VIGGS:Variant information

Chr08:2192859 - 2196602

Filter

Species
- Vigna nepalensis
Effect
- DOWNSTREAM
- INTRON
- UTR_5_PRIME

SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2193606	C	T	60	2716.77	1.00	DOWNSTREAM(\|1585\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193616	T	C	57	2477.77	1.00	DOWNSTREAM(\|1595\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193707	A	G	54	2401.77	1.00	DOWNSTREAM(\|1686\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193718	T	A	46	2027.77	1.00	DOWNSTREAM(\|1697\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193792	G	A	32	1441.77	1.00	DOWNSTREAM(\|1771\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193808	T	C	32	1394.77	1.00	DOWNSTREAM(\|1787\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193891	A	G	20	909.77	1.00	DOWNSTREAM(\|1870\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193908	G	A	20	949.77	1.00	DOWNSTREAM(\|1887\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193913	T	C	21	902.77	1.00	DOWNSTREAM(\|1892\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194019	T	C	60	2582.77	1.00	DOWNSTREAM(\|1998\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194045	A	T	59	2741.77	1.00	DOWNSTREAM(\|2024\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194070	A	G	61	2903.77	1.00	DOWNSTREAM(\|2049\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194240	G	A	60	2230.77	1.00	DOWNSTREAM(\|2219\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194271	A	T	62	2785.77	1.00	DOWNSTREAM(\|2250\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194359	T	C	57	2276.77	1.00	DOWNSTREAM(\|2338\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194419	A	G	51	2033.77	1.00	DOWNSTREAM(\|2398\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194599	G	A	63	2396.77	1.00	DOWNSTREAM(\|2578\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194780	T	G	51	2024.77	1.00	DOWNSTREAM(\|2759\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194859	T	A	63	2884.77	1.00	DOWNSTREAM(\|2838\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194862	C	T	65	2884.77	1.00	DOWNSTREAM(\|2841\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194909	G	A	53	2258.77	1.00	DOWNSTREAM(\|2888\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194950	A	G	54	2132.77	1.00	DOWNSTREAM(\|2929\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195166	T	G	69	2804.77	1.00	DOWNSTREAM(\|3145\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195241	A	C	62	2411.77	1.00	DOWNSTREAM(\|3220\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195690	C	A	61	2748.77	1.00	DOWNSTREAM(\|3669\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4925\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195752	C	T	62	2539.77	1.00	DOWNSTREAM(\|3731\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4863\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195842	A	G	65	2816.77	1.00	DOWNSTREAM(\|3821\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4773\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2196022	T	A	45	1663.73	1.00	DOWNSTREAM(\|4001\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4593\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2196048	A	C	48	1933.77	1.00	DOWNSTREAM(\|4027\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4567\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2196558	C	A	31	970.77	0.97	DOWNSTREAM(\|4057\|\|None\|Vigan.08G028600.01), DOWNSTREAM(\|4537\|\|None\|Vigan.08G028400.01), UTR_5_PRIME(\|189\|\|None\|Vigan.08G028500.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2193597	G	GTCAT	60	2790.73	1.00	DOWNSTREAM(\|1577\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193598	CG	C	61	2790.73	1.00	DOWNSTREAM(\|1578\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193684	T	TTC	46	2213.73	1.00	DOWNSTREAM(\|1664\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193782	A	AT	31	1342.73	1.00	DOWNSTREAM(\|1762\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2193970	T	TTC	46	2015.73	1.00	DOWNSTREAM(\|1950\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194107	T	TA	60	2492.73	1.00	DOWNSTREAM(\|2087\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2194273	AG	A	63	2776.73	1.00	DOWNSTREAM(\|2253\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195281	C	CTGA	64	2863.73	1.00	DOWNSTREAM(\|3261\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195694	C	CAA	63	2839.73	1.00	DOWNSTREAM(\|3674\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4920\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195712	TA	T	58	1719.73	1.00	DOWNSTREAM(\|3692\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4902\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2195832	GA	G	60	2672.73	1.00	DOWNSTREAM(\|3812\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4782\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis
2196021	T	TA	43	1445.73	1.00	DOWNSTREAM(\|4001\|\|None\|Vigan.08G028400.01), DOWNSTREAM(\|4593\|\|None\|Vigan.08G028600.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2193831	(AT)23	(AT)22	6	100.74	1.00	DOWNSTREAM(\|1811\|\|None\|Vigan.08G028400.01), INTRON(\|\|\|None\|Vigan.08G028500.01)	Vigna nepalensis