File S1 - A Two-Dimensional Pooling Strategy for Rare Variant Detection on Next-Generation Sequencing Platforms

Figure S1: Circos plot of filtered tracks, SNV calls and coverage over the region. The region of interest, a 250 kb region of chromosome 5 (5p15.33), is shown. Section A shows the genes TERT, CLPTM1L, BC034612, SLC6A3 and a portion of LPCAT1 in light green, with exons drawn in black. The grey and black tracks in section A highlight the repeat masked and self-chaining regions we excluded from analysis. Section B presents the positions of pinnable class SNVs in dark green, multiple SNVs in light green, singletons in grey and positions with some evidence but insufficient coverage (missing coverage) in black. Section C plots the depth of coverage over the region in dark green. The range of the plot is from 0× coverage at the outside of the light green band to 20,000× at the inside of the light green. Table S1: Predicted consequences of SNVs. Tables 2A, 2C, 2E and 2G show a breakdown for matrices 1, 2, 3 and 4 of the predicted consequences of pinnable, multiple and singleton SNVs. Tables 2B, 2D, 2F and 2H further list the transcription consequences for exonic variants from matrices 1 to 4 respectively. Table S2: Summary of indel class by matrix. The number of Pinnable, Multiple and Singleton indel variants identified is listed for each of the four 12×12 matrices. Also indicated is the percentage of each variant class that is catalogued in dbSNP. The number of total variants for each of the classes represents the total unique number of variants from all four matrices. Table S3: Predicted consequences of indels. The predicted consequences of the pinnable, multiple and singleton indel variants identified in matrices 1, 2, 3 and 4 are presented in Tables 3A, 3B, 3C and 3D.
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