VIGGS:Variant information

Chr08:25981373 - 25986972

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
25981947	T	C	53	2132.77	1.00	UTR_3_PRIME(\|25\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|491\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25981976	G	A	55	2055.77	1.00	UTR_3_PRIME(\|462\|\|None\|Vigan.08G257000.01), UTR_3_PRIME(\|54\|\|None\|Vigan.08G256900.01)	Vigna nepalensis
25982024	T	A	48	2067.77	1.00	UTR_3_PRIME(\|102\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|414\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982029	G	A	44	2042.77	1.00	UTR_3_PRIME(\|107\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|409\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982134	G	A	46	1961.77	1.00	UTR_3_PRIME(\|212\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|304\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982143	A	C	43	1852.77	1.00	UTR_3_PRIME(\|221\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|295\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982173	A	T	51	1981.77	1.00	UPSTREAM(\|4985\|\|None\|Vigan.08G257100.01), UTR_3_PRIME(\|251\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|265\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982345	G	A	60	2362.77	1.00	UPSTREAM(\|4813\|\|None\|Vigan.08G257100.01), UTR_3_PRIME(\|423\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|93\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982375	T	C	50	1957.77	1.00	UPSTREAM(\|4783\|\|None\|Vigan.08G257100.01), UTR_3_PRIME(\|453\|\|None\|Vigan.08G256900.01), UTR_3_PRIME(\|63\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25982447	A	C	48	1928.77	1.00	SYNONYMOUS_CODING(SILENT\|gcT/gcG\|A361\|None\|Vigan.08G257000.01), UPSTREAM(\|4711\|\|None\|Vigan.08G257100.01), UTR_3_PRIME(\|525\|\|None\|Vigan.08G256900.01)	Vigna nepalensis
25982495	A	G	67	2593.77	1.00	SYNONYMOUS_CODING(SILENT\|agT/agC\|S345\|None\|Vigan.08G257000.01), UPSTREAM(\|4663\|\|None\|Vigan.08G257100.01), UTR_3_PRIME(\|573\|\|None\|Vigan.08G256900.01)	Vigna nepalensis
25982524	A	C	65	2481.77	1.00	INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4634\|\|None\|Vigan.08G257100.01), UTR_3_PRIME(\|602\|\|None\|Vigan.08G256900.01)	Vigna nepalensis
25982708	A	G	58	2523.77	1.00	DOWNSTREAM(\|82\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4450\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25982720	A	T	59	2651.77	1.00	DOWNSTREAM(\|94\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4438\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25982749	C	T	53	2149.77	1.00	DOWNSTREAM(\|123\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4409\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25982917	A	C	61	2630.77	1.00	DOWNSTREAM(\|291\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4241\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983308	A	G	63	2404.77	1.00	DOWNSTREAM(\|682\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|3850\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983391	C	A	56	2116.77	1.00	DOWNSTREAM(\|765\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|3767\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983556	A	T	49	1954.77	1.00	DOWNSTREAM(\|930\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|3602\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983671	T	A	47	1959.77	1.00	DOWNSTREAM(\|1045\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|3487\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984258	G	A	55	1982.77	1.00	DOWNSTREAM(\|1632\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2900\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984346	C	G	47	1974.77	1.00	DOWNSTREAM(\|1720\|\|None\|Vigan.08G256900.01), SYNONYMOUS_CODING(SILENT\|gtG/gtC\|V160\|None\|Vigan.08G257000.01), UPSTREAM(\|2812\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984521	T	A	74	3033.77	1.00	DOWNSTREAM(\|1895\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2637\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984738	G	A	52	2366.77	1.00	DOWNSTREAM(\|2112\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2420\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984747	G	A	54	2316.77	1.00	DOWNSTREAM(\|2121\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2411\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984939	G	T	56	2284.77	1.00	DOWNSTREAM(\|2313\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2219\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985036	A	G	44	1830.77	1.00	DOWNSTREAM(\|2410\|\|None\|Vigan.08G256900.01), SYNONYMOUS_CODING(SILENT\|gaT/gaC\|D88\|None\|Vigan.08G257000.01), UPSTREAM(\|2122\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985207	G	C	49	1895.77	1.00	DOWNSTREAM(\|2581\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1951\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985369	G	A	62	2357.77	1.00	DOWNSTREAM(\|2743\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1789\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985594	G	A	56	2258.77	1.00	DOWNSTREAM(\|2968\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1564\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985848	A	G	56	2189.77	1.00	DOWNSTREAM(\|3222\|\|None\|Vigan.08G256900.01), SYNONYMOUS_CODING(SILENT\|caT/caC\|H59\|None\|Vigan.08G257000.01), UPSTREAM(\|1310\|\|None\|Vigan.08G257100.01), UPSTREAM(\|4774\|\|None\|Vigan.08G257200.01)	Vigna nepalensis
