Table 1 Transition-Transversion (TiTv) ratio for known and novel SNPs discovered in CONVERGE in different tranches of sensitivities to known SNPs in 1000 Genomes Phase 1 ASN Panel.

From: RETRACTED ARTICLE: 11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project

Sensitivity to Known SNPs (%)

Number of SNPs

TiTv Ratio

 

Known

Novel

Known

Novel

79

7946865

9361731

2.1783

2.1998

80

8047459

9502607

2.1786

2.2011

85

8550425

10357018

2.1817

2.204

87

8751611

10853838

2.1838

2.2042

89

8952798

11310561

2.1862

2.1961

90

9053391

11486024

2.187

2.1868

95

9556357

13089943

2.1849

1.9637

98

9858137

15716679

2.1759

1.6553

99

9958730

17362038

2.1721

1.5296

99.9

10049264

20940831

2.1683

1.353

100

10059324

22722016

2.168

1.2839

  1. This table shows the results of VQSR on all SNPs called in CONVERGE using default annotations in GATK and biallelic SNPs in 1000 Genomes Phase 1 ASN Panel as ‘known’, ‘true’, and ‘training’ sets. The first column shows the tranche defined by sensitivity to known set, the second and third column shows the number of known and novel SNPs in CONVERGE falling into each tranche, and the last two columns show the TiTv ratio of known and novel SNPs in each tranche respectively.
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