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Detailed information for vg0509824684:

Variant ID: vg0509824684 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 9824684
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTCAGGAGCTACGCATTCCTTTATATCAAGAGATTTTGTGGCAAAACACCAAATAAGGATAGAAGATCTTAGCAACCCTATGATAATATCAACCCCG[G/A]
GAAGCCAGCTACCGACTAAGCTCTTCAGCCCATCAGTAACCATAGAGATCCAAGGAGTCACTTTTCTGGCTAATCTCATCCTTCTGAGCTCTAAGAACCC

Reverse complement sequence

GGGTTCTTAGAGCTCAGAAGGATGAGATTAGCCAGAAAAGTGACTCCTTGGATCTCTATGGTTACTGATGGGCTGAAGAGCTTAGTCGGTAGCTGGCTTC[C/T]
CGGGGTTGATATTATCATAGGGTTGCTAAGATCTTCTATCCTTATTTGGTGTTTTGCCACAAAATCTCTTGATATAAAGGAATGCGTAGCTCCTGAATCA

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 91.90% 8.00% 0.15% 0.00% NA
All Indica  2759 92.60% 7.20% 0.22% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 37.90% 61.70% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 82.70% 16.60% 0.66% 0.00% NA
Indica Intermediate  786 94.30% 5.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0509824684 G -> A LOC_Os05g17150.1 missense_variant ; p.Gly470Arg; MODERATE nonsynonymous_codon ; G470R Average:59.666; most accessible tissue: Minghui63 flag leaf, score: 75.341 unknown unknown DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0509824684 8.10E-06 NA mr1131_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
vg0509824684 5.12E-07 NA mr1316_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
vg0509824684 1.70E-06 NA mr1386_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
vg0509824684 6.17E-06 NA mr1541_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
vg0509824684 5.50E-06 NA mr1743_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
vg0509824684 NA 7.20E-08 mr1762_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
vg0509824684 NA 8.50E-10 mr1818_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
vg0509824684 4.32E-06 NA mr1938_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