VIGGS:Variant information

Chr04:52751685 - 52756881

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
52752228	A	G	56	2262.77	1.00	DOWNSTREAM(\|835\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01)	Vigna nepalensis
52752352	C	A	67	2622.77	1.00	DOWNSTREAM(\|959\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|4930\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52752376	T	C	53	2321.77	1.00	DOWNSTREAM(\|983\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|4906\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52752499	T	A	46	1844.77	1.00	DOWNSTREAM(\|1106\|\|None\|Vigan.04G418500.01), SYNONYMOUS_CODING(SILENT\|ccA/ccT\|P486\|None\|Vigan.04G418600.01), UPSTREAM(\|4783\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52752566	T	G	49	1925.77	1.00	DOWNSTREAM(\|1173\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|4716\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52753408	C	G	53	2048.77	1.00	DOWNSTREAM(\|2015\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3874\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52753501	A	C	49	1934.77	1.00	DOWNSTREAM(\|2108\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3781\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52753771	A	C	40	1628.77	1.00	DOWNSTREAM(\|2378\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3511\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52753909	T	C	46	1823.77	1.00	DOWNSTREAM(\|2516\|\|None\|Vigan.04G418500.01), SYNONYMOUS_CODING(SILENT\|ggA/ggG\|G342\|None\|Vigan.04G418600.01), UPSTREAM(\|3373\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52753996	A	G	59	2255.77	1.00	DOWNSTREAM(\|2603\|\|None\|Vigan.04G418500.01), SYNONYMOUS_CODING(SILENT\|taT/taC\|Y313\|None\|Vigan.04G418600.01), UPSTREAM(\|3286\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52754093	A	T	58	2326.77	1.00	DOWNSTREAM(\|2700\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3189\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52754110	T	C	64	2810.77	1.00	DOWNSTREAM(\|2717\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3172\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52754240	G	T	46	1830.77	1.00	DOWNSTREAM(\|2847\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3042\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52754281	A	G	48	1984.77	1.00	DOWNSTREAM(\|2888\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3001\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52755149	G	C	57	2263.77	1.00	DOWNSTREAM(\|3756\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|2133\|\|None\|Vigan.04G418700.01), UPSTREAM(\|4338\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52755591	T	G	57	2344.77	1.00	DOWNSTREAM(\|4198\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|1691\|\|None\|Vigan.04G418700.01), UPSTREAM(\|3896\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52755820	C	A	66	2585.77	1.00	DOWNSTREAM(\|4427\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|1462\|\|None\|Vigan.04G418700.01), UPSTREAM(\|3667\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52755834	C	T	62	2431.77	1.00	DOWNSTREAM(\|4441\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|1448\|\|None\|Vigan.04G418700.01), UPSTREAM(\|3653\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52756064	T	C	57	2266.77	1.00	DOWNSTREAM(\|4671\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|1218\|\|None\|Vigan.04G418700.01), UPSTREAM(\|3423\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52756538	C	A	58	2285.77	1.00	INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|2949\|\|None\|Vigan.04G418800.01), UPSTREAM(\|744\|\|None\|Vigan.04G418700.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
52752372	AAT	A	52	2312.73	1.00	DOWNSTREAM(\|980\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|4909\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52752710	TA	T	50	1338.73	0.98	DOWNSTREAM(\|1318\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|4571\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52754116	ATT	A	64	2838.73	1.00	DOWNSTREAM(\|2724\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|3165\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52754518	ATAG	A	54	2366.73	1.00	DOWNSTREAM(\|3126\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|2763\|\|None\|Vigan.04G418700.01), UPSTREAM(\|4968\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52755852	AT	A	60	2101.73	1.00	DOWNSTREAM(\|4460\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|1429\|\|None\|Vigan.04G418700.01), UPSTREAM(\|3634\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52756110	CT	C	52	1741.73	1.00	DOWNSTREAM(\|4718\|\|None\|Vigan.04G418500.01), INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|1171\|\|None\|Vigan.04G418700.01), UPSTREAM(\|3376\|\|None\|Vigan.04G418800.01)	Vigna nepalensis
52756555	A	AT	54	1978.73	1.00	INTRON(\|\|\|None\|Vigan.04G418600.01), UPSTREAM(\|2931\|\|None\|Vigan.04G418800.01), UPSTREAM(\|726\|\|None\|Vigan.04G418700.01)	Vigna nepalensis
52756861	T	TC	47	1768.73	1.00	UPSTREAM(\|2625\|\|None\|Vigan.04G418800.01), UPSTREAM(\|420\|\|None\|Vigan.04G418700.01), UTR_5_PRIME(\|175\|\|None\|Vigan.04G418600.01)	Vigna nepalensis