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Detailed information for vg0136326230:

Variant ID: vg0136326230 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 36326230
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.04, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTAGGTTTGATAAGGGACAGACATACATATTTGCTCTAAGTACAGAATATAGTGCTAGCCTCTGAAGTAGGCGGTGTTGTCCCATGCTGATCATCACG[G/A]
CTATCAGTTGTGGCCTATGCATAAGCAATATTAATATAAGAATTTACAATTGTTTATATGCAAGAGAGTACACATTGCTGCAGAATGAAGCTATTAGATT

Reverse complement sequence

AATCTAATAGCTTCATTCTGCAGCAATGTGTACTCTCTTGCATATAAACAATTGTAAATTCTTATATTAATATTGCTTATGCATAGGCCACAACTGATAG[C/T]
CGTGATGATCAGCATGGGACAACACCGCCTACTTCAGAGGCTAGCACTATATTCTGTACTTAGAGCAAATATGTATGTCTGTCCCTTATCAAACCTAACT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.20% 15.70% 0.44% 1.67% NA
All Indica  2759 75.20% 24.50% 0.22% 0.11% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 46.50% 19.70% 5.58% 28.25% NA
Indica I  595 88.70% 11.30% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 60.70% 39.30% 0.00% 0.00% NA
Indica Intermediate  786 69.80% 29.00% 0.76% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0136326230 G -> A LOC_Os01g62740.1 downstream_gene_variant ; 1214.0bp to feature; MODIFIER silent_mutation Average:42.136; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0136326230 G -> A LOC_Os01g62750.1 intron_variant ; MODIFIER silent_mutation Average:42.136; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0136326230 G -> DEL N N silent_mutation Average:42.136; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0136326230 NA 2.18E-07 mr1133 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
vg0136326230 NA 1.04E-06 mr1192 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
vg0136326230 NA 3.72E-07 mr1213 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
vg0136326230 NA 6.39E-06 mr1727 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
vg0136326230 NA 1.27E-09 mr1887 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
vg0136326230 NA 1.26E-09 mr1887 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
vg0136326230 NA 1.48E-06 mr1133_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