Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population

Table 5 Accuracy of genotype imputation from 5K to 50K and computing time when using the FIMPUTE software

Scenario	CR_F^a	r²_F^b	Run time_F m:s	Mean Top10^c	Min Top10^c	Max Top10^c
7_5K50K	74.82	57.79	01:15	0.058	0.011	0.178
8_5K50K	77.10	61.64	02:14	0.076	0.036	0.210
9_5K50K	84.42	74.05	03:33	0.135	0.054	0.310
10_5K50K	87.55	79.29	05:47	0.152	0.052	0.394
11_5K50K	91.06	85.38	09:08	0.177	0.054	0.398
12_5K50K	60.93	35.25	02:04	0.085	0.055	0.168
13_5K50K	66.69	44.25	03:32	0.095	0.056	0.338
14_5K50K	72.12	52.44	05:47	0.123	0.056	0.349
15_5K50K	51.82	17.89	01:28	0.004	0.003	0.006
16_5K50K	75.18	58.25	03:07	0.117	0.052	0.259
17_5K50K	84.07	73.41	05:04	0.153	0.058	0.335
18_5K50K	92.21	86.78	00:44	0.140	0.091	0.183
19_5K50K	95.10	91.90	01:01	0.042	0.001	0.270
20_5K50K	92.8	87.77	00:55	0.045	0.001	0.187
21_5K50K	95.32	92.26	01:11	0.066	0.002	0.270
22_5K50K	77.53	62.36	01:07	0.070	0.022	0.211
23_5K50K	88.46	80.92	02:05	0.167	0.023	0.370
24_5K50K	87.99	80.14	03:34	0.204	0.055	0.417

^aCR_F = concordance rate when using the FIMPUTE software
^br²_F = Squared Pearson correlation when using the FIMPUTE software
^cMean Top10, Min Top10 and Max Top10 = mean, min and max relationship among the 10 most related animals between the reference and imputed sets

ISSN: 1297-9686