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Detailed information for vg0805076219:

Variant ID: vg0805076219 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5076219
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, C: 0.08, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TGTACAGCTAGAACCACAAAGCTATTATCAACCCGGAAAGCATTAGTAAGCTCATTAGCAGTTATAGTAGATTTTTTTATTCTGAAATAAATATTTCCTA[G/C]
GCCTGTGTGAATCAAACAAGATTTTGGAGTGTTGCATCTTATTTTTAGTGATATGCCCTAGAGGCAATCATAGAGATAGAGATGATTGTATCACATACTA

Reverse complement sequence

TAGTATGTGATACAATCATCTCTATCTCTATGATTGCCTCTAGGGCATATCACTAAAAATAAGATGCAACACTCCAAAATCTTGTTTGATTCACACAGGC[C/G]
TAGGAAATATTTATTTCAGAATAAAAAAATCTACTATAACTGCTAATGAGCTTACTAATGCTTTCCGGGTTGATAATAGCTTTGTGGTTCTAGCTGTACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.70% 26.00% 0.30% 26.01% NA
All Indica  2759 58.80% 16.30% 0.36% 24.61% NA
All Japonica  1512 15.40% 50.00% 0.26% 34.33% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 90.40% 0.50% 0.00% 9.08% NA
Indica II  465 30.30% 29.70% 0.22% 39.78% NA
Indica III  913 48.30% 25.70% 0.33% 25.63% NA
Indica Intermediate  786 63.70% 9.30% 0.76% 26.21% NA
Temperate Japonica  767 2.70% 84.10% 0.52% 12.65% NA
Tropical Japonica  504 31.90% 4.40% 0.00% 63.69% NA
Japonica Intermediate  241 21.20% 36.90% 0.00% 41.91% NA
VI/Aromatic  96 90.60% 3.10% 0.00% 6.25% NA
Intermediate  90 47.80% 25.60% 0.00% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805076219 G -> C LOC_Os08g08750.1 upstream_gene_variant ; 2696.0bp to feature; MODIFIER silent_mutation Average:31.268; most accessible tissue: Callus, score: 61.233 N N N N
vg0805076219 G -> C LOC_Os08g08760.1 downstream_gene_variant ; 3263.0bp to feature; MODIFIER silent_mutation Average:31.268; most accessible tissue: Callus, score: 61.233 N N N N
vg0805076219 G -> C LOC_Os08g08750-LOC_Os08g08760 intergenic_region ; MODIFIER silent_mutation Average:31.268; most accessible tissue: Callus, score: 61.233 N N N N
vg0805076219 G -> DEL N N silent_mutation Average:31.268; most accessible tissue: Callus, score: 61.233 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805076219 NA 2.51E-07 mr1606 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
vg0805076219 NA 3.39E-13 mr1942 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
vg0805076219 NA 5.87E-06 mr1942 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
vg0805076219 NA 8.65E-08 mr1047_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
vg0805076219 NA 3.89E-15 mr1115_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
vg0805076219 NA 9.71E-07 mr1159_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
vg0805076219 NA 7.21E-10 mr1189_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
vg0805076219 NA 2.70E-08 mr1378_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
vg0805076219 NA 4.69E-06 mr1425_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
vg0805076219 NA 8.96E-06 mr1449_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
vg0805076219 NA 1.17E-09 mr1454_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
vg0805076219 NA 7.29E-12 mr1471_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
vg0805076219 NA 1.28E-08 mr1482_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
vg0805076219 NA 8.02E-11 mr1530_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
vg0805076219 NA 7.26E-16 mr1539_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
vg0805076219 NA 6.10E-17 mr1540_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
vg0805076219 NA 4.68E-11 mr1580_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
vg0805076219 NA 9.37E-07 mr1629_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
vg0805076219 NA 2.28E-10 mr1642_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
vg0805076219 NA 3.48E-07 mr1671_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
vg0805076219 NA 6.58E-15 mr1732_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
vg0805076219 NA 1.32E-11 mr1789_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
vg0805076219 NA 5.00E-10 mr1808_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
vg0805076219 NA 3.36E-07 mr1815_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
vg0805076219 NA 5.88E-06 mr1815_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
vg0805076219 NA 5.64E-10 mr1825_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
vg0805076219 NA 2.49E-09 mr1864_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
vg0805076219 NA 8.84E-06 mr1870_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
vg0805076219 NA 9.48E-09 mr1879_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
vg0805076219 NA 7.42E-07 mr1892_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
vg0805076219 NA 3.38E-12 mr1942_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
vg0805076219 NA 4.05E-06 mr1966_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