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Detailed information for vg0523130102:

Variant ID: vg0523130102 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23130102
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


ATCTCCAGTGTTGCCAATGGTCACATTAGCAGACTTAGAGGTCTGCCCTGCAGGTGCCTTCATCCCCTTGCGTTGTGGACACTTCCTGGCCAGATAGCCA[G/A]
GTTGACCACACACAAAGCAAGTCCTCTCATCCTGATTAGGATTGTTGTTATTGTTCTTCTTCTTGAAGTTGGTGGTCTGCTGAGCTTTGTATTTCCCCTT

Reverse complement sequence

AAGGGGAAATACAAAGCTCAGCAGACCACCAACTTCAAGAAGAAGAACAATAACAACAATCCTAATCAGGATGAGAGGACTTGCTTTGTGTGTGGTCAAC[C/T]
TGGCTATCTGGCCAGGAAGTGTCCACAACGCAAGGGGATGAAGGCACCTGCAGGGCAGACCTCTAAGTCTGCTAATGTGACCATTGGCAACACTGGAGAT

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 96.50% 3.50% 0.02% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 56.10% 43.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% 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 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 64.60% 34.40% 1.04% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0523130102 G -> A LOC_Os05g39430.1 missense_variant ; p.Pro233Leu; MODERATE nonsynonymous_codon ; P233L Average:27.255; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 possibly damaging 1.728 TOLERATED 0.26

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523130102 NA 7.53E-08 mr1989 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
vg0523130102 NA 4.99E-09 mr1057_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
vg0523130102 NA 1.17E-10 mr1126_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
vg0523130102 NA 4.30E-06 mr1127_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
vg0523130102 NA 2.08E-11 mr1166_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
vg0523130102 NA 5.87E-07 mr1465_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
vg0523130102 NA 3.67E-10 mr1567_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
vg0523130102 NA 1.28E-13 mr1612_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