VIGGS:Variant information

Chr04:41040562 - 41045116

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
41040599	G	A	45	1747.77	1.00	UPSTREAM(\|4803\|\|None\|Vigan.04G288400.01), UTR_5_PRIME(\|133\|\|None\|Vigan.04G288300.01)	Vigna nepalensis
41040755	T	C	48	1837.77	1.00	SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A8\|None\|Vigan.04G288300.01), UPSTREAM(\|4647\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41041223	G	A	48	1670.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|4179\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41041282	G	T	50	2056.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|4120\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41041798	C	T	49	1935.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|3604\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41041837	A	G	51	2064.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|3565\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41042279	G	C	49	1940.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|3123\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41042750	A	G	49	2005.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|2652\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41042957	T	C	55	2110.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|2445\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41043238	G	A	46	1790.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|2164\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41043560	G	C	53	2152.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|1842\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41043624	A	G	41	1600.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|1778\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41043745	G	A	40	1612.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|cGg/cAg\|R78Q\|None\|Vigan.04G288300.01), UPSTREAM(\|1657\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41044015	T	C	59	2309.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|1387\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41044088	G	T	53	2071.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|1314\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41044137	C	A	58	2332.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|1265\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41044338	G	A	49	1967.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gGg/gAg\|G163E\|None\|Vigan.04G288300.01), UPSTREAM(\|1064\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41044492	T	G	34	1381.77	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|910\|\|None\|Vigan.04G288400.01)	Vigna nepalensis
41044905	G	A	42	1724.77	1.00	UPSTREAM(\|497\|\|None\|Vigan.04G288400.01), UTR_3_PRIME(\|61\|\|None\|Vigan.04G288300.01)	Vigna nepalensis
41045064	T	C	56	2295.77	1.00	UPSTREAM(\|338\|\|None\|Vigan.04G288400.01), UTR_3_PRIME(\|220\|\|None\|Vigan.04G288300.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
41044739	A	ATT	51	1900.73	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|662\|\|None\|Vigan.04G288400.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
41041371	(AT)9	(AT)8	42	1513.73	1.00	INTRON(\|\|\|None\|Vigan.04G288300.01), UPSTREAM(\|4030\|\|None\|Vigan.04G288400.01)	Vigna nepalensis