VIGGS:Variant information

Chr02:11850664 - 11854426

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SNPs

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
11851363	T	C	56	2112.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|4887\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11851610	C	T	77	3394.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|4640\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11851611	A	C	75	3394.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|4639\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11851967	A	C	58	2418.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|4283\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11852218	A	G	55	2139.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|4032\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11852275	A	G	49	1981.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3975\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11852758	C	T	49	1954.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3492\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11852863	A	G	54	2114.77	1.00	SYNONYMOUS_CODING(SILENT\|gcA/gcG\|A135\|None\|Vigan.02G132500.01), UPSTREAM(\|3387\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11852962	G	T	40	1503.77	1.00	SYNONYMOUS_CODING(SILENT\|gcG/gcT\|A168\|None\|Vigan.02G132500.01), UPSTREAM(\|3288\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853129	G	A	68	648.77	0.28	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3121\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853131	G	A	70	657.77	0.29	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3119\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853139	T	A	77	858.77	0.31	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3111\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853165	G	A	83	972.77	0.34	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3085\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853169	A	T	84	1052.77	0.36	INTRON(\|\|\|None\|Vigan.02G132500.01), SPLICE_SITE_REGION(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3081\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853196	A	T	67	555.77	0.27	NON_SYNONYMOUS_CODING(MISSENSE\|tAc/tTc\|Y210F\|None\|Vigan.02G132500.01), UPSTREAM(\|3054\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853211	C	T	64	450.77	0.23	NON_SYNONYMOUS_CODING(MISSENSE\|tCg/tTg\|S215L\|None\|Vigan.02G132500.01), UPSTREAM(\|3039\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853220	C	A	56	333.77	0.20	NON_SYNONYMOUS_CODING(MISSENSE\|aCt/aAt\|T218N\|None\|Vigan.02G132500.01), UPSTREAM(\|3030\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853223	G	A	56	297.77	0.20	STOP_GAINED(NONSENSE\|tGg/tAg\|W219*\|None\|Vigan.02G132500.01), UPSTREAM(\|3027\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853702	A	G	43	1988.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|2548\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853708	T	C	47	2059.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|2542\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853746	C	T	45	1702.77	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|2504\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853809	A	G	38	1466.77	1.00	SYNONYMOUS_CODING(SILENT\|gtA/gtG\|V316\|None\|Vigan.02G132500.01), UPSTREAM(\|2441\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853873	C	G	45	1746.77	1.00	NON_SYNONYMOUS_CODING(MISSENSE\|Cct/Gct\|P338A\|None\|Vigan.02G132500.01), UPSTREAM(\|2377\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11854083	C	A	44	1910.77	1.00	UPSTREAM(\|2167\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|127\|\|None\|Vigan.02G132500.01)	Vigna nepalensis
11854093	G	T	41	1832.77	1.00	UPSTREAM(\|2157\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|137\|\|None\|Vigan.02G132500.01)	Vigna nepalensis
11854135	G	T	30	1248.77	1.00	UPSTREAM(\|2115\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|179\|\|None\|Vigan.02G132500.01)	Vigna nepalensis
11854243	C	A	61	2800.77	1.00	UPSTREAM(\|2007\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|287\|\|None\|Vigan.02G132500.01)	Vigna nepalensis
11854246	C	T	64	2837.77	1.00	UPSTREAM(\|2004\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|290\|\|None\|Vigan.02G132500.01)	Vigna nepalensis
11854394	A	G	61	2485.77	1.00	UPSTREAM(\|1856\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|438\|\|None\|Vigan.02G132500.01)	Vigna nepalensis

Indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
11850763	CTA	C	43	1866.73	1.00	UTR_5_PRIME(\|31\|\|None\|Vigan.02G132500.01)	Vigna nepalensis
11853106	TATA	T	62	268.73	0.18	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3143\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853137	C	CCA	73	810.73	0.30	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3112\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11853140	TGG	T	77	846.73	0.32	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|3109\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11854191	A	AATTG	47	2149.73	1.00	UPSTREAM(\|2058\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|236\|\|None\|Vigan.02G132500.01)	Vigna nepalensis

SSR-associated indels

Position	Ref.	Alt.	Depth	Score	Freq. Of Alt.	Effect	Species
11851393	(AAT)6	(AAT)7	47	2166.73	1.00	INTRON(\|\|\|None\|Vigan.02G132500.01), UPSTREAM(\|4856\|\|None\|Vigan.02G132600.01)	Vigna nepalensis
11854177	(AT)9	(AT)4	42	1892.73	1.00	UPSTREAM(\|2072\|\|None\|Vigan.02G132600.01), UTR_3_PRIME(\|222\|\|None\|Vigan.02G132500.01)	Vigna nepalensis