Table 3

False-positive rates and false discovery rates (FDRs) were calculated for the entire set of variations called in NA07022 by extrapolating the heterozygous (Het) FDRs calculated from comparative Sanger sequencing of 291 selected novel variants (table S8) to all variants. This is a conservative approach (detailed in SOM). The total number of all types of false-positive variants is estimated at 7.5 to 16.1 per Mb.

Variation typeTotal detectedNovelHet novel FDR (table S8)Estimated false positives on genomeEstimated false positives / MbpEstimated FDR
SNP3,076,869310,6902–6%7k–17k2.3–6.10.2–0.6%
Deletion168,72661,9608–14%5k–8k1.8–3.03.0–5.0%
Insertion168,90961,93311–18%7k–11k2.3–3.93.9–6.5%
Block substitution62,78330,44511–29%3k–9k1.1–3.15.2–13.9%