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Detailed information for vg0232675158:

Variant ID: vg0232675158 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32675158
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCAATCCATCTCTGGCCCCCTACAGTTTCATGGTTTTAGATGTTCTAGTCCTCCATTTGTTCTATTCATTATATTTTTTGGCTAAATTAACGTAAATAT[A/G]
TAATCCCTTATATTCATAGACAGAGGGAGAAACTACTACACGTATATTCACAATATTTTTTTACAACATATAATTTAACTTGCATATTTGTGAAATCATA

Reverse complement sequence

TATGATTTCACAAATATGCAAGTTAAATTATATGTTGTAAAAAAATATTGTGAATATACGTGTAGTAGTTTCTCCCTCTGTCTATGAATATAAGGGATTA[T/C]
ATATTTACGTTAATTTAGCCAAAAAATATAATGAATAGAACAAATGGAGGACTAGAACATCTAAAACCATGAAACTGTAGGGGGCCAGAGATGGATTGGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.40% 8.20% 0.36% 0.00% NA
All Indica  2759 98.90% 1.10% 0.04% 0.00% NA
All Japonica  1512 77.40% 21.60% 0.93% 0.00% NA
Aus  269 91.40% 7.80% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 34.70% 62.70% 2.58% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0232675158 A -> G LOC_Os02g53380.1 upstream_gene_variant ; 1240.0bp to feature; MODIFIER silent_mutation Average:40.454; most accessible tissue: Zhenshan97 flower, score: 63.813 N N N N
vg0232675158 A -> G LOC_Os02g53384.1 upstream_gene_variant ; 3599.0bp to feature; MODIFIER silent_mutation Average:40.454; most accessible tissue: Zhenshan97 flower, score: 63.813 N N N N
vg0232675158 A -> G LOC_Os02g53380-LOC_Os02g53384 intergenic_region ; MODIFIER silent_mutation Average:40.454; most accessible tissue: Zhenshan97 flower, score: 63.813 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232675158 NA 2.99E-06 mr1443 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
vg0232675158 8.55E-07 8.55E-07 mr1050_2 Jap_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
vg0232675158 NA 4.79E-06 mr1194_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
vg0232675158 NA 7.09E-06 mr1295_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
vg0232675158 2.35E-06 1.17E-08 mr1498_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
vg0232675158 NA 3.25E-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
vg0232675158 NA 2.02E-06 mr1715_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
vg0232675158 NA 6.46E-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