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Detailed information for vg0313617458:

Variant ID: vg0313617458 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13617458
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCAATAAGTCGCTCGTAAAACATATGGTATTTGAAAAAGGCAAGCGAATACGTGTGGTCGAGAAGGACGCTGAGGCGGTTACTCAGGAATCAGACTCA[G/A]
CATATCCAGACTCCGATCTCCATGTCTCGCACATCTTCGGAGGTTCCACGACATACTCCTCAGAGCGAGAATACAAGAAGGTGAAACGTGAAGTTTGTTC

Reverse complement sequence

GAACAAACTTCACGTTTCACCTTCTTGTATTCTCGCTCTGAGGAGTATGTCGTGGAACCTCCGAAGATGTGCGAGACATGGAGATCGGAGTCTGGATATG[C/T]
TGAGTCTGATTCCTGAGTAACCGCCTCAGCGTCCTTCTCGACCACACGTATTCGCTTGCCTTTTTCAAATACCATATGTTTTACGAGCGACTTATTGAAG

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 84.40% 11.90% 1.23% 2.50% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 57.90% 32.50% 2.84% 6.81% NA
Aus  269 99.60% 0.00% 0.00% 0.37% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 92.60% 6.90% 0.39% 0.13% NA
Tropical Japonica  504 17.30% 58.70% 6.55% 17.46% NA
Japonica Intermediate  241 32.40% 58.90% 2.90% 5.81% NA
VI/Aromatic  96 19.80% 54.20% 13.54% 12.50% NA
Intermediate  90 76.70% 18.90% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0313617458 G -> A LOC_Os03g23990.1 missense_variant ; p.Ala563Thr; MODERATE nonsynonymous_codon ; A563T Average:47.96; most accessible tissue: Minghui63 flag leaf, score: 73.334 possibly damaging 1.571 DELETERIOUS 0.05
vg0313617458 G -> DEL LOC_Os03g23990.1 N frameshift_variant Average:47.96; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313617458 NA 2.88E-14 mr1084 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
vg0313617458 NA 1.46E-12 mr1205 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
vg0313617458 NA 3.15E-07 mr1206 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
vg0313617458 NA 5.79E-07 mr1319 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
vg0313617458 NA 2.10E-09 mr1322 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
vg0313617458 NA 3.44E-17 mr1330 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
vg0313617458 NA 7.22E-07 mr1330 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
vg0313617458 NA 2.63E-11 mr1332 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
vg0313617458 NA 1.71E-11 mr1336 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
vg0313617458 NA 1.35E-06 mr1338 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
vg0313617458 NA 9.37E-13 mr1454 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
vg0313617458 NA 8.46E-13 mr1521 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
vg0313617458 4.06E-06 3.01E-15 mr1579 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
vg0313617458 NA 3.91E-06 mr1579 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
vg0313617458 NA 6.81E-20 mr1580 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
vg0313617458 NA 9.90E-17 mr1701 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
vg0313617458 NA 8.01E-11 mr1775 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
vg0313617458 NA 1.89E-07 mr1779 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
vg0313617458 NA 3.82E-21 mr1825 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