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Detailed information for vg0726684254:

Variant ID: vg0726684254 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26684254
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTTGATTTGCCGTCAATGTCTTAGCTAGGGCCTGCAAAATGTATGGACATTGCTTAAAATGGCTAGTTGGTGATGTCATCAGAGTCAAGACATATCGG[T/C]
ATAAGCCTACTTAAACTGCACAACCAAAAGCAATATATTGCTCGTACATGGATAACTTGACACATGTAAAAAATGAAAAAAAATATAAGCAGCAAGAATA

Reverse complement sequence

TATTCTTGCTGCTTATATTTTTTTTCATTTTTTACATGTGTCAAGTTATCCATGTACGAGCAATATATTGCTTTTGGTTGTGCAGTTTAAGTAGGCTTAT[A/G]
CCGATATGTCTTGACTCTGATGACATCACCAACTAGCCATTTTAAGCAATGTCCATACATTTTGCAGGCCCTAGCTAAGACATTGACGGCAAATCAACTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 89.00% 11.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 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 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 80.10% 19.90% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0726684254 T -> C LOC_Os07g44700.1 upstream_gene_variant ; 4118.0bp to feature; MODIFIER silent_mutation Average:59.094; most accessible tissue: Callus, score: 86.969 N N N N
vg0726684254 T -> C LOC_Os07g44710.1 intron_variant ; MODIFIER silent_mutation Average:59.094; most accessible tissue: Callus, score: 86.969 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726684254 NA 1.52E-07 mr1922 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
vg0726684254 NA 7.36E-06 mr1153_2 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
vg0726684254 1.41E-06 NA mr1252_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
vg0726684254 NA 2.73E-06 mr1383_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