Imputation accuracy to whole-genome sequence in Nellore cattle

Table 3 SNP-wise imputation accuracy from the Bovine HD BeadChip (~ 777 K) to whole-genome sequence in Nellore cattle using FImpute3 and Minimac4 by classes of MAF and functional annotation

	Min	1st Qu	Median	Mean	3rd Qu	Max
High
Overall
FImpute3	0.00	0.70	0.90	0.78	0.97	1.00
Minimac4	0.00	0.76	0.92	0.79	0.98	1.00
Rsq_Minimac4	0.00	0.62	0.87	0.75	0.96	1.00
MAF ≤ 0.03
FImpute3	0.00	0.49	0.79	0.69	1.00	1.00
Minimac4	0.00	0.35	0.74	0.65	1.00	1.00
Rsq_Minimac4	0.11	0.34	0.48	0.49	0.63	1.00
Moderate
Overall
FImpute3	0.00	0.73	0.91	0.80	0.98	1.00
Minimac4	0.00	0.78	0.92	0.81	0.98	1.00
Rsq_Minimac4	0.00	0.65	0.87	0.77	0.96	1.00
MAF ≤ 0.03
FImpute3	0.00	0.56	0.83	0.74	1.00	1.00
Minimac4	0.00	0.49	0.74	0.69	1.00	1.00
Rsq_Minimac4	0.03	0.35	0.50	0.50	0.65	1.00
Low
Overall
FImpute3	0.00	0.80	0.93	0.85	0.99	1.00
Minimac4	0.00	0.83	0.94	0.86	0.99	1.00
Rsq_Minimac4	0.00	0.76	0.91	0.81	0.97	1.00
MAF ≤ 0.03
FImpute3	0.00	0.66	0.85	0.78	1.00	1.00
Minimac4	0.00	0.50	0.79	0.71	1.00	1.00
Rsq_Minimac4	0.02	0.37	0.52	0.52	0.66	1.00
Modifier
Overall
FImpute3	0.00	0.81	0.92	0.86	0.98	1.00
Minimac4	0.00	0.85	0.94	0.88	0.98	1.00
Rsq_Minimac4	0.00	0.79	0.92	0.84	0.97	1.00
MAF ≤ 0.03
FImpute3	0.00	0.61	0.83	0.75	1.00	1.00
Minimac4	0.00	0.49	0.74	0.70	1.00	1.00
Rsq_Minimac4	0.00	0.37	0.52	0.52	0.66	1.00

High, variants that cause premature stop codons, loss of function or trigger nonsense-mediated decay; low, variants mostly harmless or unlikely to change protein behavior; moderate, non-disruptive variants that might change protein effectiveness; modifier, non-coding variants or variants affecting non-coding genes, where predictions are difficult or there is no evidence of impact

ISSN: 1297-9686