pCADD: SNV prioritisation in Sus scrofa

Groß, Christian; Derks, Martijn; Megens, Hendrik-Jan; Bosse, Mirte; Groenen, Martien A. M.; Reinders, Marcel; de Ridder, Dick

doi:10.1186/s12711-020-0528-9

Genetics Selection Evolution

Table 5 Top 40 SNVs according to pCADD^Alt:Frq that are presumably intergenic according to the Ensembl Sus scrofa* gene build, annotated with NCBI

From: pCADD: SNV prioritisation in Sus scrofa

Chr	Pos	Ref:Frq	Alt:Frq	pCADD	pCADD*Alt:Frq	NCBI-gene build	Human-ensembl-gene build
5	14463457	T:0.014	C:0.986	26.559	26.185	lncRNA
10	45490687	G:0.007	T:0.993	24.175	24.000	RSU1
9	88698813	C:0.021	G:0.979	24.433	23.909		lncRNA
6	149549021	T:0.007	C:0.993	23.714	23.544
18	30883512	G:0.045	A:0.955	24.211	23.111	lncRNA
14	102653354	A:0.007	G:0.993	23.216	23.052	lncRNA
3	35533299	C:0.029	T:0.971	23.729	23.041	RBFOX1
8	16080284	T:0.021	G:0.979	23.540	23.035	KCNIP4
8	16090742	A:0.007	C:0.993	23.188	23.0248	KCNIP4
9	88631400	T:0.037	C:0.963	23.855	22.978		lncRNA
13	11996804	A:0.068	G:0.932	24.518	22.846		miscRNA
8	16069085	C:0.014	T:0.986	23.148	22.817	KCNIP4
1	270976051	G:0.057	A:0.943	24.148	22.768
12	10080096	C:0.029	T:0.971	23.417	22.738
15	134154371	G:0.028	A:0.972	23.388	22.729
17	15317464	T:0.035	C:0.965	23.437	22.611
8	16126909	T:0.145	G:0.855	26.331	22.515	KCNIP4
14	102708028	T:0.007	C:0.993	22.622	22.463		lncRNA
17	8460314	T:0.007	A:0.993	22.607	22.448		FAT1
3	2721065	C:0.016	T:0.984	22.794	22.438		SDK1
8	2274651	T:0.006	C:0.994	24.861	24.721	lncRNA
14	41547002	T:0.006	C:0.994	24.651	24.511	MYO1H
9	88656584	T:0.023	C:0.977	24.606	24.047		lncRNA
13	145274213	A:0.031	G:0.969	24.336	23.576	ZBTB20
5	14463352	A:0.006	G:0.994	23.526	23.393	lncRNA
2	135162568	A:0.011	C:0.989	23.305	23.043
13	196634107	A:0.011	C:0.989	23.190	22.930		lncRNA
13	203405436	G:0.006	A:0.994	23.046	22.917
17	15317464	T:0.022	C:0.978	23.436	22.910
13	203404345	T:0.017	G:0.983	23.239	22.842
18*	4227731	C:0.006	A:0.994	22.839	22.710
13	203405428	T:0.006	G:0.994	22.663	22.535
13	145279451	A:0.019	G:0.981	22.960	22.512	ZBTB20
15	134347171	T:0.006	G:0.994	22.633	22.506
5	25295998	A:0.011	G:0.989	22.731	22.476	lncRNA
15	134154371	G:0.040	A:0.960	23.387	22.457
18	42017803	T:0.017	G:0.983	22.811	22.427
15	134347189	G:0.006	C:0.994	22.471	22.345
8	16126909	T:0.152	G:0.848	26.331	22.337	KCNIP4
14	138794865	A:0.006	G:0.994	22.411	22.285		lncRNA

When no NCBI gene annotation was found, SNVs were mapped to hg38 and the Human Ensembl gene build was used. Italics: SNVs that are intergenic in the three gene builds, yet found in regions with conserved synteny
*SNV located in a region unannotated in any gene build

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ISSN: 1297-9686

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