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Table 2 Impact on imputation accuracy of splitting chromosomes into chunks

From: Imputation of missing genotypes: an empirical evaluation of IMPUTE

Accuracy
   NNC (split) NNC (non split) SCA (split) SCA (non split)
Complete missing Overall 97.42%
(0.01, 0.93, 0.99, 1)
97.42%
(0.01, 0.93, 0.99, 1)
88.29%
(0.01, 0.79, 0.95, 1)
88.29%
(0.01, 0.79, 0.95, 1)
  0.95 P.P. 99.23%
(0, 0.98, 1, 1)
99.23%
(0.00, 0.98, 1.00, 1)
97.30%
(0.00, 0.94, 1.00, 1)
97.30%
(0.00, 0.94, 1.00, 1)
80% missing Overall 97.24%
(0.01, 0.93, 0.99, 1)
97.70%
(0.01, 0.93, 0.99, 1)
88.76%
(0.01, 0.80, 0.96, 1)
88.76%
(0.01, 0.80, 0.96, 1)
  0.95 P.P. 99.28%
(0.00, 0.98, 1.00, 1)
99.30%
(0.00, 0.98, 1.00, 1)
97.44%
(0.00, 0.94, 1.00, 1)
97.44%
(0.00, 0.94, 1.00, 1)
  1. No obvious impact of splitting chromosome 2 into small chunks of 10 Mb on imputation accuracy while using the data from the NNC and SCA sets. In all tests, 10% of the SNPs on chromosome 2 were randomly selected and their genotype data were either completely removed (Complete missing), or only 80% randomly removed (80% missing).