From: Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy
 | Chromosome 1 | Chromosome 29 | ||||||
---|---|---|---|---|---|---|---|---|
 | HOL20 | MIX80 | HOL80 | MIX140 | HOL20 | MIX80 | HOL80 | MIX140 |
Sequence (n) | 1,912,451 | 1,912,451 | 1,91,2451 | 1,912,451 | 670,773 | 670,773 | 670,773 | 670,773 |
777 K chip (n) | 41,868 | 41,868 | 41,868 | 41,868 | 13,556 | 13,556 | 13,556 | 13,556 |
No variation in reference set (n)1 | 1,178,683 | 710,480 | 894,633 | 616,808 | 385,137 | 221,137 | 283,516 | 187,904 |
No variation observed in validation set (n)1 | -2 | 468,203 | 284,050 | 561,875 | -2 | 164,000 | 101,621 | 197,233 |
No variation imputed in validation set (n)1 | 19,484 | 1,005 | 1,077 | 649 | 19,284 | 4,139 | 4,267 | 3,681 |
Obtained overall imputation accuracy (n) | 672,416 | 690,895 | 690,823 | 691,251 | 252,796 | 267,941 | 267,813 | 268,399 |
average overall imputation accuracy (r) | 0.70 | 0.83 | 0.88 | 0.89 | 0.59 | 0.74 | 0.80 | 0.82 |
standard deviation of r | 0.32 | 0.27 | 0.25 | 0.24 | 0.37 | 0.32 | 0.29 | 0.28 |