VIGGS:Variant information

Chr01:63702233 - 63705711

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
63702461	T	C	53	2409.77	1.00	DOWNSTREAM(\|4041\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|Ttg/Ctg\|L47\|None\|Vigan.01G509400.01), UPSTREAM(\|3425\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702463	G	A	54	2409.77	1.00	DOWNSTREAM(\|4039\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|ttG/ttA\|L47\|None\|Vigan.01G509400.01), UPSTREAM(\|3427\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702491	C	A	55	2352.77	1.00	DOWNSTREAM(\|4011\|\|None\|Vigan.01G509500.01), NON_SYNONYMOUS_CODING(MISSENSE\|Cag/Aag\|Q57K\|None\|Vigan.01G509400.01), UPSTREAM(\|3455\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702500	A	C	50	2282.77	1.00	DOWNSTREAM(\|4002\|\|None\|Vigan.01G509500.01), NON_SYNONYMOUS_CODING(MISSENSE\|Aag/Cag\|K60Q\|None\|Vigan.01G509400.01), UPSTREAM(\|3464\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702520	T	C	51	2209.77	1.00	DOWNSTREAM(\|3982\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|taT/taC\|Y66\|None\|Vigan.01G509400.01), UPSTREAM(\|3484\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702694	A	G	49	1920.77	1.00	DOWNSTREAM(\|3808\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|3658\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702744	C	T	49	2180.77	1.00	DOWNSTREAM(\|3758\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|ggC/ggT\|G103\|None\|Vigan.01G509400.01), UPSTREAM(\|3708\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702759	A	G	49	2179.77	1.00	DOWNSTREAM(\|3743\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|acA/acG\|T108\|None\|Vigan.01G509400.01), UPSTREAM(\|3723\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702819	A	G	47	1874.77	1.00	DOWNSTREAM(\|3683\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|caA/caG\|Q128\|None\|Vigan.01G509400.01), UPSTREAM(\|3783\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702831	C	T	49	1966.77	1.00	DOWNSTREAM(\|3671\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|atC/atT\|I132\|None\|Vigan.01G509400.01), UPSTREAM(\|3795\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702873	A	G	47	1838.77	1.00	DOWNSTREAM(\|3629\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|ggA/ggG\|G146\|None\|Vigan.01G509400.01), UPSTREAM(\|3837\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703287	A	G	52	2243.77	1.00	DOWNSTREAM(\|3215\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4251\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703291	T	C	49	2220.77	1.00	DOWNSTREAM(\|3211\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4255\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703301	T	A	47	2098.77	1.00	DOWNSTREAM(\|3201\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4265\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703327	T	A	48	1900.77	1.00	DOWNSTREAM(\|3175\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4291\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703393	C	A	57	2547.77	1.00	DOWNSTREAM(\|3109\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4357\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703399	C	A	57	2569.77	1.00	DOWNSTREAM(\|3103\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4363\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703436	G	C	53	2460.77	1.00	DOWNSTREAM(\|3066\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4400\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703442	A	G	51	2350.77	1.00	DOWNSTREAM(\|3060\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4406\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703448	T	A	48	2123.77	1.00	DOWNSTREAM(\|3054\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4412\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703461	A	G	52	2330.77	1.00	DOWNSTREAM(\|3041\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4425\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703517	A	G	56	2328.77	1.00	DOWNSTREAM(\|2985\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4481\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703809	G	A	44	1739.77	1.00	DOWNSTREAM(\|2693\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|caG/caA\|Q259\|None\|Vigan.01G509400.01), UPSTREAM(\|4773\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703959	C	T	50	1757.77	1.00	DOWNSTREAM(\|2543\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|ggC/ggT\|G309\|None\|Vigan.01G509400.01), UPSTREAM(\|4923\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63704013	T	A	41	1744.77	1.00	DOWNSTREAM(\|2489\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4977\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63704030	T	A	34	1541.77	1.00	DOWNSTREAM(\|2472\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4994\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63704107	A	G	42	1714.77	1.00	DOWNSTREAM(\|2395\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|acA/acG\|T336\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704168	C	T	49	2173.77	1.00	DOWNSTREAM(\|2334\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704187	T	C	45	1983.77	1.00	DOWNSTREAM(\|2315\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704188	G	A	45	1983.77	1.00	DOWNSTREAM(\|2314\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704262	G	A	43	1633.77	1.00	DOWNSTREAM(\|2240\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704301	A	G	51	2253.77	1.00	DOWNSTREAM(\|2201\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704310	T	G	56	2485.77	1.00	DOWNSTREAM(\|2192\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704361	G	A	60	2671.77	1.00	DOWNSTREAM(\|2141\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704614	C	T	60	2631.77	1.00	DOWNSTREAM(\|1888\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704621	A	T	55	2498.77	1.00	DOWNSTREAM(\|1881\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704693	T	A	58	2271.77	1.00	DOWNSTREAM(\|1809\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704745	C	T	53	2446.77	1.00	DOWNSTREAM(\|1757\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704753	A	T	55	2536.77	1.00	DOWNSTREAM(\|1749\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704756	C	G	55	2522.77	1.00	DOWNSTREAM(\|1746\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704763	G	T	55	2472.77	1.00	DOWNSTREAM(\|1739\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704767	G	T	55	2427.77	1.00	DOWNSTREAM(\|1735\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63705459	A	G	50	1945.77	1.00	DOWNSTREAM(\|1043\|\|None\|Vigan.01G509500.01), NON_SYNONYMOUS_CODING(MISSENSE\|Agt/Ggt\|S386G\|None\|Vigan.01G509400.01)	Vigna nepalensis
63705533	T	C	51	1976.77	1.00	DOWNSTREAM(\|969\|\|None\|Vigan.01G509500.01), SYNONYMOUS_CODING(SILENT\|gcT/gcC\|A410\|None\|Vigan.01G509400.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
63703290	A	AC	51	2211.73	1.00	DOWNSTREAM(\|3211\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4255\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63703452	T	TA	48	2176.73	1.00	DOWNSTREAM(\|3049\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|4417\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63704158	TG	T	49	2149.73	1.00	DOWNSTREAM(\|2343\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704365	T	TAA	61	2753.73	1.00	DOWNSTREAM(\|2136\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis
63704706	CATTCAGTCATGCAATTTTTACACTTAAAA	C	53	2409.73	1.00	DOWNSTREAM(\|1795\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
63702634	(CTT)6	(CTT)5	50	2240.73	1.00	DOWNSTREAM(\|3867\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|3599\|\|None\|Vigan.01G509300.01)	Vigna nepalensis
63702638	(CTT)6	(CTT)4	52	2312.73	1.00	DOWNSTREAM(\|3863\|\|None\|Vigan.01G509500.01), INTRON(\|\|\|None\|Vigan.01G509400.01), UPSTREAM(\|3603\|\|None\|Vigan.01G509300.01)	Vigna nepalensis