VIGGS:Variant information

Chr05:720496 - 722817

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
720655	A	C	60	431.77	0.22	DOWNSTREAM(\|2456\|\|None\|Vigan.05G011500.01), UPSTREAM(\|381\|\|None\|Vigan.05G011600.01), UPSTREAM(\|3833\|\|None\|Vigan.05G011800.01), UTR_3_PRIME(\|298\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720661	G	A	63	531.77	0.27	DOWNSTREAM(\|2462\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3827\|\|None\|Vigan.05G011800.01), UPSTREAM(\|387\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|292\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720663	G	A	63	543.77	0.27	DOWNSTREAM(\|2464\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3825\|\|None\|Vigan.05G011800.01), UPSTREAM(\|389\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|290\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720736	T	G	44	1783.77	1.00	DOWNSTREAM(\|2537\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3752\|\|None\|Vigan.05G011800.01), UPSTREAM(\|462\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|217\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720754	G	A	62	411.77	0.21	DOWNSTREAM(\|2555\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3734\|\|None\|Vigan.05G011800.01), UPSTREAM(\|480\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|199\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720780	G	A	76	1083.77	0.41	DOWNSTREAM(\|2581\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3708\|\|None\|Vigan.05G011800.01), UPSTREAM(\|506\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|173\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
721004	G	C	100	2084.77	0.54	DOWNSTREAM(\|2805\|\|None\|Vigan.05G011500.01), NON_SYNONYMOUS_CODING(MISSENSE\|gaC/gaG\|D213E\|None\|Vigan.05G011700.01), UPSTREAM(\|3484\|\|None\|Vigan.05G011800.01), UPSTREAM(\|730\|\|None\|Vigan.05G011600.01)	Vigna nepalensis
721038	C	T	95	1503.77	0.45	DOWNSTREAM(\|2839\|\|None\|Vigan.05G011500.01), NON_SYNONYMOUS_CODING(MISSENSE\|cGt/cAt\|R202H\|None\|Vigan.05G011700.01), UPSTREAM(\|3450\|\|None\|Vigan.05G011800.01), UPSTREAM(\|764\|\|None\|Vigan.05G011600.01)	Vigna nepalensis
721373	T	C	47	1787.77	1.00	DOWNSTREAM(\|3174\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1099\|\|None\|Vigan.05G011600.01), UPSTREAM(\|3115\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721512	A	G	51	2060.77	1.00	DOWNSTREAM(\|3313\|\|None\|Vigan.05G011500.01), SYNONYMOUS_CODING(SILENT\|gtT/gtC\|V176\|None\|Vigan.05G011700.01), UPSTREAM(\|1238\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2976\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721562	A	C	61	2375.77	1.00	DOWNSTREAM(\|3363\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1288\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2926\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721583	T	C	64	2592.77	1.00	DOWNSTREAM(\|3384\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1309\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2905\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721632	G	A	58	2334.77	1.00	DOWNSTREAM(\|3433\|\|None\|Vigan.05G011500.01), SYNONYMOUS_CODING(SILENT\|aaC/aaT\|N164\|None\|Vigan.05G011700.01), UPSTREAM(\|1358\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2856\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721700	G	C	66	2213.77	0.94	DOWNSTREAM(\|3501\|\|None\|Vigan.05G011500.01), NON_SYNONYMOUS_CODING(MISSENSE\|Ccc/Gcc\|P142A\|None\|Vigan.05G011700.01), UPSTREAM(\|1426\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2788\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721751	G	A	66	210.77	0.15	DOWNSTREAM(\|3552\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1477\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2737\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721755	A	T	65	294.77	0.17	DOWNSTREAM(\|3556\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1481\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2733\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721760	G	A	66	2814.77	1.00	DOWNSTREAM(\|3561\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1486\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2728\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721770	A	C	67	432.77	0.22	DOWNSTREAM(\|3571\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1496\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2718\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721814	C	T	73	418.77	0.21	DOWNSTREAM(\|3615\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1540\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2674\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721822	A	G	74	423.77	0.20	DOWNSTREAM(\|3623\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1548\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2666\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721823	G	A	74	423.77	0.20	DOWNSTREAM(\|3624\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1549\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2665\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721830	A	C	75	450.77	0.21	DOWNSTREAM(\|3631\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1556\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2658\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721909	G	A	75	168.77	0.15	DOWNSTREAM(\|3710\|\|None\|Vigan.05G011500.01), SYNONYMOUS_CODING(SILENT\|taC/taT\|Y123\|None\|Vigan.05G011700.01), UPSTREAM(\|1635\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2579\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721941	G	T	68	2837.77	1.00	DOWNSTREAM(\|3742\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1667\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2547\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
722021	T	C	47	2073.77	1.00	DOWNSTREAM(\|3822\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1747\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2467\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
722026	A	G	44	1946.77	1.00	DOWNSTREAM(\|3827\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1752\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2462\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
722100	A	T	58	2337.77	1.00	DOWNSTREAM(\|3901\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1826\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2388\|\|None\|Vigan.05G011800.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
720637	C	CTTGCAAACCAGTAGCT	60	159.73	0.08	DOWNSTREAM(\|2439\|\|None\|Vigan.05G011500.01), UPSTREAM(\|364\|\|None\|Vigan.05G011600.01), UPSTREAM(\|3850\|\|None\|Vigan.05G011800.01), UTR_3_PRIME(\|315\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720759	C	CGGCCT	62	693.73	0.23	DOWNSTREAM(\|2561\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3728\|\|None\|Vigan.05G011800.01), UPSTREAM(\|486\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|193\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720760	A	AATG	69	732.73	0.29	DOWNSTREAM(\|2562\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3727\|\|None\|Vigan.05G011800.01), UPSTREAM(\|487\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|192\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720768	CTTGT	C	71	960.73	0.32	DOWNSTREAM(\|2570\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3719\|\|None\|Vigan.05G011800.01), UPSTREAM(\|495\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|181\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720772	T	TCCAC	65	976.73	0.35	DOWNSTREAM(\|2574\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3715\|\|None\|Vigan.05G011800.01), UPSTREAM(\|499\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|180\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720798	TTCC	T	85	1676.73	0.49	DOWNSTREAM(\|2600\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3689\|\|None\|Vigan.05G011800.01), UPSTREAM(\|525\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|152\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
720803	AAACAT	A	92	1667.73	0.49	DOWNSTREAM(\|2605\|\|None\|Vigan.05G011500.01), UPSTREAM(\|3684\|\|None\|Vigan.05G011800.01), UPSTREAM(\|530\|\|None\|Vigan.05G011600.01), UTR_3_PRIME(\|145\|\|None\|Vigan.05G011700.01)	Vigna nepalensis
721763	TG	T	63	423.73	0.21	DOWNSTREAM(\|3565\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1490\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2724\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721766	ATG	A	67	423.73	0.22	DOWNSTREAM(\|3568\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1493\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2721\|\|None\|Vigan.05G011800.01)	Vigna nepalensis
721841	CAGGAATTACAAAAGGAATAG	C	85	421.73	0.19	DOWNSTREAM(\|3643\|\|None\|Vigan.05G011500.01), INTRON(\|\|\|None\|Vigan.05G011700.01), UPSTREAM(\|1568\|\|None\|Vigan.05G011600.01), UPSTREAM(\|2646\|\|None\|Vigan.05G011800.01)	Vigna nepalensis