VIGGS:Variant information

Chr04:6038115 - 6041183

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6038205	T	C	49	1908.77	1.00	UPSTREAM(\|818\|\|None\|Vigan.04G063800.01), UTR_3_PRIME(\|157\|\|None\|Vigan.04G063900.01)	Vigna nepalensis
6038677	C	T	63	2496.77	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1290\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6038711	G	A	62	2552.77	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1324\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6038994	A	G	61	2469.77	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1607\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039078	C	T	70	166.77	0.13	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1691\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039115	A	G	87	558.77	0.22	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1728\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039116	G	A	86	564.77	0.22	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1729\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039128	T	G	82	750.77	0.28	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1741\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039132	T	C	85	750.77	0.27	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1745\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039133	A	T	85	750.77	0.27	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1746\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039146	C	A	91	2397.77	0.73	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1759\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039179	C	T	78	973.77	0.35	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1792\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039184	C	A	78	967.77	0.35	INTRON(\|\|\|None\|Vigan.04G063900.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1797\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039191	G	T	76	1027.77	0.38	NON_SYNONYMOUS_CODING(MISSENSE\|Cag/Aag\|Q256K\|None\|Vigan.04G063900.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1804\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039210	C	T	74	896.77	0.36	SYNONYMOUS_CODING(SILENT\|ggG/ggA\|G249\|None\|Vigan.04G063900.01), UPSTREAM(\|1823\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039325	G	T	52	2264.77	0.98	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1938\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039349	G	A	47	2248.77	0.98	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1962\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6040119	T	G	34	1506.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|gAc/gCc\|D175A\|None\|Vigan.04G063900.01), UPSTREAM(\|2732\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6040142	A	C	40	1705.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|atT/atG\|I167M\|None\|Vigan.04G063900.01), UPSTREAM(\|2755\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6040254	G	A	50	1925.77	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|2867\|\|None\|Vigan.04G063800.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6038269	CA	C	44	1735.73	1.00	UPSTREAM(\|883\|\|None\|Vigan.04G063800.01), UTR_3_PRIME(\|92\|\|None\|Vigan.04G063900.01)	Vigna nepalensis
6038447	A	AACC	58	2730.73	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1061\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039085	CACAGAG	C	71	3231.73	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1699\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039101	CAT	C	79	429.73	0.16	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1715\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039106	AGTT	A	88	456.73	0.19	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|1720\|\|None\|Vigan.04G063800.01)	Vigna nepalensis
6039401	T	TA	56	1975.73	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|2015\|\|None\|Vigan.04G063800.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6039969	(AC)14	(AC)0	35	1525.73	1.00	INTRON(\|\|\|None\|Vigan.04G063900.01), UPSTREAM(\|2583\|\|None\|Vigan.04G063800.01)	Vigna nepalensis