RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0221445039:

Variant ID: vg0221445039 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21445039
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCCCAGGTACACAACCCAATGGGTCAGCTTCAGCCTCCGCTCCACTACGACAGAAGCTGGCCTTTATTAAGTGCAAATGAATTTGGATCACAACTCAA[C/T]
AAACTCCACCTTGAGACAAATTCCTTCTTGTAGCATGAATCAATCCTTCACCCTGAACACAACAAAGACAAAAAAAAAACATTTTCGGCGCCAAACAGCC

Reverse complement sequence

GGCTGTTTGGCGCCGAAAATGTTTTTTTTTTGTCTTTGTTGTGTTCAGGGTGAAGGATTGATTCATGCTACAAGAAGGAATTTGTCTCAAGGTGGAGTTT[G/A]
TTGAGTTGTGATCCAAATTCATTTGCACTTAATAAAGGCCAGCTTCTGTCGTAGTGGAGCGGAGGCTGAAGCTGACCCATTGGGTTGTGTACCTGGGGAC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.70%	43.30%	0.00%	0.00%	NA
All Indica	2759	92.20%	7.80%	0.00%	0.00%	NA
All Japonica	1512	3.30%	96.70%	0.00%	0.00%	NA
Aus	269	15.60%	84.40%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	92.90%	7.10%	0.00%	0.00%	NA
Indica III	913	90.30%	9.70%	0.00%	0.00%	NA
Indica Intermediate	786	89.70%	10.30%	0.00%	0.00%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	6.20%	93.80%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	40.00%	60.00%	0.00%	0.00%	NA

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
vg0221445039	C -> T	LOC_Os02g35670.1	missense_variant ; p.Cys83Tyr; MODERATE	nonsynonymous_codon ; C83Y	Average:57.346; most accessible tissue: Zhenshan97 root, score: 64.045	unknown	unknown	DELETERIOUS	0.00

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221445039	NA	4.21E-06	mr1120	Ind_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
vg0221445039	NA	6.23E-15	mr1156	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
vg0221445039	NA	1.48E-11	mr1657	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
vg0221445039	NA	1.60E-10	mr1720	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
vg0221445039	NA	1.18E-06	mr1756	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
vg0221445039	NA	6.00E-13	mr1914	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
vg0221445039	NA	8.54E-57	mr1109_2	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
vg0221445039	NA	2.01E-13	mr1514_2	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
vg0221445039	NA	1.32E-15	mr1720_2	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 9 of 9 entries

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Search for Variation information by Variation ID:

Detailed information for vg0221445039:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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