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Detailed information for vg0228495434:

Variant ID: vg0228495434 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28495434
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CGATAACAGGCCTAAGATAATTTATAATATTCATCATTTTCGTTTTTTTCTCTCCTTAGATCATAACACGAGAAGATCAATGTACATAACCACATGCCAT[T/G]
CATGCTTACCGGCCATTAGTTCTGGTAGATATTCAGTACCATTATGAATTTATGATTGGCTTGAGAAAGAAAATCACACCAAGGTCTTTCAAAAAACAAA

Reverse complement sequence

TTTGTTTTTTGAAAGACCTTGGTGTGATTTTCTTTCTCAAGCCAATCATAAATTCATAATGGTACTGAATATCTACCAGAACTAATGGCCGGTAAGCATG[A/C]
ATGGCATGTGGTTATGTACATTGATCTTCTCGTGTTATGATCTAAGGAGAGAAAAAAACGAAAATGATGAATATTATAAATTATCTTAGGCCTGTTATCG

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 77.10% 22.80% 0.04% 0.00% NA
All Indica  2759 96.00% 4.00% 0.00% 0.00% NA
All Japonica  1512 38.60% 61.30% 0.13% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 92.30% 7.70% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 11.70% 88.00% 0.26% 0.00% NA
Tropical Japonica  504 88.50% 11.50% 0.00% 0.00% NA
Japonica Intermediate  241 19.50% 80.50% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 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
vg0228495434 T -> G LOC_Os02g46680.1 intron_variant ; MODIFIER silent_mutation Average:54.274; most accessible tissue: Callus, score: 91.199 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228495434 NA 3.96E-09 mr1019 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
vg0228495434 NA 9.41E-08 mr1364 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
vg0228495434 NA 3.45E-07 mr1443 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
vg0228495434 NA 8.03E-12 mr1471 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
vg0228495434 NA 1.73E-12 mr1790 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
vg0228495434 NA 2.02E-18 mr1790_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