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Table 1 Summary statistics of 27,500 top-ranked SNPs per call set and quality assessed by transition-to-transversion ratio (Ts/Tv) and missing genotypes

From: Comparing variant calling algorithms for target-exon sequencing in a large sample

   All SNPs Singletons %Missing genotypes
Call set #SNPs % dbSNP Known Ts/Tv Novel Ts/Tv Overall Ts/Tv #SNPs Ts/Tv
IBC 27500 25.72% 3.02 2.54 2.71 16325 (59.36%) 2.57 4.71
PBC 27500 26.87% 3.02 2.45 2.59 15877 (57.73%) 2.44 0.47
LDC 27500 26.85% 3.01 2.45 2.59 15857 (57.66%) 2.44 0.17
LDC + F 27500 26.81% 3.00 2.45 2.58 15869 (57.71%) 2.44 0.17
  1. Abbreviations: IBC = individual-based single marker caller, PBC = population-based single marker caller, LDC = LD-aware caller without flanking haplotypes, LDC + F = LD-aware caller with flanking haplotypes. Expanded table showing quality of call sets broken down by variant class is included in Additional file 1: Table S1.