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Figure 3 | BMC Genomics

Figure 3

From: High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

Figure 3

D2 vs. B6 SNPs and B6 realignment discrepancies vs. reference sequence. Custom HTS of chromosome 1 (171.6 – 174.6 Mb) data reveals D2 vs. B6 PARC SNPs and realignment discrepancies when compared to the B6 reference sequence. A) B6 vs. D2 PARC SNPs identified by Illumina's realignment of Genome Analyzer data (blue circle) and/or Applied Biosystems' realignment of SOLiD data (red circle). D2 vs. B6 SNPs annotated in the Mouse Phenome Database (MPD) are also illustrated for comparison (green circle). Of the 11,824 PARC SNPs found using custom HTS by at least one sequencing method, 7,663 were previously unknown or not annotated as D2. vs. B6 SNPs, demonstrating that public data for D2 vs. B6 SNPs is currently far from complete. B) Identification of 12 and 31 provisional discrepancies in the comparison of the B6 reference sequence to Illumina's (blue circle) and Applied Biosystems' (red circle) realignments; and confirmation (i.e., detected by both HTS platforms) of realignment discrepancies at 29 positions when compared to reference sequence.

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