VIGGS:Variant information

Chr03:39607445 - 39610251

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
39607507	A	C	60	2317.77	1.00	DOWNSTREAM(\|919\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|206\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607544	T	C	69	294.77	0.16	DOWNSTREAM(\|956\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|169\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607553	T	C	73	396.77	0.21	DOWNSTREAM(\|965\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|160\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607599	G	C	94	1359.77	0.40	DOWNSTREAM(\|1011\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|114\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607689	G	A	98	1303.77	0.38	DOWNSTREAM(\|1101\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|24\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607707	A	G	96	1149.77	0.33	DOWNSTREAM(\|1119\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|6\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607708	G	A	96	1152.77	0.33	DOWNSTREAM(\|1120\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|5\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607744	G	T	100	920.77	0.28	DOWNSTREAM(\|1156\|\|None\|Vigan.03G256800.01), NON_SYNONYMOUS_CODING(MISSENSE\|gCt/gAt\|A157D\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607746	A	G	100	962.77	0.27	DOWNSTREAM(\|1158\|\|None\|Vigan.03G256800.01), SYNONYMOUS_CODING(SILENT\|tcT/tcC\|S156\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607761	G	A	94	855.77	0.28	DOWNSTREAM(\|1173\|\|None\|Vigan.03G256800.01), SYNONYMOUS_CODING(SILENT\|tgC/tgT\|C151\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607768	C	T	93	720.77	0.24	DOWNSTREAM(\|1180\|\|None\|Vigan.03G256800.01), NON_SYNONYMOUS_CODING(MISSENSE\|gGa/gAa\|G149E\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607786	G	A	84	372.77	0.17	DOWNSTREAM(\|1198\|\|None\|Vigan.03G256800.01), NON_SYNONYMOUS_CODING(MISSENSE\|gCt/gTt\|A143V\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607795	C	T	88	331.77	0.16	DOWNSTREAM(\|1207\|\|None\|Vigan.03G256800.01), NON_SYNONYMOUS_CODING(MISSENSE\|gGa/gAa\|G140E\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607856	C	T	56	2295.77	1.00	DOWNSTREAM(\|1268\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607892	T	C	57	2322.77	1.00	DOWNSTREAM(\|1304\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39608475	A	G	48	1853.77	1.00	DOWNSTREAM(\|1887\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39608522	A	G	44	1647.77	1.00	DOWNSTREAM(\|1934\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|4987\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39608567	T	A	55	2216.77	1.00	DOWNSTREAM(\|1979\|\|None\|Vigan.03G256800.01), SYNONYMOUS_CODING(SILENT\|ccA/ccT\|P113\|None\|Vigan.03G256900.01), UPSTREAM(\|4942\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609675	G	T	60	2701.77	1.00	DOWNSTREAM(\|3087\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3834\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609685	C	G	61	2739.77	1.00	DOWNSTREAM(\|3097\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3824\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609757	A	G	53	2160.77	1.00	DOWNSTREAM(\|3169\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3752\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609836	T	G	50	1930.77	1.00	DOWNSTREAM(\|3248\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3673\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609914	A	G	39	1580.77	1.00	DOWNSTREAM(\|3326\|\|None\|Vigan.03G256800.01), SYNONYMOUS_CODING(SILENT\|acT/acC\|T55\|None\|Vigan.03G256900.01), UPSTREAM(\|3595\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609999	A	G	48	1826.77	1.00	DOWNSTREAM(\|3411\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3510\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39610217	A	G	54	2073.77	1.00	DOWNSTREAM(\|3629\|\|None\|Vigan.03G256800.01), START_GAINED(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3292\|\|None\|Vigan.03G257000.01), UTR_5_PRIME(\|23\|\|None\|Vigan.03G256900.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
39607480	TG	T	50	1829.73	1.00	DOWNSTREAM(\|893\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|232\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39607552	GT	G	65	1163.73	0.77	DOWNSTREAM(\|965\|\|None\|Vigan.03G256800.01), UTR_3_PRIME(\|160\|\|None\|Vigan.03G256900.01)	Vigna nepalensis
39609178	G	GA	29	512.87	0.90	DOWNSTREAM(\|2591\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|4330\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609347	GT	G	44	1328.73	1.00	DOWNSTREAM(\|2760\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|4161\|\|None\|Vigan.03G257000.01)	Vigna nepalensis
39609825	G	GA	52	1794.73	1.00	DOWNSTREAM(\|3238\|\|None\|Vigan.03G256800.01), INTRON(\|\|\|None\|Vigan.03G256900.01), UPSTREAM(\|3683\|\|None\|Vigan.03G257000.01)	Vigna nepalensis