VIGGS:Variant information

Chr06:21770888 - 21776262

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
21770918	C	T	58	2175.77	1.00	UTR_5_PRIME(\|96\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771039	C	T	43	1741.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|tCt/tTt\|S9F\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771070	C	T	50	1976.77	1.00	SYNONYMOUS_CODING(SILENT\|ttC/ttT\|F19\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771103	C	T	54	1934.77	1.00	SYNONYMOUS_CODING(SILENT\|ccC/ccT\|P30\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771210	G	A	43	1975.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771215	C	T	46	2049.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771229	G	C	44	1676.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771300	G	C	50	2245.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771308	G	A	52	2326.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771340	G	A	45	1742.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771383	C	T	54	2136.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771912	T	A	57	2167.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21772142	T	A	53	2069.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21772349	G	C	51	1979.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21772732	T	C	65	2680.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21772816	T	A	51	1982.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773090	T	C	40	1588.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773585	C	A	60	2383.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773619	A	T	68	2938.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773636	T	C	59	2656.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773699	A	G	53	2090.77	1.00	SYNONYMOUS_CODING(SILENT\|ccA/ccG\|P244\|None\|Vigan.06G112600.01)	Vigna nepalensis
21774039	C	A	58	2268.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21774191	C	T	59	2273.77	0.98	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21774470	C	T	63	2422.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21774876	C	G	65	2569.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21774929	C	T	74	2795.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775248	T	A	48	2024.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775303	G	A	45	1900.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775548	T	C	59	2375.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775622	G	C	51	2073.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775774	C	T	59	2423.77	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775910	A	C	56	2483.77	1.00	UTR_3_PRIME(\|3\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775911	A	G	55	2483.77	1.00	UTR_3_PRIME(\|4\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21775951	A	G	41	1655.77	1.00	UTR_3_PRIME(\|44\|\|None\|Vigan.06G112600.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
21771050	A	AGC	46	2122.73	1.00	FRAME_SHIFT(\|atc/aGCtc\|I13S?\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771052	CAT	C	48	2257.73	1.00	FRAME_SHIFT(\|atc/\|I14\|None\|Vigan.06G112600.01)	Vigna nepalensis
21771057	T	TCGC	51	2297.73	1.00	CODON_CHANGE_PLUS_CODON_INSERTION(\|gtt/gtCGCt\|V15VA\|None\|Vigan.06G112600.01)	Vigna nepalensis
21772291	AT	A	48	1336.73	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21772429	AT	A	56	1706.73	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773131	A	AC	50	2257.73	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773136	CA	C	53	2335.73	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis
21773870	TC	T	57	2255.73	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
21771658	(AAT)13	(AAT)5	47	1747.73	1.00	INTRON(\|\|\|None\|Vigan.06G112600.01)	Vigna nepalensis