Table 2 Concordant variant calls among the vendors

From: Measuring coverage and accuracy of whole-exome sequencing in clinical context

  

Heterozygous variants

Homozygous variants

  

SNVs

Indels

SNVs

Indels

V1-V2-V3 (≥10 ×)

Union of variants

18,702.4 (17,085–21,939)

1,961.4 (1,740–2,139)

9,945.3 (9,647–10,270)

607.7 (527–695)

 

Concordant variants

17,478.1 (15,923–20,561)

1,051.7 (941–1,187)

9,839.6 (9,559–10,121)

501.0 (448–556)

 

Concordance (%)

93.4±0.85

53.7±3.34

98.9±0.34

82.6±2.19

V1-V2 (≥10 ×)

Union of variants

19,369.8 (17,598–22,848)

2,298.4 (2,188–2,442)

10,397.9 (10,086–10,793)

697.9 (646–749)

 

Concordant variants

18,356.2 (16,673–21,722)

1,426.9 (1,261–1,627)

10,304.0 (10,008–10,628)

580.2 (536–618)

 

Concordance (%)

94.7±0.68

62.0 ± 2.99

99.1±0.26

83.2±1.10

V1-V2 (≥20 ×)

Union of variants

18,488.9 (16,755–21,840)

1,888.1 (1,786–2,013)

9,923.4 (9,637–10,229)

593.9 (546–637)

 

Concordant variants

17,649.0 (15,994–20,929)

1,234.8 (1,108–1,417)

9,856.4 (9,566–10,129)

515.7 (481–552)

 

Concordance (%)

95.4±0.71

67.7±3.12

99.5±0.09

89.0±1.19

  1. Overall concordance rates of called variants are significantly different across variant types. For each variant type, we calculate the proportion of concordant variants among the union of variants called by the three vendors. A total of 58,870 unique variants were called including 682 multiallelic variants. Mean and range across the nine individuals are shown for the number of union and concordant variants, and mean and standard deviation are shown for concordance rates. “V1-V2-V3” refers to results from variants covered with ≥10 × in all three vendors, and “V1-V2” refers to results from variants covered with ≥10 × or 20 × by both V1 and V2. Concordant variants in “V1-V2-V3” include the ones with complete concordance among the three vendors.
  2. SNV, single-nucleotide variant.
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