VIGGS:Variant information

Chr08:13185049 - 13187691

Filter

SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
13185054	T	C	40	1816.77	1.00	DOWNSTREAM(\|3567\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4686\|\|None\|Vigan.08G148400.01), UTR_5_PRIME(\|49\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185056	C	A	41	1881.77	1.00	DOWNSTREAM(\|3569\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4684\|\|None\|Vigan.08G148400.01), UTR_5_PRIME(\|47\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185065	G	A	39	1741.77	1.00	DOWNSTREAM(\|3578\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4675\|\|None\|Vigan.08G148400.01), UTR_5_PRIME(\|38\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185376	A	T	51	2333.77	1.00	DOWNSTREAM(\|3889\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4364\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185378	A	T	51	2333.77	1.00	DOWNSTREAM(\|3891\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4362\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185413	G	A	47	1907.77	1.00	DOWNSTREAM(\|3926\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4327\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185463	A	C	56	2469.77	1.00	DOWNSTREAM(\|3976\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4277\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185469	C	T	54	2401.77	1.00	DOWNSTREAM(\|3982\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4271\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185479	A	C	48	2221.77	1.00	DOWNSTREAM(\|3992\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4261\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185483	G	C	47	2086.77	1.00	DOWNSTREAM(\|3996\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4257\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185511	C	A	33	1456.77	1.00	DOWNSTREAM(\|4024\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4229\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185820	T	A	55	2137.77	1.00	DOWNSTREAM(\|3920\|\|None\|Vigan.08G148400.01), DOWNSTREAM(\|4333\|\|None\|Vigan.08G148200.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185890	G	A	59	2278.77	1.00	DOWNSTREAM(\|3850\|\|None\|Vigan.08G148400.01), DOWNSTREAM(\|4403\|\|None\|Vigan.08G148200.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185937	A	C	63	2802.77	1.00	DOWNSTREAM(\|3803\|\|None\|Vigan.08G148400.01), DOWNSTREAM(\|4450\|\|None\|Vigan.08G148200.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185962	A	T	63	2884.77	1.00	DOWNSTREAM(\|3778\|\|None\|Vigan.08G148400.01), DOWNSTREAM(\|4475\|\|None\|Vigan.08G148200.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185964	T	C	64	2884.77	1.00	DOWNSTREAM(\|3776\|\|None\|Vigan.08G148400.01), DOWNSTREAM(\|4477\|\|None\|Vigan.08G148200.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186104	A	C	59	2256.77	1.00	DOWNSTREAM(\|3636\|\|None\|Vigan.08G148400.01), DOWNSTREAM(\|4617\|\|None\|Vigan.08G148200.01), SYNONYMOUS_CODING(SILENT\|Aga/Cga\|R112\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186511	C	T	32	1372.77	1.00	DOWNSTREAM(\|3229\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186519	C	T	32	1453.77	1.00	DOWNSTREAM(\|3221\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186526	T	A	31	1438.77	1.00	DOWNSTREAM(\|3214\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186554	C	T	40	1771.77	1.00	DOWNSTREAM(\|3186\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186575	T	C	39	1771.77	1.00	DOWNSTREAM(\|3165\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186612	C	A	29	1276.77	1.00	DOWNSTREAM(\|3128\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186614	G	A	29	1276.77	1.00	DOWNSTREAM(\|3126\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186746	C	T	27	1203.77	1.00	DOWNSTREAM(\|2994\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186748	G	T	28	1290.77	1.00	DOWNSTREAM(\|2992\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186760	A	T	32	1463.77	1.00	DOWNSTREAM(\|2980\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186782	G	A	38	1615.77	1.00	DOWNSTREAM(\|2958\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186787	T	A	38	1615.77	1.00	