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Detailed information for vg0802685134:

Variant ID: vg0802685134 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2685134
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTTAGCTATTTATTTTATGGATATGCATGGAATATCTAGAGAGGATAAGTAACAGAAGTGATCAACAAACACATAACAAATGGCTACAGCTATATATC[A/T]
TGATTAGATAGTTTAGGATGCCCGAGGAAGTGCAGTGACTATGAAGTGTGCTGTGATTGACGAAACGTTGGGTGTGCTTTATGGATCAAATCGAGTGTTA

Reverse complement sequence

TAACACTCGATTTGATCCATAAAGCACACCCAACGTTTCGTCAATCACAGCACACTTCATAGTCACTGCACTTCCTCGGGCATCCTAAACTATCTAATCA[T/A]
GATATATAGCTGTAGCCATTTGTTATGTGTTTGTTGATCACTTCTGTTACTTATCCTCTCTAGATATTCCATGCATATCCATAAAATAAATAGCTAAGGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.90% 1.60% 0.42% 0.00% NA
All Indica  2759 99.60% 0.00% 0.33% 0.00% NA
All Japonica  1512 94.40% 4.90% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.00% 1.18% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 85.50% 13.30% 1.19% 0.00% NA
Japonica Intermediate  241 95.90% 2.90% 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
vg0802685134 A -> T LOC_Os08g05150-LOC_Os08g05160 intergenic_region ; MODIFIER silent_mutation Average:46.262; most accessible tissue: Callus, score: 73.449 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802685134 2.52E-06 2.52E-06 mr1761 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