VIGGS:Variant information

Chr01:20222744 - 20232530

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Species
- Vigna nepalensis
Effect
- INTRON
- SYNONYMOUS_CODING
- UTR_5_PRIME

SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
20223061	C	G	36	1410.77	1.00	SYNONYMOUS_CODING(SILENT\|ctC/ctG\|L65\|None\|Vigan.01G174500.01)	Vigna nepalensis
20223211	T	C	26	972.77	1.00	SYNONYMOUS_CODING(SILENT\|atT/atC\|I115\|None\|Vigan.01G174500.01)	Vigna nepalensis
20223463	T	C	63	2408.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20224027	G	T	46	1822.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20224238	T	C	68	2661.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20225130	A	C	41	1693.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20225279	T	C	52	1986.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20225712	C	T	60	2457.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20225749	A	G	59	2655.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20225751	G	T	59	2655.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226018	T	G	35	260.77	0.31	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226034	A	G	30	1290.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226057	C	T	35	834.77	0.60	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226069	G	A	43	219.77	0.19	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226073	G	A	47	139.77	0.15	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226074	T	G	48	930.77	0.48	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226084	C	T	53	793.77	0.38	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226095	A	G	65	1231.77	0.52	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226105	T	C	78	3537.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226446	T	C	34	84.77	0.18	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20226474	T	G	5	166.9	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228178	C	T	10	23.79	0.30	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228185	C	T	11	97.77	0.36	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228211	T	C	16	32.77	0.19	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228220	C	G	22	116.73	0.32	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228374	C	A	62	152.77	0.18	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228445	A	G	24	1093.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228452	C	A	24	506.77	0.71	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228454	T	C	24	1081.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228677	G	T	26	73.77	0.15	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228683	G	A	26	73.77	0.15	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228870	G	A	7	221.28	0.86	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228876	A	T	6	241.84	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20229125	T	C	21	325.77	0.62	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20229829	G	A	10	239.89	0.90	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230053	T	C	45	103.77	0.13	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230070	C	T	59	145.77	0.19	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230141	G	C	96	198.77	0.18	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230196	C	T	44	114.77	0.18	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230210	C	T	24	84.77	0.21	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230220	C	T	14	111.77	0.36	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230295	A	G	8	264.78	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230429	A	G	19	707.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230464	G	C	25	1032.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230528	A	G	43	1449.77	0.93	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20230906	A	G	52	2127.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20231161	T	C	59	2339.77	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
20222795	CCACAGAG	C	38	1631.73	1.00	UTR_5_PRIME(\|65\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20224640	TTTCCTTCAAAAGGATA	T	69	3032.73	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20224861	CTT	C	48	1616.73	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228421	GCAC	G	42	228.73	0.24	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis
20228887	ACT	A	5	187.87	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
20225474	(TG)9	(TG)5	56	2439.73	1.00	INTRON(\|\|\|None\|Vigan.01G174500.01)	Vigna nepalensis