VIGGS:Variant information

Chr02:13964789 - 13970535

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
13964834	A	G	58	2392.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|2813\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13964851	T	G	58	2390.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|2796\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13964997	T	G	64	2632.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|2650\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13965355	T	A	59	2322.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|2292\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13965947	G	T	64	2554.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1700\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13965966	T	C	61	2492.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1681\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966025	A	T	68	2769.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1622\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966078	G	A	77	3058.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1569\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966105	G	A	74	3211.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1542\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966113	T	A	68	3053.77	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1534\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966957	A	C	62	2890.77	1.00	UPSTREAM(\|4189\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|103\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|690\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966966	T	G	62	2851.77	1.00	UPSTREAM(\|4180\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|112\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|681\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966980	T	C	61	2780.77	1.00	UPSTREAM(\|4166\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|126\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|667\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13967049	T	C	46	1802.77	1.00	UPSTREAM(\|4097\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|195\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|598\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13967257	A	T	42	1526.77	1.00	UPSTREAM(\|3889\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|390\|\|None\|Vigan.02G150600.01), UTR_3_PRIME(\|403\|\|None\|Vigan.02G150500.01)	Vigna nepalensis
13967326	A	G	52	2025.77	1.00	UPSTREAM(\|3820\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|321\|\|None\|Vigan.02G150600.01), UTR_3_PRIME(\|472\|\|None\|Vigan.02G150500.01)	Vigna nepalensis
13967371	C	T	50	1964.77	1.00	UPSTREAM(\|3775\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|276\|\|None\|Vigan.02G150600.01), UTR_3_PRIME(\|517\|\|None\|Vigan.02G150500.01)	Vigna nepalensis
13967501	T	A	48	1942.77	1.00	UPSTREAM(\|3645\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|146\|\|None\|Vigan.02G150600.01), UTR_3_PRIME(\|647\|\|None\|Vigan.02G150500.01)	Vigna nepalensis
13967914	G	C	58	2393.77	1.00	DOWNSTREAM(\|36\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|3232\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13967939	G	A	49	1999.77	1.00	DOWNSTREAM(\|61\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|3207\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13967975	G	T	56	2140.77	1.00	DOWNSTREAM(\|97\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|3171\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13968063	C	G	54	2173.77	1.00	DOWNSTREAM(\|185\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|3083\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13968247	A	T	63	2472.77	1.00	DOWNSTREAM(\|369\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|2899\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13968499	T	C	49	2235.77	1.00	DOWNSTREAM(\|621\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|2647\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13968521	A	T	53	2318.77	1.00	DOWNSTREAM(\|643\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|2625\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13968747	A	G	50	2008.77	1.00	DOWNSTREAM(\|869\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|2399\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13969033	G	A	61	2379.77	1.00	DOWNSTREAM(\|1155\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|2113\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13969921	A	C	53	2159.77	1.00	DOWNSTREAM(\|2043\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|1225\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13970102	A	G	53	2104.77	1.00	DOWNSTREAM(\|2224\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|1044\|\|None\|Vigan.02G150700.01)	Vigna nepalensis
13970235	C	T	29	1099.77	1.00	DOWNSTREAM(\|2357\|\|None\|Vigan.02G150500.01), NON_SYNONYMOUS_CODING(MISSENSE\|atG/atA\|M15I\|None\|Vigan.02G150600.01), UPSTREAM(\|911\|\|None\|Vigan.02G150700.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
13965215	CTT	C	51	2221.73	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|2430\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13965862	AT	A	62	1733.73	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|1784\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966194	TA	T	49	1457.73	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UPSTREAM(\|4951\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|1452\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966712	GCTAGTTTAAAATTTCATGTT	G	46	2001.73	1.00	INTRON(\|\|\|None\|Vigan.02G150500.01), UPSTREAM(\|4433\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|915\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13966933	ATT	A	52	2283.73	1.00	UPSTREAM(\|4212\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|712\|\|None\|Vigan.02G150600.01), UTR_3_PRIME(\|80\|\|None\|Vigan.02G150500.01)	Vigna nepalensis
13967123	T	TG	39	819.73	0.92	UPSTREAM(\|4022\|\|None\|Vigan.02G150700.01), UTR_3_PRIME(\|270\|\|None\|Vigan.02G150500.01), UTR_3_PRIME(\|523\|\|None\|Vigan.02G150600.01)	Vigna nepalensis
13968086	C	CA	57	1909.73	1.00	DOWNSTREAM(\|209\|\|None\|Vigan.02G150500.01), INTRON(\|\|\|None\|Vigan.02G150600.01), UPSTREAM(\|3059\|\|None\|Vigan.02G150700.01)	Vigna nepalensis