25985997	A	G	46	1824.77	1.00	DOWNSTREAM(\|3371\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1161\|\|None\|Vigan.08G257100.01), UPSTREAM(\|4625\|\|None\|Vigan.08G257200.01)	Vigna nepalensis
25986052	G	A	47	1856.77	1.00	DOWNSTREAM(\|3426\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1106\|\|None\|Vigan.08G257100.01), UPSTREAM(\|4570\|\|None\|Vigan.08G257200.01)	Vigna nepalensis
25986086	T	C	53	2130.77	1.00	DOWNSTREAM(\|3460\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1072\|\|None\|Vigan.08G257100.01), UPSTREAM(\|4536\|\|None\|Vigan.08G257200.01)	Vigna nepalensis
25986137	G	A	46	1878.77	1.00	DOWNSTREAM(\|3511\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1021\|\|None\|Vigan.08G257100.01), UPSTREAM(\|4485\|\|None\|Vigan.08G257200.01)	Vigna nepalensis
25986489	G	A	29	1112.77	1.00	DOWNSTREAM(\|3863\|\|None\|Vigan.08G256900.01), SYNONYMOUS_CODING(SILENT\|ttC/ttT\|F52\|None\|Vigan.08G257000.01), UPSTREAM(\|4133\|\|None\|Vigan.08G257200.01), UPSTREAM(\|669\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25986667	A	G	50	2218.77	1.00	DOWNSTREAM(\|4041\|\|None\|Vigan.08G256900.01), UPSTREAM(\|3955\|\|None\|Vigan.08G257200.01), UPSTREAM(\|491\|\|None\|Vigan.08G257100.01), UTR_5_PRIME(\|23\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25986861	G	A	49	1956.77	1.00	DOWNSTREAM(\|4235\|\|None\|Vigan.08G256900.01), UPSTREAM(\|297\|\|None\|Vigan.08G257100.01), UPSTREAM(\|3761\|\|None\|Vigan.08G257200.01), UTR_5_PRIME(\|217\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25986922	G	C	36	1390.77	1.00	DOWNSTREAM(\|4296\|\|None\|Vigan.08G256900.01), UPSTREAM(\|236\|\|None\|Vigan.08G257100.01), UPSTREAM(\|3700\|\|None\|Vigan.08G257200.01), UTR_5_PRIME(\|278\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25986962	C	T	14	736.77	1.00	DOWNSTREAM(\|4336\|\|None\|Vigan.08G256900.01), UPSTREAM(\|196\|\|None\|Vigan.08G257100.01), UPSTREAM(\|3660\|\|None\|Vigan.08G257200.01), UTR_5_PRIME(\|318\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25986965	G	A	14	601.77	1.00	DOWNSTREAM(\|4339\|\|None\|Vigan.08G256900.01), UPSTREAM(\|193\|\|None\|Vigan.08G257100.01), UPSTREAM(\|3657\|\|None\|Vigan.08G257200.01), UTR_5_PRIME(\|321\|\|None\|Vigan.08G257000.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
25982930	T	TTTCTTATTTTTGAGCAAATATTACAA	60	3695.73	1.00	DOWNSTREAM(\|305\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4227\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25982933	TTGG	T	65	3067.73	1.00	DOWNSTREAM(\|308\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4224\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25982938	TC	T	67	3067.73	1.00	DOWNSTREAM(\|313\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4219\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25982941	T	TGCAAA	66	3065.73	1.00	DOWNSTREAM(\|316\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4216\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983031	AT	A	59	2576.73	1.00	DOWNSTREAM(\|406\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4126\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983033	ATACGCAACACAGTAATACGAATTAAGCTATTCTTAAGTAACAGTTGAAAGCATACGCCACTCATAAATATTCTACAGGATGATGTTTGCAAGAAT	A	59	2578.73	1.00	DOWNSTREAM(\|408\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|4124\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25983355	C	CA	55	1841.73	1.00	DOWNSTREAM(\|730\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|3802\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984622	ATTTTTTTTT	A	50	2280.73	1.00	DOWNSTREAM(\|1997\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2535\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25984631	T	TAAAAAAA	50	2279.73	1.00	DOWNSTREAM(\|2006\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|2526\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985190	GT	G	46	1685.73	1.00	DOWNSTREAM(\|2565\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1967\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25985263	TG	T	46	1602.73	1.00	DOWNSTREAM(\|2638\|\|None\|Vigan.08G256900.01), INTRON(\|\|\|None\|Vigan.08G257000.01), UPSTREAM(\|1894\|\|None\|Vigan.08G257100.01)	Vigna nepalensis
25986658	G	GTCT	48	2241.73	1.00	DOWNSTREAM(\|4033\|\|None\|Vigan.08G256900.01), UPSTREAM(\|3963\|\|None\|Vigan.08G257200.01), UPSTREAM(\|499\|\|None\|Vigan.08G257100.01), UTR_5_PRIME(\|15\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25986956	C	CT	20	944.73	1.00	DOWNSTREAM(\|4331\|\|None\|Vigan.08G256900.01), UPSTREAM(\|201\|\|None\|Vigan.08G257100.01), UPSTREAM(\|3665\|\|None\|Vigan.08G257200.01), UTR_5_PRIME(\|313\|\|None\|Vigan.08G257000.01)	Vigna nepalensis
25986958	A	ATATATATATATAT	21	1079.73	1.00	DOWNSTREAM(\|4333\|\|None\|Vigan.08G256900.01), UPSTREAM(\|199\|\|None\|Vigan.08G257100.01), UPSTREAM(\|3663\|\|None\|Vigan.08G257200.01), UTR_5_PRIME(\|315\|\|None\|Vigan.08G257000.01)	Vigna nepalensis