TABLE 3

Leave-one-out imputation error rates of 12 resequenced classical inbred strains using Mouse HapMap SNPs, WTCHG SNPs, and gap-filling Perlegen SNPs

Genotype confidence
SNP qualityHigh confidence (%)Medium confidence (%)Low confidence (%)Total (%)
Fully resequenced0.27 (46.1)6.40 (2.79)19.0 (2.73)1.59 (51.7)
Mostly resequenced0.40 (25.3)3.94 (3.50)16.1 (2.98)2.26 (31.8)
Poorly resequenced0.76 (9.59)4.05 (2.62)15.8 (4.29)5.18 (16.5)
Total0.37 (81.1)4.74 (8.91)16.8 (10.0)2.40 (100)
  • The percentage of imputed genotypes in each category is shown within parentheses.