VIGGS:Variant information

Chr06:34537359 - 34545342

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
34537494	A	T	55	2094.77	1.00	UTR_5_PRIME(\|244\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34537899	T	C	42	1813.77	1.00	SYNONYMOUS_CODING(SILENT\|cgT/cgC\|R54\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538198	G	A	57	2501.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538208	G	A	52	2319.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538332	T	C	66	2683.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538922	G	A	51	2032.77	1.00	SYNONYMOUS_CODING(SILENT\|aaG/aaA\|K123\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539107	C	T	59	2402.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539124	C	A	59	2323.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539215	C	T	64	2607.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539267	A	G	59	2407.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539357	A	T	63	2377.77	0.98	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539375	A	C	65	2616.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539474	T	C	51	2033.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540011	T	C	44	1751.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540283	C	T	62	2416.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540350	T	G	56	2219.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540410	T	G	34	1589.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540419	T	G	36	1582.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540450	T	A	30	1301.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540467	T	A	30	588.77	0.93	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540510	G	T	40	1666.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540865	T	G	57	2238.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gTt/gGt\|V240G\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541153	C	T	47	1885.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541297	G	A	51	2046.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541469	A	G	53	2057.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541651	T	C	52	2015.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541688	T	A	55	2136.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541765	T	C	49	2181.77	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34542050	T	C	47	1968.77	1.00	DOWNSTREAM(\|4824\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34542156	A	T	45	1796.77	1.00	DOWNSTREAM(\|4718\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34542799	G	A	60	2493.77	1.00	DOWNSTREAM(\|4075\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34542966	T	G	53	2456.77	1.00	DOWNSTREAM(\|3908\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34542973	C	A	60	2619.77	1.00	DOWNSTREAM(\|3901\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543042	A	G	58	2262.77	1.00	DOWNSTREAM(\|3832\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543074	T	C	50	2248.77	1.00	DOWNSTREAM(\|3800\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543098	A	C	52	2342.77	1.00	DOWNSTREAM(\|3776\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543211	C	T	62	2416.77	1.00	DOWNSTREAM(\|3663\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543297	G	C	50	2336.77	1.00	DOWNSTREAM(\|3577\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543300	C	T	54	2369.77	1.00	DOWNSTREAM(\|3574\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543402	C	T	41	1680.77	1.00	DOWNSTREAM(\|3472\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543585	A	G	48	2085.77	1.00	DOWNSTREAM(\|3289\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543898	G	A	59	2347.77	1.00	DOWNSTREAM(\|2976\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543977	G	A	54	2401.77	1.00	DOWNSTREAM(\|2897\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543978	G	C	54	2401.77	1.00	DOWNSTREAM(\|2896\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34544110	C	T	52	2107.77	1.00	DOWNSTREAM(\|2764\|\|None\|Vigan.06G211200.01), SYNONYMOUS_CODING(SILENT\|ccC/ccT\|P443\|None\|Vigan.06G211100.01)	Vigna nepalensis
34545029	A	G	49	1906.77	1.00	DOWNSTREAM(\|1845\|\|None\|Vigan.06G211200.01), UTR_3_PRIME(\|288\|\|None\|Vigan.06G211100.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
34537906	GTCCC	G	43	1852.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01), SPLICE_SITE_DONOR(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538204	A	AT	55	2502.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538413	G	GT	37	1281.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538486	CTT	C	27	920.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34538737	T	TCATA	50	2280.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539302	A	AT	64	2355.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539432	TA	T	54	2020.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539898	AT	A	46	1547.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539903	AT	A	45	1362.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34539926	T	TGTG	57	2526.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540408	CT	C	34	1580.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34540602	G	GT	41	1236.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34541751	TGATCCTCGAA	T	46	2097.73	1.00	INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543494	GAAAA	G	46	2032.73	1.00	DOWNSTREAM(\|3379\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis
34543599	CTA	C	57	2508.73	1.00	DOWNSTREAM(\|3274\|\|None\|Vigan.06G211200.01), INTRON(\|\|\|None\|Vigan.06G211100.01)	Vigna nepalensis