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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.