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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.