Skip to main content

Table 1 Genotype concordance between genotyping and sequencing platforms

From: Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics

Comparison PPA (%) NPA (%) No Calls (Average)
Accuracy, .4x vs PMRA 98.22% 99.82% 2535
Accuracy, .6x vs PMRA 98.76% 99.85% 1848
Accuracy, .8x vs PMRA 99.01% 99.86% 1508
Accuracy, 1x vs PMRA 99.19% 99.88% 1251
  1. In all cases the genotyping array was treated as ‘Truth’. Positive % Agreement (PPA)– The percent of non-reference calls in the Truth dataset detected by Test, ignoring no calls in Test. (True Positives / True Positives + False Negatives). Negative % Agreement (NPA) – The percent of reference calls in the Truth dataset detected by Test, ignoring no calls in Test. (True Negatives / True Negatives + False Positives). No Calls– Count of No Calls in test that were variant in Truth. No calls are averaged across all 79 individuals. The total number of overlapping variants between the PMRA and the imputed sequence data is ~ 423 k
\