VIGGS:Variant information

Chr10:4589357 - 4595509

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
4589413	C	T	64	2483.77	1.00	UTR_5_PRIME(\|65\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589425	C	G	62	2487.77	1.00	UTR_5_PRIME(\|53\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589459	G	T	56	2232.77	1.00	START_GAINED(\|\|\|None\|Vigan.10G045700.01), UTR_5_PRIME(\|19\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589523	C	T	53	2406.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Ctt/Ttt\|L16F\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589533	T	G	60	2646.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|tTc/tGc\|F19C\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589579	C	T	63	2757.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589590	T	A	60	2754.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589640	T	C	56	2413.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589655	G	T	57	2457.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589684	T	C	60	2662.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589686	T	C	59	2662.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589718	C	G	57	2457.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589737	T	A	49	2112.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589766	T	A	48	1872.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589798	G	C	53	2191.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589850	T	G	57	2262.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589874	T	C	51	2212.77	1.00	SYNONYMOUS_CODING(SILENT\|gtT/gtC\|V34\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589884	G	A	47	2109.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Gat/Aat\|D38N\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589911	G	A	37	1467.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Gtt/Att\|V47I\|None\|Vigan.10G045700.01)	Vigna nepalensis
4589954	C	T	37	1482.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gCa/gTa\|A61V\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590021	T	C	43	1719.77	1.00	SYNONYMOUS_CODING(SILENT\|aaT/aaC\|N83\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590048	T	C	43	1906.77	1.00	SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A92\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590049	A	G	43	1906.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Atg/Gtg\|M93V\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590153	G	T	37	1563.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590275	T	A	50	2235.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590293	T	C	57	2528.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590342	C	A	48	2068.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590366	T	A	45	2031.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590392	C	T	43	1896.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590404	G	A	51	2356.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590420	T	C	54	2536.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590444	C	T	60	2671.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590458	C	A	57	2626.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590463	A	T	58	2626.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590465	A	G	58	2716.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590475	T	C	59	2716.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590493	G	T	54	2328.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590523	T	A	48	1907.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590606	G	A	59	2393.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590634	T	C	59	2425.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590708	C	T	47	2078.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590716	A	G	45	2049.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590774	A	G	53	2019.77	1.00	SYNONYMOUS_CODING(SILENT\|caA/caG\|Q111\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590875	T	C	41	1677.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590901	C	G	42	1726.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590949	A	G	52	2361.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591042	G	A	61	2391.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591080	T	G	58	2333.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591129	T	A	52	2009.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591142	A	G	47	2116.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591147	G	A	45	1975.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591179	G	A	45	1996.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591180	C	T	45	1996.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591276	G	A	54	2125.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591345	A	G	45	1797.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591427	G	T	38	1558.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591481	G	C	43	1695.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591507	T	A	49	2198.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591514	C	T	47	2147.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591523	G	T	45	2011.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591556	T	A	51	1968.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591608	C	A	54	2392.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591630	A	T	59	2593.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591690	G	A	64	2553.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591726	G	C	59	2410.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591832	A	G	68	2796.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591858	A	G	66	2681.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591906	T	C	69	2780.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4591943	C	T	61	2495.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592011	T	C	69	2730.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592260	T	A	56	2491.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592261	C	G	56	2491.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592287	T	C	56	2523.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592288	T	C	56	2523.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592315	T	C	53	2378.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592330	G	A	50	2181.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592366	C	G	42	1754.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592420	C	T	52	2319.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592435	A	T	51	2255.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592470	G	A	51	2248.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592478	C	T	51	2398.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592485	C	T	53	2446.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592542	A	G	43	1936.77	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4593231	C	A	56	2221.77	1.00	DOWNSTREAM(\|4670\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4593264	A	C	56	2258.77	1.00	DOWNSTREAM(\|4637\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4593791	T	C	49	1982.77	1.00	DOWNSTREAM(\|4110\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4593948	G	T	42	1625.77	1.00	DOWNSTREAM(\|3953\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594062	A	G	55	2131.77	1.00	DOWNSTREAM(\|3839\|\|None\|Vigan.10G045800.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.10G045700.01), SYNONYMOUS_CODING(SILENT\|ctA/ctG\|L229\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594102	A	G	43	1730.77	1.00	DOWNSTREAM(\|3799\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594343	A	T	28	672.88	0.89	DOWNSTREAM(\|3558\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594458	G	T	50	1983.77	1.00	DOWNSTREAM(\|3443\|\|None\|Vigan.10G045800.01), NON_SYNONYMOUS_CODING(MISSENSE\|Gct/Tct\|A252S\|None\|Vigan.10G045700.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594506	A	C	52	2317.77	1.00	DOWNSTREAM(\|3395\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594516	A	G	53	2341.77	1.00	DOWNSTREAM(\|3385\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594813	T	G	47	1876.77	1.00	DOWNSTREAM(\|3088\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4595421	G	A	65	2849.77	1.00	DOWNSTREAM(\|2480\|\|None\|Vigan.10G045800.01), UTR_3_PRIME(\|312\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4595426	T	C	65	2877.77	1.00	DOWNSTREAM(\|2475\|\|None\|Vigan.10G045800.01), UTR_3_PRIME(\|317\|\|None\|Vigan.10G045700.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
4589601	TTTTGTATTA	T	58	2617.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590137	T	TC	38	1521.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590276	TG	T	51	2226.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590362	AG	A	46	2111.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590547	A	AC	55	2020.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4590943	GCACC	G	54	2352.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592201	C	CA	52	1905.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592231	C	CTG	56	2469.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592502	CACATCCCCTCAAACTCAGGACTGG	C	47	2167.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4592703	GGTTT	G	51	2229.73	1.00	INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594163	AT	A	36	1412.73	1.00	DOWNSTREAM(\|3737\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594195	ATGAATATCT	A	37	1605.73	1.00	DOWNSTREAM(\|3705\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594671	T	TG	68	2179.73	1.00	DOWNSTREAM(\|3229\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis
4594827	C	CTA	56	2454.73	1.00	DOWNSTREAM(\|3073\|\|None\|Vigan.10G045800.01), INTRON(\|\|\|None\|Vigan.10G045700.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.10G045700.01)	Vigna nepalensis