Rare and population-specific functional variation across pig lines

Table 4 Frequency of the alternative allele by predicted consequence type and prevalence level

Consequence type	Frequency of the alternative allele by prevalence level
Consequence type	1	2	3	4	5	6	7	8	9	Total
Loss-of-function	0.0010	0.017	0.048	0.062	0.089	0.114	0.151	0.223	0.489	0.020
Frameshift indel	0.4816	0.758	0.757	0.420	0.302	0.260	0.339	0.456	0.693	0.634
In-frame indel	0.8893	0.903	0.910	0.898	0.812	0.785	0.702	0.595	0.572	0.735
Deleterious missense	0.0006	0.018	0.043	0.061	0.078	0.092	0.125	0.170	0.350	0.010
Tolerated missense	0.0011	0.027	0.047	0.066	0.083	0.106	0.143	0.202	0.443	0.074
Synonymous	0.0037	0.032	0.049	0.066	0.086	0.107	0.151	0.205	0.447	0.110
Promoter + UTR	0.0019	0.034	0.059	0.078	0.099	0.122	0.166	0.226	0.475	0.102
Intronic	0.0015	0.035	0.059	0.080	0.102	0.126	0.171	0.235	0.485	0.110
Intergenic	0.0015	0.033	0.058	0.080	0.105	0.129	0.173	0.237	0.483	0.116

ISSN: 1297-9686