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Detailed information for vg0715008269:

Variant ID: vg0715008269 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15008269
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGCAATCTCCAAATTAGGGTTTTTTTTGGCGGGCCGGGGGAGGGGCGAAAGAATCGAAATTTTGGAAGTTTCGGAAAATTTCTGAGCCGAAATTATTT[A/G]
GAAGTTTTACGTATTTTTAATGAATTTGAATTAACTTCGAACAAATTGAAAAAATGAAAAAAAACCCGTAAATTTCAGACGAGATTTGTGTTTACCTGTG

Reverse complement sequence

CACAGGTAAACACAAATCTCGTCTGAAATTTACGGGTTTTTTTTCATTTTTTCAATTTGTTCGAAGTTAATTCAAATTCATTAAAAATACGTAAAACTTC[T/C]
AAATAATTTCGGCTCAGAAATTTTCCGAAACTTCCAAAATTTCGATTCTTTCGCCCCTCCCCCGGCCCGCCAAAAAAAACCCTAATTTGGAGATTGCAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 5.90% 0.00% 0.00% NA
All Indica  2759 95.00% 5.00% 0.00% 0.00% NA
All Japonica  1512 94.30% 5.70% 0.00% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 89.10% 10.90% 0.00% 0.00% NA
Temperate Japonica  767 89.20% 10.80% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 61.50% 38.50% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0715008269 A -> G LOC_Os07g26120.1 downstream_gene_variant ; 2803.0bp to feature; MODIFIER silent_mutation Average:58.53; most accessible tissue: Callus, score: 70.874 N N N N
vg0715008269 A -> G LOC_Os07g26120-LOC_Os07g26130 intergenic_region ; MODIFIER silent_mutation Average:58.53; most accessible tissue: Callus, score: 70.874 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715008269 8.78E-06 8.77E-06 mr1369_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
vg0715008269 4.41E-06 4.40E-06 mr1453_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
vg0715008269 4.86E-06 4.87E-06 mr1766_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