VIGGS:Variant information

Chr08:8367994 - 8376185

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
8368483	T	C	62	2601.77	1.00	DOWNSTREAM(\|884\|\|None\|Vigan.08G099500.01), SYNONYMOUS_CODING(SILENT\|Tta/Cta\|L113\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369011	A	C	8	68.77	0.38	DOWNSTREAM(\|1412\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369013	A	C	8	64.77	0.38	DOWNSTREAM(\|1414\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369158	T	C	46	1982.77	1.00	DOWNSTREAM(\|1559\|\|None\|Vigan.08G099500.01), SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A166\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369167	G	T	41	1898.77	1.00	DOWNSTREAM(\|1568\|\|None\|Vigan.08G099500.01), SYNONYMOUS_CODING(SILENT\|cgG/cgT\|R169\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369245	A	G	47	1772.77	1.00	DOWNSTREAM(\|1646\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369773	C	T	57	2120.77	1.00	DOWNSTREAM(\|2174\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369787	A	G	65	2505.77	1.00	DOWNSTREAM(\|2188\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369798	T	C	62	2411.77	1.00	DOWNSTREAM(\|2199\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369884	C	T	48	1964.77	1.00	DOWNSTREAM(\|2285\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8370262	A	C	62	2415.77	1.00	DOWNSTREAM(\|2663\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8370632	T	C	65	2647.77	1.00	DOWNSTREAM(\|3033\|\|None\|Vigan.08G099500.01), NON_SYNONYMOUS_CODING(MISSENSE\|Tct/Cct\|S329P\|None\|Vigan.08G099600.01)	Vigna nepalensis
8370829	A	G	52	2107.77	1.00	DOWNSTREAM(\|3230\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8370932	G	C	49	1956.77	1.00	DOWNSTREAM(\|3333\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371037	G	A	43	1732.77	1.00	DOWNSTREAM(\|3438\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371440	C	T	44	1819.77	1.00	DOWNSTREAM(\|3841\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371497	T	C	48	2131.77	1.00	DOWNSTREAM(\|3898\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371509	T	C	45	2112.77	1.00	DOWNSTREAM(\|3910\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371543	A	G	48	2067.77	1.00	DOWNSTREAM(\|3944\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371726	T	C	55	2145.77	1.00	DOWNSTREAM(\|4127\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371788	C	T	52	1841.77	1.00	DOWNSTREAM(\|4189\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371879	T	G	48	2121.77	1.00	DOWNSTREAM(\|4280\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371885	G	T	46	2126.77	1.00	DOWNSTREAM(\|4286\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371934	A	T	40	1723.77	1.00	DOWNSTREAM(\|4335\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8372071	A	G	63	2431.77	1.00	DOWNSTREAM(\|4472\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8372407	T	C	68	2622.77	1.00	DOWNSTREAM(\|4808\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373111	T	C	63	2760.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373136	C	T	67	3026.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373377	T	C	46	1805.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373522	A	C	54	2230.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373865	G	A	49	2074.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gGt/gAt\|G441D\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373970	A	T	44	1729.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8374080	A	G	59	2293.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8374578	A	T	56	2206.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8374615	A	G	65	2583.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8374857	G	A	64	2612.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375024	A	G	67	2939.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375030	C	T	65	2962.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375310	G	A	42	1662.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375381	T	C	53	1910.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375524	T	G	52	2065.77	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375754	G	T	60	2360.77	1.00	UTR_3_PRIME(\|62\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375868	T	C	51	2096.77	1.00	UTR_3_PRIME(\|176\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8376123	C	A	44	1739.77	1.00	UTR_3_PRIME(\|431\|\|None\|Vigan.08G099600.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
8368625	CTTTTTAGTTTCT	C	45	1990.73	1.00	DOWNSTREAM(\|1027\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8368943	TA	T	40	1568.73	1.00	DOWNSTREAM(\|1345\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369346	GT	G	62	1636.73	0.98	DOWNSTREAM(\|1748\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8369753	TA	T	46	1342.73	1.00	DOWNSTREAM(\|2155\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371279	TGCTATGTTCACTTCTATTGAATTGCATAGATTTGCAAAGATGGATTA	T	24	1040.73	1.00	DOWNSTREAM(\|3681\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371521	T	TTAATAATAA	49	2300.73	1.00	DOWNSTREAM(\|3923\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371797	C	CGTGAAATCCTTCCACTCAAATGAACACACCCTGAGTGAATATCTCT	33	2388.73	1.00	DOWNSTREAM(\|4199\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371894	GAGATCTT	G	41	1885.73	1.00	DOWNSTREAM(\|4296\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8371953	TAGCTAGTATTGGCA	T	44	2017.73	1.00	DOWNSTREAM(\|4355\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8372117	CTTT	C	54	2392.73	1.00	DOWNSTREAM(\|4519\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8372169	A	AT	56	2251.73	1.00	DOWNSTREAM(\|4571\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8373160	ATTTAAT	A	36	1566.73	1.00	INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis
8375917	A	AT	51	1443.73	1.00	UTR_3_PRIME(\|226\|\|None\|Vigan.08G099600.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
8369001	(TA)25	(TA)21	11	196.73	0.55	DOWNSTREAM(\|1403\|\|None\|Vigan.08G099500.01), INTRON(\|\|\|None\|Vigan.08G099600.01)	Vigna nepalensis