VIGGS:Variant information

Chr05:12891182 - 12897755

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
12891525	G	A	61	2374.77	1.00	DOWNSTREAM(\|1163\|\|None\|Vigan.05G156900.01), SYNONYMOUS_CODING(SILENT\|atC/atT\|I479\|None\|Vigan.05G157000.01)	Vigna nepalensis
12891626	T	C	46	1815.77	1.00	DOWNSTREAM(\|1264\|\|None\|Vigan.05G156900.01), NON_SYNONYMOUS_CODING(MISSENSE\|Agc/Ggc\|S446G\|None\|Vigan.05G157000.01)	Vigna nepalensis
12891989	A	C	57	2221.77	1.00	DOWNSTREAM(\|1627\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12892010	G	C	55	2141.77	1.00	DOWNSTREAM(\|1648\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12892027	A	G	58	2242.77	1.00	DOWNSTREAM(\|1665\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12892191	C	G	48	1924.77	1.00	DOWNSTREAM(\|1829\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12892582	T	C	59	2400.77	1.00	DOWNSTREAM(\|2220\|\|None\|Vigan.05G156900.01), SYNONYMOUS_CODING(SILENT\|ctA/ctG\|L267\|None\|Vigan.05G157000.01)	Vigna nepalensis
12892780	A	C	61	2455.77	1.00	DOWNSTREAM(\|2418\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12892993	A	T	54	2180.77	1.00	DOWNSTREAM(\|2631\|\|None\|Vigan.05G156900.01), SYNONYMOUS_CODING(SILENT\|gcT/gcA\|A195\|None\|Vigan.05G157000.01)	Vigna nepalensis
12893119	T	C	63	2507.77	1.00	DOWNSTREAM(\|2757\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12893209	T	G	65	2589.77	1.00	DOWNSTREAM(\|2847\|\|None\|Vigan.05G156900.01), SYNONYMOUS_CODING(SILENT\|ggA/ggC\|G160\|None\|Vigan.05G157000.01)	Vigna nepalensis
12893374	A	G	50	1981.77	1.00	DOWNSTREAM(\|3012\|\|None\|Vigan.05G156900.01), SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A105\|None\|Vigan.05G157000.01)	Vigna nepalensis
12893568	G	A	54	2180.77	1.00	DOWNSTREAM(\|3206\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12893661	C	A	49	1956.77	1.00	DOWNSTREAM(\|3299\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12893845	A	G	56	2279.77	1.00	DOWNSTREAM(\|3483\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12894343	C	T	61	2352.77	1.00	DOWNSTREAM(\|3981\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12894508	T	G	65	2522.77	1.00	DOWNSTREAM(\|4146\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12894910	C	T	57	2378.77	1.00	DOWNSTREAM(\|4548\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12894938	T	C	55	2340.77	1.00	DOWNSTREAM(\|4576\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12894992	G	A	53	1961.77	1.00	DOWNSTREAM(\|4630\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12895280	T	G	43	1728.77	1.00	DOWNSTREAM(\|4918\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12895582	T	G	41	1803.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12895716	A	C	47	1753.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896029	C	G	40	1576.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896121	A	T	52	2049.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896535	G	A	57	2550.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896832	A	C	73	2818.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896918	T	A	77	2994.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896950	A	C	54	2528.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896960	T	G	53	2341.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12897003	T	C	51	2374.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12897018	G	C	53	2371.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12897121	T	A	62	2352.77	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12897635	A	T	68	2807.77	1.00	UTR_5_PRIME(\|114\|\|None\|Vigan.05G157000.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
12895148	G	GT	70	1993.73	1.00	DOWNSTREAM(\|4787\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12895464	CACACACACATATATATATATATATATATATATATATATATATATATATATATATATATATATAT	C	49	2038.73	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896298	AG	A	62	2393.73	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896512	TA	T	57	2402.73	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12896956	GTT	G	55	2517.73	1.00	INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis
12897556	T	TTG	52	2363.73	1.00	UTR_5_PRIME(\|36\|\|None\|Vigan.05G157000.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
12894159	(TA)33	(TA)11	47	2049.73	1.00	DOWNSTREAM(\|3798\|\|None\|Vigan.05G156900.01), INTRON(\|\|\|None\|Vigan.05G157000.01)	Vigna nepalensis