VIGGS:Variant information

Chr08:12165235 - 12168438

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
12165348	C	T	69	2751.77	1.00	UPSTREAM(\|3470\|\|None\|Vigan.08G137800.01), UTR_5_PRIME(\|150\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12165480	T	C	56	2239.77	1.00	UPSTREAM(\|3602\|\|None\|Vigan.08G137800.01), UTR_5_PRIME(\|18\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12165614	A	C	47	1870.77	1.00	SYNONYMOUS_CODING(SILENT\|ctA/ctC\|L39\|None\|Vigan.08G137900.01), UPSTREAM(\|3736\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165733	A	T	59	2573.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3855\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165743	G	C	61	2659.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3865\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165774	T	A	61	2640.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3896\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165846	C	T	44	1999.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3968\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165850	G	T	40	1929.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3972\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165871	T	A	37	1603.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3993\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165941	G	A	63	2856.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Gca/Aca\|A75T\|None\|Vigan.08G137900.01), UPSTREAM(\|4063\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165958	A	G	67	2962.77	1.00	SYNONYMOUS_CODING(SILENT\|ccA/ccG\|P80\|None\|Vigan.08G137900.01), UPSTREAM(\|4080\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166031	G	C	47	1967.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|4153\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166042	T	G	45	1753.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|4164\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166159	C	T	50	1761.77	0.98	SYNONYMOUS_CODING(SILENT\|taC/taT\|Y116\|None\|Vigan.08G137900.01), UPSTREAM(\|4281\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166423	G	A	49	1879.77	1.00	SYNONYMOUS_CODING(SILENT\|caG/caA\|Q204\|None\|Vigan.08G137900.01), UPSTREAM(\|4545\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166460	G	A	45	1793.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Gct/Act\|A217T\|None\|Vigan.08G137900.01), UPSTREAM(\|4582\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166722	A	T	57	2351.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|4844\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166754	A	G	55	2474.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|4876\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166755	C	T	55	2474.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|4877\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12166956	A	T	61	2391.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167124	A	G	55	2127.77	1.00	SYNONYMOUS_CODING(SILENT\|gaA/gaG\|E328\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167196	A	G	49	2010.77	1.00	SYNONYMOUS_CODING(SILENT\|gaA/gaG\|E352\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167228	A	T	48	1771.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gAg/gTg\|E363V\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167256	G	T	57	2288.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|caG/caT\|Q372H\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167284	C	T	58	2383.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Ctt/Ttt\|L382F\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167337	C	T	54	2011.77	1.00	SYNONYMOUS_CODING(SILENT\|gaC/gaT\|D399\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167427	A	C	50	2007.77	1.00	SYNONYMOUS_CODING(SILENT\|atA/atC\|I429\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167529	G	A	55	2196.77	1.00	SYNONYMOUS_CODING(SILENT\|ccG/ccA\|P463\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167544	T	C	57	2286.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167565	G	A	58	2360.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167591	T	G	58	2343.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167604	G	A	52	2110.77	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167803	T	C	48	2166.77	1.00	SYNONYMOUS_CODING(SILENT\|atT/atC\|I528\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167806	C	T	50	2205.77	1.00	SYNONYMOUS_CODING(SILENT\|ggC/ggT\|G529\|None\|Vigan.08G137900.01)	Vigna nepalensis
12167845	C	T	47	1629.77	1.00	SYNONYMOUS_CODING(SILENT\|gcC/gcT\|A542\|None\|Vigan.08G137900.01)	Vigna nepalensis
12168154	A	T	55	2109.77	1.00	SYNONYMOUS_CODING(SILENT\|cgA/cgT\|R645\|None\|Vigan.08G137900.01)	Vigna nepalensis
12168319	G	C	53	2381.77	1.00	UTR_3_PRIME(\|102\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12168322	G	A	53	2347.77	1.00	UTR_3_PRIME(\|105\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12168382	T	C	55	2206.77	1.00	UTR_3_PRIME(\|165\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12168410	A	G	48	2066.77	1.00	UTR_3_PRIME(\|193\|\|None\|Vigan.08G137900.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
12165417	C	CA	66	2917.73	1.00	UPSTREAM(\|3540\|\|None\|Vigan.08G137800.01), UTR_5_PRIME(\|80\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12165419	CA	C	64	2917.73	1.00	UPSTREAM(\|3542\|\|None\|Vigan.08G137800.01), UTR_5_PRIME(\|78\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12165788	T	TA	55	2496.73	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3911\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12165800	T	TG	54	2393.73	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01), UPSTREAM(\|3923\|\|None\|Vigan.08G137800.01)	Vigna nepalensis
12167578	TA	T	56	1890.73	1.00	INTRON(\|\|\|None\|Vigan.08G137900.01)	Vigna nepalensis
12168425	GC	G	52	2204.73	1.00	UTR_3_PRIME(\|209\|\|None\|Vigan.08G137900.01)	Vigna nepalensis