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Detailed information for vg0126711643:

Variant ID: vg0126711643 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 26711643
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.11, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TCATTTTACGTGCCATATCAATCCTCATCTTCATCTATCTCAAATGGGGTATGTGCATTAGAAATCAATATTTAGTTATGAACCGCTGGCATTTTCATAT[G/A]
GCTACTATTTAACAAGAGAACTAATCGCTGTAATTACATTGTACGTCTACCTATTAAAGAAGAGAGAATCCCTTATATGCCATTAAAATTTGGTCCGATC

Reverse complement sequence

GATCGGACCAAATTTTAATGGCATATAAGGGATTCTCTCTTCTTTAATAGGTAGACGTACAATGTAATTACAGCGATTAGTTCTCTTGTTAAATAGTAGC[C/T]
ATATGAAAATGCCAGCGGTTCATAACTAAATATTGATTTCTAATGCACATACCCCATTTGAGATAGATGAAGATGAGGATTGATATGGCACGTAAAATGA

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 56.90% 43.10% 0.06% 0.00% NA
All Indica  2759 90.80% 9.20% 0.00% 0.00% NA
All Japonica  1512 5.00% 94.90% 0.07% 0.00% NA
Aus  269 23.80% 75.80% 0.37% 0.00% NA
Indica I  595 80.80% 19.20% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 93.40% 6.60% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.40% 0.00% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 13.50% 86.30% 0.20% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 41.10% 57.80% 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
vg0126711643 G -> A LOC_Os01g46820.1 upstream_gene_variant ; 919.0bp to feature; MODIFIER silent_mutation Average:53.656; most accessible tissue: Minghui63 root, score: 62.438 N N N N
vg0126711643 G -> A LOC_Os01g46830.1 downstream_gene_variant ; 651.0bp to feature; MODIFIER silent_mutation Average:53.656; most accessible tissue: Minghui63 root, score: 62.438 N N N N
vg0126711643 G -> A LOC_Os01g46820-LOC_Os01g46830 intergenic_region ; MODIFIER silent_mutation Average:53.656; most accessible tissue: Minghui63 root, score: 62.438 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0126711643 NA 2.57E-07 mr1717 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
vg0126711643 2.82E-06 2.82E-06 mr1812 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
vg0126711643 NA 3.84E-06 mr1121_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