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Detailed information for vg0234423363:

Variant ID: vg0234423363 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34423363
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


ATAAAAAAAATAAAAAAAATTGATAACATAGATTAATATTAAATATATCATTCCACAAACATGCAAGACCAAATTTAACTTCTATAAATTGCAACAAAGA[T/A]
AACAAATTAAACTGAAAATAGTTATCGCACATTCGCAACTATATCTATTATTTTTGTTATAACTTATAGAAGTTGAATTTAAACTTATGTGTTTATGGAG

Reverse complement sequence

CTCCATAAACACATAAGTTTAAATTCAACTTCTATAAGTTATAACAAAAATAATAGATATAGTTGCGAATGTGCGATAACTATTTTCAGTTTAATTTGTT[A/T]
TCTTTGTTGCAATTTATAGAAGTTAAATTTGGTCTTGCATGTTTGTGGAATGATATATTTAATATTAATCTATGTTATCAATTTTTTTTATTTTTTTTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.40% 15.50% 0.17% 0.00% NA
All Indica  2759 81.10% 18.60% 0.29% 0.00% NA
All Japonica  1512 99.00% 1.00% 0.00% 0.00% NA
Aus  269 46.10% 53.90% 0.00% 0.00% NA
Indica I  595 80.00% 19.80% 0.17% 0.00% NA
Indica II  465 91.40% 8.40% 0.22% 0.00% NA
Indica III  913 83.70% 16.00% 0.33% 0.00% NA
Indica Intermediate  786 72.90% 26.70% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0234423363 T -> A LOC_Os02g56260.1 intron_variant ; MODIFIER silent_mutation Average:43.983; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0234423363 NA 6.55E-06 mr1042 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
vg0234423363 NA 1.10E-06 mr1042 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
vg0234423363 NA 4.30E-06 mr1043 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
vg0234423363 NA 7.91E-06 mr1479 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
vg0234423363 3.82E-06 1.44E-08 mr1892 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
vg0234423363 NA 2.35E-06 mr1975 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
vg0234423363 NA 9.86E-06 mr1723_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