VIGGS:Variant information

Chr03:6490811 - 6495382

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6491039	A	G	67	2631.77	1.00	UTR_3_PRIME(\|130\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491155	G	C	59	2415.77	1.00	UTR_3_PRIME(\|14\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491387	T	C	51	2002.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491432	T	G	56	2441.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491441	C	G	55	2514.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491450	T	C	55	2527.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491507	C	T	58	2581.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491508	T	C	58	2581.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491511	T	C	57	2581.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491568	T	A	46	2048.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491586	C	T	42	1906.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491611	G	A	42	2041.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491619	T	C	46	2116.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491620	A	G	47	2116.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491621	G	A	48	2116.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491666	T	C	39	1816.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491668	A	G	41	1861.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491669	C	T	41	1861.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491677	A	G	40	1902.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491678	A	T	40	1902.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6491679	C	G	41	1812.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492662	A	C	66	2652.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492693	G	T	67	2697.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492788	G	A	74	3481.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492887	A	C	60	2641.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492901	A	T	65	2853.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493087	A	G	54	2151.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493135	T	C	46	1791.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493972	C	T	54	2394.77	1.00	SYNONYMOUS_CODING(SILENT\|gtG/gtA\|V174\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493975	A	G	53	2356.77	1.00	SYNONYMOUS_CODING(SILENT\|taT/taC\|Y173\|None\|Vigan.03G067100.01)	Vigna nepalensis
6494079	T	C	39	1483.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Acc/Gcc\|T139A\|None\|Vigan.03G067100.01)	Vigna nepalensis
6494517	T	A	71	2667.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6494634	G	A	59	2361.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6494716	G	T	65	2707.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6494763	C	A	54	2221.77	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6495159	T	C	48	1835.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Act/Gct\|T21A\|None\|Vigan.03G067100.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6491671	TACAA	T	41	1852.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492246	C	CA	51	1298.73	0.96	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492417	GT	G	38	1034.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492561	C	CAGAAGTGTTTCTG	49	2473.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492782	A	AAATAAGG	79	3664.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492790	TTAATTTCC	T	72	3292.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492799	GTCC	G	72	3202.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6492804	TATTA	T	67	3112.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493195	A	AT	43	1291.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493339	T	TA	46	1602.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493521	GA	G	40	1184.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis
6493618	TA	T	47	1854.73	1.00	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6493239	(TA)15	(TA)12	35	1277.73	0.97	INTRON(\|\|\|None\|Vigan.03G067100.01)	Vigna nepalensis