DOWNSTREAM(\|2953\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186789	G	A	38	1615.77	1.00	DOWNSTREAM(\|2951\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186790	T	A	38	1615.77	1.00	DOWNSTREAM(\|2950\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186791	T	A	38	1615.77	1.00	DOWNSTREAM(\|2949\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186800	T	A	38	1615.77	1.00	DOWNSTREAM(\|2940\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186806	T	G	38	1615.77	1.00	DOWNSTREAM(\|2934\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186931	A	T	56	2301.77	1.00	DOWNSTREAM(\|2809\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186959	G	A	55	2174.77	1.00	DOWNSTREAM(\|2781\|\|None\|Vigan.08G148400.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.08G148300.01), SYNONYMOUS_CODING(SILENT\|ggG/ggA\|G203\|None\|Vigan.08G148300.01)	Vigna nepalensis
13187076	C	G	54	2148.77	1.00	DOWNSTREAM(\|2664\|\|None\|Vigan.08G148400.01), NON_SYNONYMOUS_CODING(MISSENSE\|gaC/gaG\|D242E\|None\|Vigan.08G148300.01)	Vigna nepalensis
13187149	G	A	51	1987.77	1.00	DOWNSTREAM(\|2591\|\|None\|Vigan.08G148400.01), NON_SYNONYMOUS_CODING(MISSENSE\|Gac/Aac\|D267N\|None\|Vigan.08G148300.01)	Vigna nepalensis
13187313	C	A	59	2310.77	1.00	DOWNSTREAM(\|2427\|\|None\|Vigan.08G148400.01), SYNONYMOUS_CODING(SILENT\|cgC/cgA\|R321\|None\|Vigan.08G148300.01)	Vigna nepalensis
13187601	T	G	65	2961.77	1.00	DOWNSTREAM(\|2139\|\|None\|Vigan.08G148400.01), UTR_3_PRIME(\|264\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13187606	T	A	68	3075.77	1.00	DOWNSTREAM(\|2134\|\|None\|Vigan.08G148400.01), UTR_3_PRIME(\|269\|\|None\|Vigan.08G148300.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
13185088	CT	C	43	1493.73	1.00	DOWNSTREAM(\|3602\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4651\|\|None\|Vigan.08G148400.01), UTR_5_PRIME(\|14\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185362	T	TCC	39	1483.73	0.97	DOWNSTREAM(\|3876\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4377\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185500	T	TA	38	1762.73	1.00	DOWNSTREAM(\|4014\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4239\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185513	GTTTTGTA	G	31	1447.73	1.00	DOWNSTREAM(\|4027\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4226\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13185522	A	AACAG	30	1312.73	1.00	DOWNSTREAM(\|4036\|\|None\|Vigan.08G148200.01), DOWNSTREAM(\|4217\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186560	TGA	T	40	1762.73	1.00	DOWNSTREAM(\|3179\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186593	AAAATAAAAT	A	35	1672.73	1.00	DOWNSTREAM(\|3146\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186743	T	TACA	25	1150.73	1.00	DOWNSTREAM(\|2996\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186750	ATAAGAG	A	30	1365.73	1.00	DOWNSTREAM(\|2989\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186762	G	GTT	34	1454.73	1.00	DOWNSTREAM(\|2977\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186765	TGGTGAA	T	34	1454.73	1.00	DOWNSTREAM(\|2974\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186775	T	TCC	35	1575.73	1.00	DOWNSTREAM(\|2964\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186777	TTG	T	37	1606.73	1.00	DOWNSTREAM(\|2962\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186793	GTGA	G	38	1606.73	1.00	DOWNSTREAM(\|2946\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186801	CTT	C	38	1606.73	1.00	DOWNSTREAM(\|2938\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186809	ATGAT	A	38	1605.73	1.00	DOWNSTREAM(\|2930\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186815	CAACACACGTGTGT	C	38	1604.73	1.00	DOWNSTREAM(\|2924\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13186833	A	AAGAGT	38	1603.73	1.00	DOWNSTREAM(\|2906\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis
13187514	TAGTA	T	42	1846.73	1.00	DOWNSTREAM(\|2225\|\|None\|Vigan.08G148400.01), UTR_3_PRIME(\|178\|\|None\|Vigan.08G148300.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
13186835	(TA)10	(TA)3	32	1603.73	1.00	DOWNSTREAM(\|2904\|\|None\|Vigan.08G148400.01), INTRON(\|\|\|None\|Vigan.08G148300.01)	Vigna nepalensis