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Detailed information for vg0218008797:

Variant ID: vg0218008797 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18008797
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTACATACAAGTTACAGTGTAATTATACTACGATTGTACTATAATTACATCTGTCAAATTTTCAGAAGAAAATTTGTCGACAAATGTATAGGTGGTCCCG[T/G]
CCTTTTTTAGCCAACTTTTTAGTTGTTCATCGGTGTTCCGCGCGTGCCAACACTGTAGATTTTTTAGAGAGGAAATAATAACTGTAGATGGTTCCAGAAC

Reverse complement sequence

GTTCTGGAACCATCTACAGTTATTATTTCCTCTCTAAAAAATCTACAGTGTTGGCACGCGCGGAACACCGATGAACAACTAAAAAGTTGGCTAAAAAAGG[A/C]
CGGGACCACCTATACATTTGTCGACAAATTTTCTTCTGAAAATTTGACAGATGTAATTATAGTACAATCGTAGTATAATTACACTGTAACTTGTATGTAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.10% 8.30% 2.60% 0.00% NA
All Indica  2759 99.70% 0.10% 0.14% 0.00% NA
All Japonica  1512 66.90% 25.30% 7.80% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 36.40% 48.90% 14.73% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 3.30% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0218008797 T -> G LOC_Os02g30270.1 upstream_gene_variant ; 4808.0bp to feature; MODIFIER silent_mutation Average:59.616; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg0218008797 T -> G LOC_Os02g30280.1 downstream_gene_variant ; 2421.0bp to feature; MODIFIER silent_mutation Average:59.616; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg0218008797 T -> G LOC_Os02g30290.1 downstream_gene_variant ; 2620.0bp to feature; MODIFIER silent_mutation Average:59.616; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N
vg0218008797 T -> G LOC_Os02g30280-LOC_Os02g30290 intergenic_region ; MODIFIER silent_mutation Average:59.616; most accessible tissue: Zhenshan97 flower, score: 75.657 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218008797 2.60E-06 NA mr1926 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
vg0218008797 NA 1.33E-06 mr1355_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
vg0218008797 NA 6.76E-06 mr1627_2 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
vg0218008797 NA 9.45E-06 mr1899_2 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