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Detailed information for vg0901967595:

Variant ID: vg0901967595 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1967595
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGGAAAATTTCAGAGAGTATAATTAACCATGGAGAAGTTAATGAAAATTAAATCCAGCCATGCTTTATATTTAGGAAATTTTATTTCCCACATTTAAC[A/T]
TCACTTGTAAATTAATGAACATTTAATATAAATTCTAATAATAATTTATTAAATAATTTATAAATCATAAGAAGAAAATCAAGATGTGACAATTTCATCC

Reverse complement sequence

GGATGAAATTGTCACATCTTGATTTTCTTCTTATGATTTATAAATTATTTAATAAATTATTATTAGAATTTATATTAAATGTTCATTAATTTACAAGTGA[T/A]
GTTAAATGTGGGAAATAAAATTTCCTAAATATAAAGCATGGCTGGATTTAATTTTCATTAACTTCTCCATGGTTAATTATACTCTCTGAAATTTTCCTGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.20% 22.00% 4.87% 2.01% NA
All Indica  2759 92.00% 1.80% 4.17% 1.99% NA
All Japonica  1512 26.40% 64.20% 7.14% 2.31% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.80% 4.40% 2.35% 0.50% NA
Indica II  465 90.10% 1.30% 6.02% 2.58% NA
Indica III  913 92.60% 0.10% 4.38% 2.96% NA
Indica Intermediate  786 92.00% 2.20% 4.20% 1.65% NA
Temperate Japonica  767 2.20% 96.70% 0.39% 0.65% NA
Tropical Japonica  504 57.30% 21.40% 16.47% 4.76% NA
Japonica Intermediate  241 38.60% 49.80% 9.13% 2.49% NA
VI/Aromatic  96 92.70% 1.00% 2.08% 4.17% NA
Intermediate  90 74.40% 18.90% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0901967595 A -> DEL N N silent_mutation Average:50.402; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 N N N N
vg0901967595 A -> T LOC_Os09g03870.1 intron_variant ; MODIFIER silent_mutation Average:50.402; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0901967595 NA 3.16E-14 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901967595 NA 1.69E-12 Grain_width Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901967595 2.13E-06 NA mr1008 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
vg0901967595 2.34E-06 9.24E-11 mr1008 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
vg0901967595 4.06E-07 NA mr1009 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
vg0901967595 4.30E-07 2.49E-11 mr1009 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
vg0901967595 NA 7.28E-06 mr1014 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
vg0901967595 8.89E-06 NA mr1015 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
vg0901967595 6.09E-06 1.51E-07 mr1015 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
vg0901967595 NA 1.45E-07 mr1190 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
vg0901967595 NA 6.56E-06 mr1295 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
vg0901967595 NA 1.55E-09 mr1368 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
vg0901967595 NA 5.17E-06 mr1445 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
vg0901967595 NA 2.04E-07 mr1125_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
vg0901967595 NA 1.49E-10 mr1552_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
vg0901967595 NA 4.46E-08 mr1578_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