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Detailed information for vg0805577197:

Variant ID: vg0805577197 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5577197
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, A: 0.42, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TACAGATTTAGTGATTAAGTTATCAAAGAATTACATATTCTAGAGCTTAGATCATAGCACTATTATTTATTTAATTTAAAGTTATAAAAATTATAGTTTT[G/A]
TGATAAAATAGTTTTTAAATGTGTAGTTTTGTAATAAAATAGTTGTTAAATCAATAGTTTTGTGATATAATATCTTAAATCTGTAGTTCCATGATAAATT

Reverse complement sequence

AATTTATCATGGAACTACAGATTTAAGATATTATATCACAAAACTATTGATTTAACAACTATTTTATTACAAAACTACACATTTAAAAACTATTTTATCA[C/T]
AAAACTATAATTTTTATAACTTTAAATTAAATAAATAATAGTGCTATGATCTAAGCTCTAGAATATGTAATTCTTTGATAACTTAATCACTAAATCTGTA

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 42.00% 33.50% 1.23% 23.23% NA
All Indica  2759 23.60% 45.10% 0.65% 30.74% NA
All Japonica  1512 85.80% 1.10% 0.33% 12.83% NA
Aus  269 0.40% 98.90% 0.00% 0.74% NA
Indica I  595 40.80% 17.80% 0.67% 40.67% NA
Indica II  465 40.40% 15.50% 0.43% 43.66% NA
Indica III  913 8.00% 76.90% 0.44% 14.68% NA
Indica Intermediate  786 18.60% 46.20% 1.02% 34.22% NA
Temperate Japonica  767 96.10% 0.50% 0.13% 3.26% NA
Tropical Japonica  504 74.00% 1.40% 0.60% 24.01% NA
Japonica Intermediate  241 77.60% 2.10% 0.41% 19.92% NA
VI/Aromatic  96 3.10% 33.30% 31.25% 32.29% NA
Intermediate  90 38.90% 30.00% 5.56% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805577197 G -> A LOC_Os08g09640.1 upstream_gene_variant ; 2813.0bp to feature; MODIFIER silent_mutation Average:24.752; most accessible tissue: Callus, score: 47.778 N N N N
vg0805577197 G -> A LOC_Os08g09660.1 upstream_gene_variant ; 3380.0bp to feature; MODIFIER silent_mutation Average:24.752; most accessible tissue: Callus, score: 47.778 N N N N
vg0805577197 G -> A LOC_Os08g09650.1 intron_variant ; MODIFIER silent_mutation Average:24.752; most accessible tissue: Callus, score: 47.778 N N N N
vg0805577197 G -> DEL N N silent_mutation Average:24.752; most accessible tissue: Callus, score: 47.778 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805577197 NA 4.74E-10 mr1063 Ind_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
vg0805577197 NA 2.53E-06 mr1177 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
vg0805577197 NA 5.88E-07 mr1177 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
vg0805577197 NA 2.76E-11 mr1180 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
vg0805577197 NA 1.57E-07 mr1180 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
vg0805577197 NA 1.83E-07 mr1183 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
vg0805577197 NA 3.94E-07 mr1221 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
vg0805577197 NA 5.01E-06 mr1236 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
vg0805577197 NA 3.31E-07 mr1343 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
vg0805577197 NA 4.60E-07 mr1352 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
vg0805577197 NA 4.97E-07 mr1503 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
vg0805577197 NA 1.96E-06 mr1510 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
vg0805577197 NA 1.73E-07 mr1583 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
vg0805577197 NA 2.88E-08 mr1740 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
vg0805577197 NA 3.40E-08 mr1803 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
vg0805577197 NA 4.34E-06 mr1807 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
vg0805577197 NA 4.13E-08 mr1870 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
vg0805577197 NA 8.50E-13 mr1063_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
vg0805577197 NA 1.77E-10 mr1170_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
vg0805577197 NA 1.37E-10 mr1180_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
vg0805577197 NA 6.43E-09 mr1183_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
vg0805577197 NA 3.65E-11 mr1221_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
vg0805577197 NA 1.45E-06 mr1236_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
vg0805577197 NA 1.32E-07 mr1236_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
vg0805577197 NA 3.16E-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
vg0805577197 NA 7.40E-07 mr1583_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
vg0805577197 NA 5.52E-08 mr1792_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
vg0805577197 NA 1.34E-12 mr1803_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
vg0805577197 NA 1.73E-07 mr1807_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
vg0805577197 NA 7.31E-09 mr1850_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
vg0805577197 NA 2.60E-10 mr1870_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