Number of identified novel and known single nucleotide variants. SNVs were called with SamTools pileup, and the called variants were filtered based on the allele quality ratio in VCP. Numbers are given for variants with a minimum sequencing depth of 20× in the capture target region (CTR) and CCDS annotated exon regions (CCDS) for the control I sample. Mean numbers for the variants found in the CTRs of the additional samples are also given (CTR Mean). Dark grey bars represent Agilent SureSelect (left panel) and SureSelect 50 Mb (right panel); black bars represent NimbleGen SeqCap (left panel) and SeqCap v2.0 (right panel); light grey bars represent novel SNPs (according to dbSNP b130).