Fawcett et al. BMC Genomics 2011, 12:311 http://www.biomedcentral.com/1471-2164/12/311 Table 1 Bioinformatically validated SNPs 17573 Sanger 17573 SOLiD r1766 r02120 Sub-species comparison MamuSNP ENCODE dbSNP egeno.assembly.hets egeno.17573.SOLiD egeno.r1766.frag egeno.r02120.frag egeno.sub-species comp 1,056,266 22,665 5,734 4,185 389 29 11 – – – – – 412,920 103,323 6,519 781 76 12 421,234 – 155,454 41,836 677 328,910 1,070 159 14 5 64,584 109,485 – 69,424 743 226 33 7 0 41,607 61,941 93,016 – 443 17573 Sanger 17573 SOLiD r1766 r02120 Sub-species comparison MamuSNP ENCODE dbSNP Unique non-overlapping validated SNPs identified in each pair-wise comparison are displayed. Validated SNPs were determined on the basis of both alleles at a genomic location being identified in at least two data sets and one of either multiple animals or multiple chemistries. Validated SNPs that fit into multiple cells were represented in the left-most appropriate cell. 34,339 19 0 0 9 17 3 – 1 0 – – – – – Page 3 of 13 0 – – – – – – – – – – Figure 1 Validation by category, direct comparison examples. Only the largest data sets are shown. (A) Validation in a single animal with multiple chemistries. All data for the reference animal 17573 are displayed by chemistry. SNPs falling into the overlap region are considered to be validated. (B) Validation in multiple animals with a single chemistry and with multiple chemistries. SOLiD data from re- sequencing efforts were compared to the unrelated animals r1766 and r02120. A large number (603,463) of additional SNPs not identified in the reference animal were identified and validated by comparing r02120and r1766. We observed roughly one-third the number of validated SNPs from r02120 that were obtained using the sequence data from r1766, due to reduced uniquely mapping sequence coverage in r02120 (Table 1). were validated through comparisons among the pre- viously published data. These 20 SNPs were not found in our new SOLiD re-sequencing data (Figure S1, Addi- tional file 1). The genomic distribution of the validated SNPs appears to be random across the autosomes (Figure 2). SNP distribution by chromosome was consistent with chromosome length, except for the X chromosome. X chromosome SNP discovery is limited in this study because one of the three study animals was male (r02120). Across the autosomes, the density of SNPs per Mb fits within one standard deviation (195.3 SNPs/Mb) from the overall means (1,057.1 SNPs/Mb). We retained lists of the unvalidated SNPs in order to facilitate future efforts at SNP discovery in genomic/genic regions where coverage is relatively sparse. This data is provided in our Genboree website (http://genboree.org/java-bin/project. jsp?projectName=Rhesus%20SNPs%20using%20Next- Gen%20Sequencing&isPublic=Yes[30]) in the “Rhesus SNPs” database in a track called “Unvalidated:SNPs”. Unidentified nearly identical duplications of sequence (e.g. unrecognized segmental duplications) in the rhesus whole genome assembly are one potential cause of false positive SNPs. If nearly identical duplications were mis- takenly collapsed in the genome assembly, then wher- ever there are single base differences between two copies of a sequence, the reference animal would appear heterozygous for a SNP. The other two animals would also appear heterozygous for the same SNP, thus provid- ing false validation. We addressed this issue in several ways. First, we note that this problem would produce false heterozygote calls across all three animals, and we