VIGGS:Variant information

Chr04:6144043 - 6148581

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6144760	G	A	53	2313.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6144771	C	T	51	2387.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6144789	T	C	49	2014.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6144959	A	G	55	2441.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6144977	G	T	63	2735.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6145034	T	A	54	2171.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6145314	A	G	47	1798.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4736\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145337	C	T	41	1576.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4713\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145463	A	T	55	2249.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4587\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145523	C	T	71	2794.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4527\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145558	A	G	65	2624.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4492\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145623	A	G	46	2183.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4427\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145629	G	T	46	2164.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4421\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145633	T	C	45	2041.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4417\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145642	C	T	46	2015.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4408\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145691	T	C	35	1395.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4359\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145735	G	A	51	2257.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4315\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145736	G	A	50	2257.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4314\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145761	C	A	59	2595.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4289\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145972	T	A	64	2496.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4078\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6146012	G	T	58	2397.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4038\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6146668	C	T	45	1943.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|3382\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6146693	C	G	41	1707.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|3357\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6146748	T	G	47	1901.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|3302\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6146828	G	T	45	1972.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|3222\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147249	A	C	62	2396.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2801\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147427	G	A	57	2338.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2623\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147822	A	G	58	2543.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2228\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147823	T	A	56	2543.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2227\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147834	A	G	57	2196.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2216\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147888	A	C	65	2586.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2162\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6147961	G	C	47	1864.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|2089\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6148147	A	G	54	2238.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|1903\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6148216	G	C	42	1643.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|1834\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6148339	G	A	43	1614.77	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|1711\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6148565	C	A	48	1953.77	1.00	START_GAINED(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|1485\|\|None\|Vigan.04G065000.01), UTR_5_PRIME(\|31\|\|None\|Vigan.04G064900.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6144549	AT	A	66	2428.73	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6144769	T	TTCA	51	2458.73	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6144822	G	GTGAAACC	46	2076.73	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01)	Vigna nepalensis
6145575	AT	A	63	1923.73	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4474\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6145766	GTCCTTCTAACTCCCAAAATATAAAATTCATAATTTAAT	G	59	2641.73	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|4283\|\|None\|Vigan.04G065000.01)	Vigna nepalensis
6146830	T	TA	44	1991.73	1.00	INTRON(\|\|\|None\|Vigan.04G064900.01), UPSTREAM(\|3219\|\|None\|Vigan.04G065000.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
6148535	(TC)9	(TC)7	34	1445.73	1.00	UPSTREAM(\|1514\|\|None\|Vigan.04G065000.01), UTR_5_PRIME(\|2\|\|None\|Vigan.04G064900.01)	Vigna nepalensis