VIGGS:Variant information

Chr04:48813554 - 48817538

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
48813695	A	G	37	1462.77	1.00	UPSTREAM(\|4886\|\|None\|Vigan.04G368600.01), UTR_5_PRIME(\|203\|\|None\|Vigan.04G368500.01)	Vigna nepalensis
48813793	T	C	49	2088.77	1.00	UPSTREAM(\|4788\|\|None\|Vigan.04G368600.01), UTR_5_PRIME(\|105\|\|None\|Vigan.04G368500.01)	Vigna nepalensis
48813802	C	G	45	2028.77	1.00	UPSTREAM(\|4779\|\|None\|Vigan.04G368600.01), UTR_5_PRIME(\|96\|\|None\|Vigan.04G368500.01)	Vigna nepalensis
48813816	T	G	45	1806.77	1.00	UPSTREAM(\|4765\|\|None\|Vigan.04G368600.01), UTR_5_PRIME(\|82\|\|None\|Vigan.04G368500.01)	Vigna nepalensis
48813880	C	T	38	1576.77	1.00	START_GAINED(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4701\|\|None\|Vigan.04G368600.01), UTR_5_PRIME(\|18\|\|None\|Vigan.04G368500.01)	Vigna nepalensis
48813933	A	C	49	2119.77	1.00	SYNONYMOUS_CODING(SILENT\|ctA/ctC\|L12\|None\|Vigan.04G368500.01), UPSTREAM(\|4648\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48813942	C	G	48	2143.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gaC/gaG\|D15E\|None\|Vigan.04G368500.01), UPSTREAM(\|4639\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814017	A	G	51	1968.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4564\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814074	A	G	50	1989.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4507\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814103	T	G	49	2210.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4478\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814104	C	T	49	2210.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4477\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814123	A	G	50	2221.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4458\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814132	T	G	47	2176.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4449\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814146	C	T	49	2239.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4435\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814283	T	C	47	2152.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4298\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814284	C	T	49	2152.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4297\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814343	G	A	55	2378.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4238\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814370	T	C	56	2626.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4211\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814386	T	C	51	2273.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4195\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814415	C	T	57	2234.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4166\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814450	C	T	55	2450.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4131\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814472	G	A	54	2364.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4109\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814569	C	A	55	2196.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4012\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814583	T	A	54	2128.77	0.98	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3998\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814642	C	T	49	1910.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3939\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814687	G	A	49	2188.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3894\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814697	A	G	52	2247.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3884\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814826	C	G	42	1698.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3755\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814895	A	G	59	2623.77	1.00	SYNONYMOUS_CODING(SILENT\|aaA/aaG\|K52\|None\|Vigan.04G368500.01), UPSTREAM(\|3686\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814910	T	C	59	2637.77	1.00	SYNONYMOUS_CODING(SILENT\|ggT/ggC\|G57\|None\|Vigan.04G368500.01), UPSTREAM(\|3671\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48815001	C	A	52	2106.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3580\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48815038	G	A	54	2244.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3543\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48815235	A	T	53	2105.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3346\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48815285	T	C	62	2624.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3296\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48815352	T	C	55	2149.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|3229\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48816346	A	G	53	2166.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|2235\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4758\|\|None\|Vigan.04G368700.01)	Vigna nepalensis
48816652	C	A	40	1606.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|1929\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4452\|\|None\|Vigan.04G368700.01)	Vigna nepalensis
48816724	A	C	41	1816.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|1857\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4380\|\|None\|Vigan.04G368700.01)	Vigna nepalensis
48816727	A	C	41	1946.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|1854\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4377\|\|None\|Vigan.04G368700.01)	Vigna nepalensis
48816754	A	G	48	2081.77	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|1827\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4350\|\|None\|Vigan.04G368700.01)	Vigna nepalensis
48817277	A	G	53	1950.77	1.00	SYNONYMOUS_CODING(SILENT\|gaA/gaG\|E322\|None\|Vigan.04G368500.01), UPSTREAM(\|1304\|\|None\|Vigan.04G368600.01), UPSTREAM(\|3827\|\|None\|Vigan.04G368700.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
48813991	T	TC	48	1671.73	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4589\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814111	CG	C	46	2167.73	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4469\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48814363	T	TC	52	2613.73	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|4217\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48815794	A	AGT	63	2827.73	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|2786\|\|None\|Vigan.04G368600.01)	Vigna nepalensis
48816954	CA	C	44	1337.73	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|1626\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4149\|\|None\|Vigan.04G368700.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
48816712	(TAA)9	(TAA)6	39	1762.73	1.00	INTRON(\|\|\|None\|Vigan.04G368500.01), UPSTREAM(\|1868\|\|None\|Vigan.04G368600.01), UPSTREAM(\|4391\|\|None\|Vigan.04G368700.01)	Vigna nepalensis