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Table 1 Mean concordance and discordance rates of INDEL detection between WGS and WES data in different regions

From: Reducing INDEL calling errors in whole genome and exome sequencing data

Concordance rate

Without filtering

≥1 read

≥20 reads

≥40 reads

≥60 reads

≥80 reads

Exact-match

53% (0.8%)

62% (1.1%)

69% (1.5%)

73% (2.3%)

76% (1.6%)

74% (1.3%)

Position-match

55% (0.8%)

66% (1.0%)

73% (1.1%)

77% (1.8%)

79% (1.1%)

76% (1.3%)

Discordance rate

Without filtering

≥1 read

≥20 reads

≥40 reads

≥60 reads

≥80 reads

WGS-specific

34% (1.4%)

20% (1.5%)

14% (1.6%)

14% (2.2%)

15% (2.5%)

20% (3.2%)

WES-specific

11% (1.2%)

14% (1.4%)

13% (1.3%)

9% (2.6%)

6% (2.2%)

4% (1.5%)

  1. The data are shown in the following order: (1) regions without filtering, and regions filtered by requiring base coverage to be at least (2) one read, (3) 20 reads, (4) 40 reads, (5) 60 reads, or (6) 80 reads in both data. The mean discordance rate is calculated based on position-match, which is the percentage of INDELs specific to either data set. The standard deviation is shown in parentheses.