VIGGS:Variant information

Chr02:2609929 - 2613617

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2609930	T	A	6	232.84	1.00	UTR_5_PRIME(\|109\|\|None\|Vigan.02G034700.01)	Vigna nepalensis
2609960	A	G	19	909.77	1.00	START_GAINED(\|\|\|None\|Vigan.02G034700.01), UTR_5_PRIME(\|79\|\|None\|Vigan.02G034700.01)	Vigna nepalensis
2609970	T	C	24	1032.77	1.00	UTR_5_PRIME(\|69\|\|None\|Vigan.02G034700.01)	Vigna nepalensis
2610062	A	C	16	530.77	1.00	SYNONYMOUS_CODING(SILENT\|atA/atC\|I8\|None\|Vigan.02G034700.01)	Vigna nepalensis
2610652	G	A	20	806.77	1.00	INTRON(\|\|\|None\|Vigan.02G034700.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.02G034700.01)	Vigna nepalensis
2611057	T	C	51	1951.77	1.00	DOWNSTREAM(\|4788\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|4698\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2611270	T	A	44	1940.77	1.00	DOWNSTREAM(\|4575\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|4485\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2611283	G	A	47	2144.77	1.00	DOWNSTREAM(\|4562\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|4472\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2611410	T	C	48	1972.77	1.00	DOWNSTREAM(\|4435\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|4345\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2611507	C	A	46	1830.77	1.00	DOWNSTREAM(\|4338\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|4248\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612171	G	A	55	2228.77	1.00	DOWNSTREAM(\|3674\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3584\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612377	C	A	59	2203.77	1.00	DOWNSTREAM(\|3468\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3378\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612413	C	G	54	2137.77	1.00	DOWNSTREAM(\|3432\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3342\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612453	A	G	53	2146.77	1.00	DOWNSTREAM(\|3392\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3302\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612464	G	T	51	2092.77	1.00	DOWNSTREAM(\|3381\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3291\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612514	A	C	62	2474.77	1.00	DOWNSTREAM(\|3331\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3241\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612680	T	C	49	2200.77	1.00	DOWNSTREAM(\|3165\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3075\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612688	G	A	52	2416.77	1.00	DOWNSTREAM(\|3157\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3067\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612721	T	C	61	2462.77	1.00	DOWNSTREAM(\|3124\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3034\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612886	C	T	71	2748.77	1.00	DOWNSTREAM(\|2959\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|2869\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2612939	G	T	54	2234.77	1.00	DOWNSTREAM(\|2906\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|2816\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2613134	G	A	49	1908.77	1.00	DOWNSTREAM(\|2711\|\|None\|Vigan.02G034900.01), NON_SYNONYMOUS_CODING(MISSENSE\|cGt/cAt\|R237H\|None\|Vigan.02G034700.01), UPSTREAM(\|2621\|\|None\|Vigan.02G034800.01)	Vigna nepalensis
2613536	T	G	45	1808.77	1.00	DOWNSTREAM(\|2309\|\|None\|Vigan.02G034900.01), UPSTREAM(\|2219\|\|None\|Vigan.02G034800.01), UTR_3_PRIME(\|290\|\|None\|Vigan.02G034700.01)	Vigna nepalensis
2613604	A	G	50	2142.77	1.00	DOWNSTREAM(\|2241\|\|None\|Vigan.02G034900.01), UPSTREAM(\|2151\|\|None\|Vigan.02G034800.01), UTR_3_PRIME(\|358\|\|None\|Vigan.02G034700.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
2609927	CGT	C	6	249.77	1.00	INTERGENIC(\|\|\|\|), INTRAGENIC(\|\|\|None\|), UPSTREAM(\|1\|\|None\|Vigan.02G034700.01), UTR_5_PRIME(\|110\|\|None\|Vigan.02G034700.01)	Vigna nepalensis
2612690	TG	T	54	2365.73	1.00	DOWNSTREAM(\|3154\|\|None\|Vigan.02G034900.01), INTRON(\|\|\|None\|Vigan.02G034700.01), UPSTREAM(\|3064\|\|None\|Vigan.02G034800.01)	Vigna nepalensis