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Detailed information for vg0232298835:

Variant ID: vg0232298835 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32298835
Reference Allele: GAlternative Allele: T
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGATTAGTAGCATCTTGTATCTTTTACTTATGACCTCTTATATGTTTTTGAGTTATTTGATTACAGGTGGCAGCTTGATTATTTAACTAAGCTGAAGT[G/T]
GCCTCAAATTGAACACGAGAATGCACCATGGGCATCACGTACCCCATTGTGTAGTCTGCATAGCTGGTCATTTACTGGGATATTTCCTGAGCCAGCACCT

Reverse complement sequence

AGGTGCTGGCTCAGGAAATATCCCAGTAAATGACCAGCTATGCAGACTACACAATGGGGTACGTGATGCCCATGGTGCATTCTCGTGTTCAATTTGAGGC[C/A]
ACTTCAGCTTAGTTAAATAATCAAGCTGCCACCTGTAATCAAATAACTCAAAAACATATAAGAGGTCATAAGTAAAAGATACAAGATGCTACTAATCACA

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 97.10% 1.90% 1.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.20% 5.60% 3.17% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 85.10% 9.00% 5.87% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 2.10% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0232298835 G -> T LOC_Os02g52820.1 downstream_gene_variant ; 144.0bp to feature; MODIFIER silent_mutation Average:57.104; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N
vg0232298835 G -> T LOC_Os02g52830.1 downstream_gene_variant ; 939.0bp to feature; MODIFIER silent_mutation Average:57.104; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N
vg0232298835 G -> T LOC_Os02g52820-LOC_Os02g52830 intergenic_region ; MODIFIER silent_mutation Average:57.104; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232298835 8.93E-06 8.93E-06 mr1499_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
vg0232298835 NA 6.29E-06 mr1706_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
vg0232298835 7.49E-06 2.92E-07 mr1712_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
vg0232298835 8.73E-08 1.14E-09 mr1946_2 Jap_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
vg0232298835 8.73E-08 1.14E-09 mr1948_2 Jap_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
vg0232298835 1.81E-07 1.25E-09 mr1977_2 Jap_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