TABLE 2

Classification of imputed genotypes that are untyped or experimentally missing

Genotype confidence
SNP qualityHigh confidenceMedium confidenceLow confidenceTotal
Ungenotyped 8.22 million NIEHS/Perlegen genotypes over 78 nonresequenced strains
Fully resequenced235,728,507 (36.7)48,532,073 (7.57)13,431,178 (2.09)297,691,758 (46.4)
Mostly resequenced137,628,908 (21.5)34,464,866 (5.37)21,237,494 (3.31)193,331,268 (30.2)
Poorly resequenced72,753,547 (11.3)25,350,239 (3.95)52,284,738 (8.15)150,388,524 (23.4)
Total446,110,962 (69.5)108,347,178 (16.9)86,953,410 (13.6)641,411,550 (100)
Experimentally missing NIEHS/Perlegen genotypes over 16 resequenced strains
Mostly resequenced1,109,113 (7.58)958,986 (6.56)1,316,561 (9.00)3,384,660 (23.1)
Poorly resequenced1,407,303 (9.62)1,753,637 (12.0)8,077,233 (55.2)11,238,223 (76.9)
Total2,516,416 (17.2)2,712,673 (18.6)9,393,794 (64.2)14,622,883 (100)
Missing genotypes in the combined set
Total744,725 (58.8)263,196 (20.8)257,847 (20.4)1,265,768 (100)
Grand total449,372,103 (68.4)111,323,047 (16.9)96,605,051 (14.7)657,300,201 (100)
  • The percentage of imputed genotypes in each category is shown within parentheses. The confidence level corresponds to the predicted posterior probability of the imputation method. The level of resequencing corresponds to the number of missing genotypes in the 16 resequenced strains.