RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0216547473:

Variant ID: vg0216547473 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 16547473
Reference Allele: TTG	Alternative Allele: TGTGTGTG,TGTGTG,TGTGTGTGTG,TGTG,GTG,T
Primary Allele: TGTGTGTG	Secondary Allele: TGTG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGGAGTCTAGAGTGGAGTTGTTAATCGCTCTGAACCCCAGCCTCACCCCTCTAGTTCATTTTTTCATAATACTCTAGCCCACTCCACTCTTTATTTCTT[TTG/TGTGTGTG,TGTGTG,TGTGTGTGTG,TGTG,GTG,T]
TGTGTGTGTGTGTGTGTTGCTAGAGGAACTATACATCGCACTGACACCCCCCCCTCTAGTTCATTTTTTTCAAATCACTCCAATCGGGAATGGGAATCCC

Reverse complement sequence

GGGATTCCCATTCCCGATTGGAGTGATTTGAAAAAAATGAACTAGAGGGGGGGGTGTCAGTGCGATGTATAGTTCCTCTAGCAACACACACACACACACA[CAA/CACACACA,CACACA,CACACACACA,CACA,CAC,A]
AAGAAATAAAGAGTGGAGTGGGCTAGAGTATTATGAAAAAATGAACTAGAGGGGTGAGGCTGGGGTTCAGAGCGATTAACAACTCCACTCTAGACTCCGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of TGTGTGTG(primary allele)	Frequency of TGTG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	17.40%	14.80%	16.91%	1.21%	TTG: 14.03%; TGTGTG: 12.65%; T: 9.52%; TGTGTGTGTG: 7.30%; GTG: 6.18%
All Indica	2759	27.70%	19.10%	18.41%	0.11%	TGTGTGTGTG: 11.74%; TGTGTG: 11.42%; GTG: 8.52%; T: 2.50%; TTG: 0.51%
All Japonica	1512	0.60%	4.90%	11.44%	1.59%	TTG: 41.87%; T: 24.60%; TGTGTG: 12.83%; GTG: 1.85%; TGTGTGTGTG: 0.33%
Aus	269	15.20%	32.30%	13.01%	0.00%	TGTGTG: 29.74%; GTG: 7.81%; TGTGTGTGTG: 1.86%
Indica I	595	23.40%	20.70%	31.76%	0.00%	TGTGTGTGTG: 11.43%; TGTGTG: 7.39%; GTG: 5.38%
Indica II	465	8.80%	29.50%	13.76%	0.00%	TGTGTGTGTG: 29.03%; T: 7.31%; GTG: 7.10%; TGTGTG: 2.80%; TTG: 1.72%
Indica III	913	39.80%	14.30%	7.89%	0.11%	TGTGTG: 22.56%; GTG: 11.61%; T: 2.30%; TGTGTGTGTG: 0.99%; TTG: 0.44%
Indica Intermediate	786	28.10%	17.30%	23.28%	0.25%	TGTGTGTGTG: 14.25%; GTG: 8.14%; TGTGTG: 6.62%; T: 1.78%; TTG: 0.25%
Temperate Japonica	767	0.00%	2.30%	8.47%	1.96%	TTG: 66.88%; T: 19.17%; TGTGTG: 0.52%; TGTGTGTGTG: 0.39%; GTG: 0.26%
Tropical Japonica	504	1.60%	7.10%	15.08%	0.99%	TGTGTG: 34.92%; T: 22.82%; TTG: 12.50%; GTG: 4.76%; TGTGTGTGTG: 0.20%
Japonica Intermediate	241	0.40%	8.30%	13.28%	1.66%	T: 45.64%; TTG: 23.65%; TGTGTG: 5.81%; GTG: 0.83%; TGTGTGTGTG: 0.41%
VI/Aromatic	96	0.00%	2.10%	60.42%	27.08%	GTG: 5.21%; TTG: 3.12%; T: 2.08%
Intermediate	90	10.00%	10.00%	27.78%	4.44%	TTG: 14.44%; TGTGTGTGTG: 12.22%; TGTGTG: 10.00%; T: 7.78%; GTG: 3.33%

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0216547473	TTG -> T	LOC_Os02g27950.1	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> T	LOC_Os02g27950.2	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> T	LOC_Os02g27960.1	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> T	LOC_Os02g27960.2	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> T	LOC_Os02g27950-LOC_Os02g27960	intergenic_region ; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTGTG	LOC_Os02g27950.1	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTGTG	LOC_Os02g27950.2	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTGTG	LOC_Os02g27960.1	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTGTG	LOC_Os02g27960.2	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTGTG	LOC_Os02g27950-LOC_Os02g27960	intergenic_region ; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTG	LOC_Os02g27950.1	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTG	LOC_Os02g27950.2	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTG	LOC_Os02g27960.1	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTG	LOC_Os02g27960.2	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTGTG	LOC_Os02g27950-LOC_Os02g27960	intergenic_region ; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTG	LOC_Os02g27950.1	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTG	LOC_Os02g27950.2	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTG	LOC_Os02g27960.1	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTG	LOC_Os02g27960.2	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTG	LOC_Os02g27950-LOC_Os02g27960	intergenic_region ; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> DEL	N	N	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTG	LOC_Os02g27950.1	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTG	LOC_Os02g27950.2	upstream_gene_variant ; 1728.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTG	LOC_Os02g27960.1	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTG	LOC_Os02g27960.2	downstream_gene_variant ; 2708.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> TGTGTG	LOC_Os02g27950-LOC_Os02g27960	intergenic_region ; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> GTG	LOC_Os02g27950.1	upstream_gene_variant ; 1727.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> GTG	LOC_Os02g27950.2	upstream_gene_variant ; 1727.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> GTG	LOC_Os02g27960.1	downstream_gene_variant ; 2709.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> GTG	LOC_Os02g27960.2	downstream_gene_variant ; 2709.0bp to feature; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg0216547473	TTG -> GTG	LOC_Os02g27950-LOC_Os02g27960	intergenic_region ; MODIFIER	silent_mutation	Average:69.491; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N

Showing 1 to 31 of 31 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216547473	4.59E-06	NA	mr1089	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	1.68E-06	mr1089	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	6.12E-14	mr1089	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	4.28E-15	mr1093	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	2.39E-09	mr1109	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	3.69E-06	NA	mr1129	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	5.30E-10	mr1129	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	1.04E-09	mr1129	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	4.64E-07	3.33E-16	mr1235	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0216547473	NA	6.72E-09	mr1243	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251

Showing 1 to 10 of 96 entries

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Search for Variation information by Variation ID:

Detailed information for vg0216547473:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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