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Table 4 Comparison between SNP predictions made by the three base callers and the 'CG-HQ' high-quality set of variant calls from Complete Genomics.

From: All Your Base: a fast and accurate probabilistic approach to base calling

  Match Δ% Mismatch Extra Complex Total FDR
AYB 339908 +6.65 299 36524 13251 389982 8.79 × 10-4
Bustard 318725   284 32165 12476 363650 8.90 × 10-4
Ibis 319907 +0.37 342 42865 14210 377324 10.68 × 10-4
  1. SNP predictions for sites that are SNPs in CG-HQ either 'match' or 'mismatch' depending on whether they agree; for AYB and Ibis matches we also record the percent improvement over Bustard (Δ%). 'Extra' SNP predictions are those for sites that are not present in the CG-HQ data. Predicted SNPs at sites for which the CG-HQ results indicate complex variations from GRCh37, mainly insertions and deletions, are counted as 'complex'. The false discovery rate (FDR) is calculated across matches and mismatches only, since the high level of congruence across base callers in the 'extra' category suggests many of these predicted SNPs may be correct (see text for details). Only variant calls for the autosomal, × or mitochondrial chromosomes are considered.