VIGGS:Variant information

Chr01:58484143 - 58488370

Filter

[SNPs] [Indels] [SSR-associated indels]

SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
58484203	C	A	53	2144.77	1.00	UPSTREAM(\|3390\|\|None\|Vigan.01G454300.01), UTR_3_PRIME(\|539\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58484254	C	T	58	2381.77	1.00	UPSTREAM(\|3441\|\|None\|Vigan.01G454300.01), UTR_3_PRIME(\|488\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58484471	T	C	68	2617.77	1.00	UPSTREAM(\|3658\|\|None\|Vigan.01G454300.01), UTR_3_PRIME(\|271\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58484534	T	C	56	2369.77	1.00	UPSTREAM(\|3721\|\|None\|Vigan.01G454300.01), UTR_3_PRIME(\|208\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58485153	A	T	58	2619.77	1.00	DOWNSTREAM(\|4385\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01), UPSTREAM(\|4340\|\|None\|Vigan.01G454300.01)	Vigna nepalensis
58485154	T	C	59	2619.77	1.00	DOWNSTREAM(\|4384\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01), UPSTREAM(\|4341\|\|None\|Vigan.01G454300.01)	Vigna nepalensis
58486092	A	T	58	2302.77	1.00	DOWNSTREAM(\|3446\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58486122	G	A	64	2544.77	1.00	DOWNSTREAM(\|3416\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58486497	C	A	50	2080.77	1.00	DOWNSTREAM(\|3041\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58487529	T	C	69	2648.77	1.00	DOWNSTREAM(\|2009\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58487552	C	T	67	2541.77	1.00	DOWNSTREAM(\|1986\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58487772	C	T	59	2362.77	1.00	DOWNSTREAM(\|1766\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58488335	G	C	33	1338.77	1.00	DOWNSTREAM(\|1203\|\|None\|Vigan.01G454500.01), START_GAINED(\|\|\|None\|Vigan.01G454400.01), UTR_5_PRIME(\|421\|\|None\|Vigan.01G454400.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
58484934	GCCGGTA	G	37	1553.73	1.00	CODON_CHANGE_PLUS_CODON_DELETION(\|ggtaccggc/ggc\|GTG137G\|None\|Vigan.01G454400.01), DOWNSTREAM(\|4603\|\|None\|Vigan.01G454500.01), UPSTREAM(\|4122\|\|None\|Vigan.01G454300.01)	Vigna nepalensis
58485812	ACT	A	55	2375.73	1.00	DOWNSTREAM(\|3725\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01), UPSTREAM(\|5000\|\|None\|Vigan.01G454300.01)	Vigna nepalensis
58486045	TC	T	54	1884.73	1.00	DOWNSTREAM(\|3492\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58486769	TA	T	43	1306.73	1.00	DOWNSTREAM(\|2768\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis
58486972	GTAAA	G	64	2685.73	1.00	DOWNSTREAM(\|2565\|\|None\|Vigan.01G454500.01), INTRON(\|\|\|None\|Vigan.01G454400.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
58488165	(ACT)6	(ACT)5	39	1703.73	1.00	DOWNSTREAM(\|1372\|\|None\|Vigan.01G454500.01), UTR_5_PRIME(\|252\|\|None\|Vigan.01G454400.01)	Vigna nepalensis