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.