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Detailed information for vg0113344604:

Variant ID: vg0113344604 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13344604
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, T: 0.20, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTCAATGTTTACATTTAATGAAAATGATTTTATATTGTAGATGTTGAAAATGAGTTTAACTTGAAAAAAATGTCAAAACGACTTATAATACAAAATA[T/A]
AATGGAGGAAGTAGATTGCAACGTAACGCAGATTGATTTAAGTTTAAATTCGAATTAGATCAACAAGGACTACTTGGTTTTTTGAGCCATCAATGATCTT

Reverse complement sequence

AAGATCATTGATGGCTCAAAAAACCAAGTAGTCCTTGTTGATCTAATTCGAATTTAAACTTAAATCAATCTGCGTTACGTTGCAATCTACTTCCTCCATT[A/T]
TATTTTGTATTATAAGTCGTTTTGACATTTTTTTCAAGTTAAACTCATTTTCAACATCTACAATATAAAATCATTTTCATTAAATGTAAACATTGAATAT

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 54.90% 45.00% 0.04% 0.00% NA
All Indica  2759 66.80% 33.10% 0.07% 0.00% NA
All Japonica  1512 23.60% 76.40% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 89.40% 10.60% 0.00% 0.00% NA
Indica II  465 49.90% 50.10% 0.00% 0.00% NA
Indica III  913 60.70% 39.30% 0.00% 0.00% NA
Indica Intermediate  786 66.80% 33.00% 0.25% 0.00% NA
Temperate Japonica  767 16.90% 83.10% 0.00% 0.00% NA
Tropical Japonica  504 38.10% 61.90% 0.00% 0.00% NA
Japonica Intermediate  241 14.50% 85.50% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg0113344604 T -> A LOC_Os01g23700.1 upstream_gene_variant ; 3883.0bp to feature; MODIFIER silent_mutation Average:59.662; most accessible tissue: Callus, score: 74.181 N N N N
vg0113344604 T -> A LOC_Os01g23730.1 upstream_gene_variant ; 3964.0bp to feature; MODIFIER silent_mutation Average:59.662; most accessible tissue: Callus, score: 74.181 N N N N
vg0113344604 T -> A LOC_Os01g23705.1 downstream_gene_variant ; 1946.0bp to feature; MODIFIER silent_mutation Average:59.662; most accessible tissue: Callus, score: 74.181 N N N N
vg0113344604 T -> A LOC_Os01g23710.1 intron_variant ; MODIFIER silent_mutation Average:59.662; most accessible tissue: Callus, score: 74.181 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113344604 9.36E-06 9.35E-06 mr1193 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
vg0113344604 NA 3.02E-08 mr1030_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
vg0113344604 NA 3.37E-08 mr1654_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
vg0113344604 NA 4.42E-08 mr1994_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
vg0113344604 NA 4.46E-06 mr1994_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