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500 RSE capture primers designed using Antholigo. The genomic position (HG19) of the primers as well as the sequence and spacing between primers is provided in addition to other design criteria metrics including deltaG, Tm, and GC%. Table S2: List of qPCR primers and probe sequences designed to amplify regions within several genes (ACTB, EGFR, CLEC16A, BRCA2, CETP, KCNJ2, KCNE1, NOS3) as well as five MHC locations (MHC-1, MHC-2, MHC-3, MHC-4 and MHC-5 as indicated by arrows in Fig. 5a). Table S3: PCR primer location and sequences designed to validate high-confidence variant calls from NGS results. Table S4: Results from Sanger validation of high confidence variants identified by NGS. Table S5: 46 RSE primers designed to capture the four genes (~700 kb in total) in order to examine the effect of RSE primer spacing on capture efficiency (Fig. 3). Figure S1: Read segregation problems caused by reference sequence error in regional duplication. A 2.5 kb duplication (a) within the MHC presented difficulties during the alignment of reads to this region. Reads at the beginning and ends of the duplicated regions segregated cleanly due to polymorphic differences between the duplications. But reads aligning to the middle of the duplication identified a variant position (marked by an *) (b). Sanger sequencing of this region identified that the reference sequence incorrectly identified the * base in the second duplication as a T, when it was actually a C, creating a false variant position. After correcting the reference sequence (c), the central reads segregated correctly and the false variant was eliminated. (PDF 1372 kb)