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Detailed information for vg0233324652:

Variant ID: vg0233324652 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 33324652
Reference Allele: AAlternative Allele: T,AT
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.02, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


TCATCTGTGTATTTGAATCAAGTGTTCATTACAAACTGATGGGGATTAAAGGAGGAAAAAGGAAAATAATTTCTGCAAAATGTCGAATAATACCCAAAAA[A/T,AT]
ATATATATAGTAGAAACCATTTCATTCCCCAAAATTAACCAACAATGTATAACGCATGTCCAATTCCAATCGATGGATCCTCTGTTTCTAGTTTATCTTG

Reverse complement sequence

CAAGATAAACTAGAAACAGAGGATCCATCGATTGGAATTGGACATGCGTTATACATTGTTGGTTAATTTTGGGGAATGAAATGGTTTCTACTATATATAT[T/A,AT]
TTTTTGGGTATTATTCGACATTTTGCAGAAATTATTTTCCTTTTTCCTCCTTTAATCCCCATCAGTTTGTAATGAACACTTGATTCAAATACACAGATGA

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 56.10% 43.90% 0.02% 0.00% AT: 0.02%
All Indica  2759 92.40% 7.60% 0.00% 0.00% AT: 0.04%
All Japonica  1512 0.70% 99.20% 0.07% 0.00% NA
Aus  269 22.70% 77.30% 0.00% 0.00% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 90.80% 9.10% 0.00% 0.00% AT: 0.11%
Indica Intermediate  786 89.10% 10.90% 0.00% 0.00% NA
Temperate Japonica  767 1.00% 98.80% 0.13% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 32.20% 67.80% 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
vg0233324652 A -> T LOC_Os02g54370.1 3_prime_UTR_variant ; 88.0bp to feature; MODIFIER silent_mutation Average:57.107; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0233324652 A -> T LOC_Os02g54350.1 upstream_gene_variant ; 4194.0bp to feature; MODIFIER silent_mutation Average:57.107; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0233324652 A -> T LOC_Os02g54360.1 upstream_gene_variant ; 2113.0bp to feature; MODIFIER silent_mutation Average:57.107; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0233324652 A -> AT LOC_Os02g54370.1 3_prime_UTR_variant ; 87.0bp to feature; MODIFIER silent_mutation Average:57.107; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0233324652 A -> AT LOC_Os02g54350.1 upstream_gene_variant ; 4195.0bp to feature; MODIFIER silent_mutation Average:57.107; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg0233324652 A -> AT LOC_Os02g54360.1 upstream_gene_variant ; 2114.0bp to feature; MODIFIER silent_mutation Average:57.107; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233324652 NA 1.11E-08 mr1047 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
vg0233324652 NA 2.63E-15 mr1164 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
vg0233324652 NA 6.35E-10 mr1379 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
vg0233324652 NA 5.15E-08 mr1559 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
vg0233324652 NA 1.14E-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
vg0233324652 NA 3.85E-17 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
vg0233324652 NA 2.68E-08 mr1084_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
vg0233324652 NA 6.35E-15 mr1133_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
vg0233324652 NA 2.39E-15 mr1148_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
vg0233324652 NA 3.96E-10 mr1198_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
vg0233324652 NA 1.85E-07 mr1205_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
vg0233324652 NA 2.12E-06 mr1227_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
vg0233324652 NA 2.30E-11 mr1228_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
vg0233324652 NA 1.01E-06 mr1548_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
vg0233324652 NA 1.73E-57 mr1558_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
vg0233324652 NA 5.36E-33 mr1571_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
vg0233324652 NA 7.64E-14 mr1575_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
vg0233324652 NA 2.27E-14 mr1579_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
vg0233324652 NA 9.03E-34 mr1580_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
vg0233324652 NA 9.60E-10 mr1646_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
vg0233324652 NA 7.37E-06 mr1677_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
vg0233324652 NA 2.07E-10 mr1680_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
vg0233324652 NA 4.42E-15 mr1686_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
vg0233324652 NA 1.18E-22 mr1698_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
vg0233324652 NA 2.51E-33 mr1825_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
vg0233324652 NA 7.50E-22 mr1922_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
vg0233324652 NA 2.08E-22 mr1924_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
vg0233324652 NA 1.43E-09 mr1940_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
vg0233324652 NA 5.77E-15 mr1950_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