VIGGS:Variant information

Chr01:6560661 - 6566297

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6560729	T	G	53	2079.77	1.00	START_GAINED(\|\|\|None\|Vigan.01G080700.01), UTR_5_PRIME(\|122\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6561009	C	A	44	1710.77	1.00	SYNONYMOUS_CODING(SILENT\|cgC/cgA\|R53\|None\|Vigan.01G080700.01)	Vigna nepalensis
6561478	T	G	77	3215.74	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6561503	A	G	71	2870.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6561631	G	A	68	2794.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6561667	C	A	54	2132.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6562187	T	G	58	2281.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4901\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6562565	C	A	58	2338.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4523\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6562580	C	T	53	2155.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4508\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6562693	A	C	54	2247.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4395\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6562725	A	G	49	1947.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4363\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6562862	T	A	52	1877.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4226\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6562906	T	C	50	1833.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|4182\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563194	T	G	59	2393.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3894\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563206	A	T	60	2426.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3882\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563273	T	C	54	2124.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3815\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563304	A	T	50	2011.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3784\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563355	G	A	41	1644.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3733\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563488	T	C	44	2018.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3600\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563497	C	A	45	1977.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3591\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563581	C	T	41	1783.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3507\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563591	T	C	38	1706.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3497\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563781	T	C	63	2455.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3307\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6563964	C	A	66	2721.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3124\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564113	G	C	58	2511.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2975\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564136	A	G	56	2441.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2952\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564246	C	T	49	2017.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2842\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564370	T	C	47	1880.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2718\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564433	C	G	54	2168.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2655\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564539	C	G	64	2576.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2549\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564748	C	G	63	2572.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2340\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564950	C	A	63	2569.77	1.00	SYNONYMOUS_CODING(SILENT\|ccC/ccA\|P185\|None\|Vigan.01G080700.01), UPSTREAM(\|2138\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564977	T	A	68	2826.77	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2111\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565234	G	T	60	2359.77	1.00	DOWNSTREAM(\|4955\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1854\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565262	A	G	54	2166.77	1.00	DOWNSTREAM(\|4927\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1826\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565306	G	A	55	2159.77	1.00	DOWNSTREAM(\|4883\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1782\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565395	G	A	46	1912.77	1.00	DOWNSTREAM(\|4794\|\|None\|Vigan.01G080900.01), SYNONYMOUS_CODING(SILENT\|gaG/gaA\|E245\|None\|Vigan.01G080700.01), UPSTREAM(\|1693\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565455	T	A	47	1815.77	1.00	DOWNSTREAM(\|4734\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1633\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565469	C	A	48	1833.77	1.00	DOWNSTREAM(\|4720\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1619\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565556	T	C	50	1948.77	1.00	DOWNSTREAM(\|4633\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1532\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565675	G	C	44	1721.77	1.00	DOWNSTREAM(\|4514\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1413\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565737	G	A	52	1946.77	1.00	DOWNSTREAM(\|4452\|\|None\|Vigan.01G080900.01), INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|1351\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565917	G	A	62	2502.77	1.00	DOWNSTREAM(\|4272\|\|None\|Vigan.01G080900.01), UPSTREAM(\|1171\|\|None\|Vigan.01G080800.01), UTR_3_PRIME(\|78\|\|None\|Vigan.01G080700.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6560672	T	TTTATTATAATTATAAATTAATATTACAC	42	2289.73	1.00	UTR_5_PRIME(\|178\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6561834	CGT	C	63	2797.73	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6564084	G	GAAA	39	1801.73	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|3003\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564186	TAGTAGACATTAACGTTTAGGA	T	58	2504.73	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2901\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564715	CT	C	57	1774.73	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2372\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6564809	GTTCTAGATTAT	G	57	2524.73	1.00	INTRON(\|\|\|None\|Vigan.01G080700.01), UPSTREAM(\|2278\|\|None\|Vigan.01G080800.01)	Vigna nepalensis
6565928	T	TA	59	2059.73	1.00	DOWNSTREAM(\|4260\|\|None\|Vigan.01G080900.01), UPSTREAM(\|1159\|\|None\|Vigan.01G080800.01), UTR_3_PRIME(\|90\|\|None\|Vigan.01G080700.01)	Vigna nepalensis
6565995	CGT	C	58	2542.73	1.00	DOWNSTREAM(\|4193\|\|None\|Vigan.01G080900.01), UPSTREAM(\|1092\|\|None\|Vigan.01G080800.01), UTR_3_PRIME(\|157\|\|None\|Vigan.01G080700.01)	Vigna nepalensis