VIGGS:Variant information

Chr11:15273415 - 15277760

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
15273509	A	G	60	2377.77	1.00	UTR_5_PRIME(\|95\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15273964	C	T	45	1768.77	1.00	SYNONYMOUS_CODING(SILENT\|ccC/ccT\|P76\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274011	G	A	50	2221.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274014	T	A	50	2221.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274040	T	G	55	2264.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274095	G	C	45	1912.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274346	C	A	62	2704.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274374	A	T	59	2711.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274381	T	A	55	2456.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274462	T	A	44	1770.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274767	C	G	52	2124.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274897	C	A	53	2182.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275504	C	G	59	2324.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275519	G	A	58	2373.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275578	T	C	70	3146.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275909	C	T	48	2221.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275930	A	G	51	2309.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275973	G	C	56	2489.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275987	A	T	56	2579.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276010	C	A	52	2329.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276036	T	C	51	2040.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276101	C	T	63	2851.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276109	A	G	62	2871.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276110	T	C	61	2960.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276131	T	A	66	2953.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276169	A	T	59	2669.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276195	A	G	57	2564.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276204	A	G	55	2610.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276250	C	T	65	2619.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276431	C	G	58	2547.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276437	T	G	57	2507.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276456	T	G	55	2212.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276482	T	A	56	2210.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277039	A	G	69	2634.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277102	T	C	76	3055.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277150	T	G	71	2839.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277179	T	C	68	2657.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277220	C	T	71	3144.77	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277554	G	C	47	1942.77	1.00	UTR_3_PRIME(\|75\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277568	C	G	50	1982.77	1.00	UTR_3_PRIME(\|89\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277624	G	C	46	1972.77	1.00	UTR_3_PRIME(\|145\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277635	A	T	43	1942.77	1.00	UTR_3_PRIME(\|156\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277674	C	G	39	1739.77	1.00	UTR_3_PRIME(\|195\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277686	C	G	45	2111.77	1.00	UTR_3_PRIME(\|207\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277733	G	C	42	1840.77	1.00	UTR_3_PRIME(\|254\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277738	A	G	40	1803.77	1.00	UTR_3_PRIME(\|259\|\|None\|Vigan.11G108800.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
15274368	A	AT	54	2527.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274435	T	TA	39	1174.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274949	T	TA	37	1048.25	0.92	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15274950	T	TA	48	1948.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275574	A	ATTG	71	3226.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275735	TA	T	55	1642.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15275896	G	GTTATAACTA	43	2048.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276074	AC	A	55	2465.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276079	TC	T	55	2564.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276179	A	AACCTCTAG	59	2772.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15276321	G	GCAA	69	3032.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277215	CGTA	C	70	3135.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis
15277691	TC	T	49	2122.73	1.00	UTR_3_PRIME(\|213\|\|None\|Vigan.11G108800.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
15273825	(TCT)8	(TCT)6	50	2181.73	1.00	INTRON(\|\|\|None\|Vigan.11G108800.01)	Vigna nepalensis