that the animal with the lowest coverage, r02120, limits the number of SNPs identified as heterozygous in all sequenced animals). Among the 306,782 SNPs that are heterozygous in all subjects, we can evaluate the impact of cryptic sequence duplication in two ways. We compared Sanger read coverage for these 306,782 SNPs against an equivalent number of SNPs that were scored as heterozygous in two animals and homozygous in one animal. Unrecognized duplications should have higher than average read coverage in the original 5.2 × Sanger whole genome read data. We found (Figure S2, Addi- tional file 2) that the mean coverage and read coverage distributions for the two sets of SNPs is virtually identi- cal. If a substantial fraction of the “three heterozygote” SNPs were false positives due to unrecognized duplica- tions in the genome assembly, we would expect a higher mean read coverage for that set compared with the con- trol SNPs that are not scored as heterozygous in all three animals. The percentage of SNPs with read cover- age of 11 or greater (i.e. twice the genome-wide average) was only 3.8% for SNPs detected in all three individuals and 3.5% for SNPs detected in only two individuals (0.38% and 0.35% respectively of all of our validated SNPs). An alternative hypothesis is that duplicated sequences within the rhesus assembly were not assembled in the chromosome scaffolds and were instead placed in the “chromosome unknown” or chrUr bin. The tendency for duplications to be included in unknown chromosomes has been noted in other whole genome shotgun