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Detailed information for vg0503118625:

Variant ID: vg0503118625 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3118625
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


GTAAAAAGCTTTGATCAACTGCATTGACCTTCTTTTACTCTTCAATAGTACATTCGCCATTTTTGTTCCACTAATTTATTTAAGTAACTCAAGGAGATTA[A/C]
GTGCAAAGTATATGAAAAACTCGATTATTCTTTATTCTTGCACACAATAGGATATAGAAAAAATTACTATCCTTAAAGAGGTACCTATAGGTATCACACT

Reverse complement sequence

AGTGTGATACCTATAGGTACCTCTTTAAGGATAGTAATTTTTTCTATATCCTATTGTGTGCAAGAATAAAGAATAATCGAGTTTTTCATATACTTTGCAC[T/G]
TAATCTCCTTGAGTTACTTAAATAAATTAGTGGAACAAAAATGGCGAATGTACTATTGAAGAGTAAAAGAAGGTCAATGCAGTTGATCAAAGCTTTTTAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.40% 3.90% 0.76% 0.00% NA
All Indica  2759 99.50% 0.40% 0.04% 0.00% NA
All Japonica  1512 86.80% 10.80% 2.31% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 63.10% 30.60% 6.35% 0.00% NA
Japonica Intermediate  241 94.60% 4.10% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0503118625 A -> C LOC_Os05g06200.1 downstream_gene_variant ; 1363.0bp to feature; MODIFIER silent_mutation Average:32.301; most accessible tissue: Callus, score: 47.077 N N N N
vg0503118625 A -> C LOC_Os05g06190-LOC_Os05g06200 intergenic_region ; MODIFIER silent_mutation Average:32.301; most accessible tissue: Callus, score: 47.077 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503118625 NA 3.58E-07 mr1422 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
vg0503118625 NA 1.65E-08 mr1583 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
vg0503118625 9.97E-08 2.05E-10 mr1218_2 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
vg0503118625 NA 1.52E-06 mr1422_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
vg0503118625 NA 7.50E-07 mr1583_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
vg0503118625 4.73E-06 4.95E-10 mr1850_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