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Detailed information for vg0234311021:

Variant ID: vg0234311021 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34311021
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TTATTACAAAGTCCACACACGAACAAACTCAGCACACACTGACATAATGTAAAGAAAACATAAACTAAAAGACACCAACACAAGATAAAAGAACCCTCAA[T/G]
TATTGAATTCTATTCGAGAATCTCCATCCGAAATTTTCTTCATGTTGGTACAATTAGAATTGAGATGCAGAAATTTCTCACAATTTGATCCACATGCCTT

Reverse complement sequence

AAGGCATGTGGATCAAATTGTGAGAAATTTCTGCATCTCAATTCTAATTGTACCAACATGAAGAAAATTTCGGATGGAGATTCTCGAATAGAATTCAATA[A/C]
TTGAGGGTTCTTTTATCTTGTGTTGGTGTCTTTTAGTTTATGTTTTCTTTACATTATGTCAGTGTGTGCTGAGTTTGTTCGTGTGTGGACTTTGTAATAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.50% 0.06% 0.00% NA
All Indica  2759 85.50% 14.40% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 70.80% 29.00% 0.22% 0.00% NA
Indica III  913 82.90% 16.90% 0.22% 0.00% NA
Indica Intermediate  786 88.50% 11.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0234311021 T -> G LOC_Os02g56040.1 upstream_gene_variant ; 3292.0bp to feature; MODIFIER silent_mutation Average:35.041; most accessible tissue: Callus, score: 76.724 N N N N
vg0234311021 T -> G LOC_Os02g56060.1 upstream_gene_variant ; 1685.0bp to feature; MODIFIER silent_mutation Average:35.041; most accessible tissue: Callus, score: 76.724 N N N N
vg0234311021 T -> G LOC_Os02g56050.1 intron_variant ; MODIFIER silent_mutation Average:35.041; most accessible tissue: Callus, score: 76.724 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234311021 NA 4.86E-07 mr1032 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
vg0234311021 NA 9.96E-07 mr1165 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
vg0234311021 NA 7.94E-06 mr1415 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
vg0234311021 NA 1.28E-06 mr1478 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
vg0234311021 NA 7.94E-06 mr1567 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
vg0234311021 3.57E-06 3.57E-06 mr1664 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
vg0234311021 4.09E-06 4.09E-06 mr1664 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
vg0234311021 NA 2.27E-09 mr1829 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
vg0234311021 NA 9.53E-07 mr1165_2 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
vg0234311021 NA 1.65E-09 mr1478_2 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
vg0234311021 NA 4.26E-07 mr1971_2 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