Fig. 3

Hybrid-capture and LR-PCR are concordant for SNVs and indels. a Hypothetical examples to describe the concordance table for comparison of hybrid capture and LR-PCR data. All examples assume the reference base is A and the alternate (“alt”) base is T. (i) Example of a true positive (dark blue) where an alt allele is present in PMS2CL. (ii) Example of a permissible dosage error (light blue), where PMS2CL is homozygous for the alt allele but hybrid capture only calls one alt allele instead of two. (iii) Example of a false positive (light orange), where only hybrid capture detected an alt allele. (iv) Example of a false negative (dark orange), where an alt allele in PMS2CL was missed by hybrid capture. Shaded matrix on the right indicates cells that represent true positives, permissible dosage errors, false positives, and false negatives. Numbers on axes denote the total number of alt alleles in either the hybrid capture data or the PMS2/PMS2CL LR-PCR data. b Diploid SNV and indel concordance for exon 11 of PMS2. Numbers on axes denote the number of alt alleles where 0 is equivalent to 0/0, 1 is equivalent to 0/1, and 2 is equivalent to 1/1. 95% confidence intervals in brackets. c Four-copy SNV and indel concordance for exons 12–15 of PMS2/PMS2CL, as explained in (a)