Fig. 5

Sequencing depth of coverage map for RSE-extracted MHC region. a MHC sequencing coverage is displayed for the entire enriched 4 Mb of the PGF MHC region along with 300 kbp of non-targeted sequence on either side. Each qPCR probe assay is marked by a numbered arrow. b 50 kbp regions around each of three qPCR assays is shown to demonstrate differing levels of coverage. RSE capture primer positions are marked with a green marker. The red circle shows the approximate depth of coverage at the qPCR probe position. While regions 2 and 5 have differing average depth of coverage, the qPCR results at the site of capture are very similar (930 vs 1010 copies/μl) which suggest similar amounts of enrichment that is validated by the sequencing depth of coverage results (130 vs 95). Region 3 shows enhanced depth of coverage and suggests higher enrichment that is validated by the higher qPCR results (2569 copies/μl). The depth of coverage results correlate well to the qPCR copy number estimates of the extracted material: higher enrichment = higher depth of coverage