Table 6. Numbers of data points per chromosome after imputation with barley genome, Chinese Spring survey sequence (CSSS), W7984 and IWGSC RefSeq v1.0 references and imputation accuracy calculated by comparing imputed data of five, six and seven runs with actual SNP data generated from eight sequencing runs.
| Run | Reference | Missing data points | A genome | B genome | D genome | Total |
|---|---|---|---|---|---|---|
| Five runs | Barley | Total data points | 157,689 | 221,204 | 85,281 | 464,174 |
| Correctly imputed | 141,111 | 195,450 | 77,230 | 413,791 | ||
| Accuracy | 89.49 | 88.36 | 90.56 | 89.15 | ||
| CSSS | Total data points | 374,452 | 448,904 | 125,864 | 949,220 | |
| Correctly imputed | 339,919 | 401,393 | 114,507 | 855,819 | ||
| Accuracy | 90.78 | 89.42 | 90.98 | 90.16 | ||
| W7984 | Total data points | 556,620 | 637,680 | 186,281 | 1,380,581 | |
| Correctly imputed | 502,417 | 568,400 | 169,075 | 1,239,892 | ||
| Accuracy | 90.26 | 89.14 | 90.76 | 89.81 | ||
| IWGSC RefSeq v1.0 | Total data points | 691,863 | 841,893 | 243,017 | 1,776,773 | |
| Correctly imputed | 584,917 | 694,667 | 209,385 | 1,488,969 | ||
| Accuracy | 84.54 | 82.51 | 86.16 | 83.80 | ||
| Six runs | Barley | Total data points | 23,138 | 22,979 | 11,552 | 57,669 |
| Correctly imputed | 20,356 | 20,016 | 10,294 | 50,666 | ||
| Accuracy | 87.98 | 87.11 | 89.11 | 87.86 | ||
| CSSS | Total data points | 74,520 | 103,888 | 29,095 | 207,503 | |
| Correctly imputed | 63,312 | 86,484 | 25,494 | 175,290 | ||
| Accuracy | 84.96 | 83.25 | 87.62 | 84.48 | ||
| W7984 | Total data points | 393,307 | 517,916 | 154,857 | 1,066,080 | |
| Correctly imputed | 363,152 | 473,970 | 143,550 | 980,672 | ||
| Accuracy | 92.33 | 91.51 | 92.70 | 91.99 | ||
| IWGSC RefSeq v1.0 | Total data points | 467,224 | 574,541 | 162,471 | 1,204,236 | |
| Correctly imputed | 397,638 | 475,980 | 140,790 | 1,014,408 | ||
| Accuracy | 85.11 | 82.85 | 86.66 | 84.24 | ||
| Seven runs | Barley | Total data points | 25,242 | 33,810 | 12,195 | 71,247 |
| Correctly imputed | 22,637 | 29,634 | 11,207 | 63,478 | ||
| Accuracy | 89.68 | 87.65 | 91.90 | 89.10 | ||
| CSSS | Total data points | 67,293 | 104,296 | 25,254 | 196,843 | |
| Correctly imputed | 59,247 | 89,933 | 22,647 | 171,827 | ||
| Accuracy | 88.04 | 86.23 | 89.68 | 87.29 | ||
| W7984 | Total data points | 154,672 | 214,222 | 59,594 | 428,488 | |
| Correctly imputed | 135,735 | 186,183 | 53,429 | 375,347 | ||
| Accuracy | 87.76 | 86.91 | 89.65 | 87.60 | ||
| IWGSC RefSeq v1.0 | Total data points | 233,321 | 289,654 | 80,048 | 603,023 | |
| Correctly imputed | 199,037 | 240,517 | 69,725 | 509,279 | ||
| Accuracy | 85.31 | 83.04 | 87.10 | 84.45 |