VIGGS:Variant information

Chr09:36631905 - 36634992

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
36632312	A	T	52	2057.77	1.00	DOWNSTREAM(\|4632\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|1341\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36632533	C	T	71	2888.77	1.00	DOWNSTREAM(\|4411\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|1562\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36632764	T	G	56	2515.77	1.00	DOWNSTREAM(\|4180\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|1793\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633202	C	T	57	2250.77	1.00	DOWNSTREAM(\|3742\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2231\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633452	C	A	63	2479.77	1.00	DOWNSTREAM(\|3492\|\|None\|Vigan.09G224800.01), SYNONYMOUS_CODING(SILENT\|Cga/Aga\|R142\|None\|Vigan.09G224700.01), UPSTREAM(\|2481\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633672	T	C	58	2317.77	1.00	DOWNSTREAM(\|3272\|\|None\|Vigan.09G224800.01), SYNONYMOUS_CODING(SILENT\|ccT/ccC\|P187\|None\|Vigan.09G224700.01), UPSTREAM(\|2701\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633702	T	C	52	2306.77	1.00	DOWNSTREAM(\|3242\|\|None\|Vigan.09G224800.01), SYNONYMOUS_CODING(SILENT\|ttT/ttC\|F197\|None\|Vigan.09G224700.01), UPSTREAM(\|2731\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633717	T	A	54	2407.77	1.00	DOWNSTREAM(\|3227\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2746\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633746	G	C	53	2441.77	1.00	DOWNSTREAM(\|3198\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2775\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633752	G	A	55	2621.77	1.00	DOWNSTREAM(\|3192\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2781\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633755	G	C	59	2671.77	1.00	DOWNSTREAM(\|3189\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2784\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633767	T	G	66	3031.77	1.00	DOWNSTREAM(\|3177\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2796\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633777	C	A	62	2894.77	1.00	DOWNSTREAM(\|3167\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2806\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633787	G	A	59	2626.77	1.00	DOWNSTREAM(\|3157\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2816\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633827	C	A	63	2893.77	1.00	DOWNSTREAM(\|3117\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2856\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633864	A	T	62	2887.77	1.00	DOWNSTREAM(\|3080\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2893\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4984\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36633918	G	C	36	1530.77	1.00	DOWNSTREAM(\|3026\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2947\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4930\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634293	T	C	24	1051.77	1.00	DOWNSTREAM(\|2651\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3322\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4555\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634301	A	G	25	1141.77	1.00	DOWNSTREAM(\|2643\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3330\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4547\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634304	A	C	26	1141.77	1.00	DOWNSTREAM(\|2640\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3333\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4544\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634306	C	T	26	1231.77	1.00	DOWNSTREAM(\|2638\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3335\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4542\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634313	A	G	30	1290.77	1.00	DOWNSTREAM(\|2631\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3342\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4535\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634331	T	A	40	1816.77	1.00	DOWNSTREAM(\|2613\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3360\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4517\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634337	A	C	44	1996.77	1.00	DOWNSTREAM(\|2607\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3366\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4511\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634340	T	A	46	2041.77	1.00	DOWNSTREAM(\|2604\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3369\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4508\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634344	C	T	45	2041.77	1.00	DOWNSTREAM(\|2600\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3373\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4504\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634345	A	G	45	1996.77	1.00	DOWNSTREAM(\|2599\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3374\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4503\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634380	G	A	41	1641.77	1.00	DOWNSTREAM(\|2564\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3409\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4468\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634446	A	G	40	1805.77	1.00	DOWNSTREAM(\|2498\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3475\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4402\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634521	G	A	41	1669.77	1.00	DOWNSTREAM(\|2423\|\|None\|Vigan.09G224800.01), NON_SYNONYMOUS_CODING(MISSENSE\|Gta/Ata\|V222I\|None\|Vigan.09G224700.01), UPSTREAM(\|3550\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4327\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634588	C	T	55	2515.77	1.00	DOWNSTREAM(\|2356\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3617\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4260\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634593	G	C	60	2634.77	1.00	DOWNSTREAM(\|2351\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3622\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4255\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634618	T	G	58	2324.77	1.00	DOWNSTREAM(\|2326\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3647\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4230\|\|None\|Vigan.09G224900.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
36632759	A	ACAATAT	54	2635.73	1.00	DOWNSTREAM(\|4184\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|1789\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633352	AATTAAGTTGTG	A	47	2059.73	1.00	DOWNSTREAM(\|3591\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2382\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633840	T	TTC	65	3018.73	1.00	DOWNSTREAM(\|3103\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2870\|\|None\|Vigan.09G224600.01)	Vigna nepalensis
36633876	T	TG	65	2851.73	1.00	DOWNSTREAM(\|3067\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2906\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4971\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36633931	T	TAAAAACTTAGGATTGGAAACAACTTTCCAATGTTCCTTTTGGAAACG	26	1218.73	1.00	DOWNSTREAM(\|3012\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|2961\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4916\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634282	T	TC	21	737.73	1.00	DOWNSTREAM(\|2661\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3312\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4565\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634308	C	CA	28	1222.73	1.00	DOWNSTREAM(\|2635\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3338\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4539\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634444	G	GT	41	1796.73	1.00	DOWNSTREAM(\|2499\|\|None\|Vigan.09G224800.01), INTRON(\|\|\|None\|Vigan.09G224700.01), UPSTREAM(\|3474\|\|None\|Vigan.09G224600.01), UPSTREAM(\|4403\|\|None\|Vigan.09G224900.01)	Vigna nepalensis
36634911	T	TTTAGC	40	1728.73	1.00	DOWNSTREAM(\|2032\|\|None\|Vigan.09G224800.01), UPSTREAM(\|3936\|\|None\|Vigan.09G224900.01), UPSTREAM(\|3941\|\|None\|Vigan.09G224600.01), UTR_3_PRIME(\|116\|\|None\|Vigan.09G224700.01)	Vigna nepalensis