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Detailed information for vg0432977710:

Variant ID: vg0432977710 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32977710
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.81, C: 0.19, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGGATTACTTTCGCATTCACAAGCTTCCGAATGTAGAGCTTCAGATTTTTTAATACTTACTTTGTCCTATTTTAAGCGCAGCCATGAGTTTCCGTGT[C/T]
TAACTTTAATTGTCGGTCTTATTTAAAAAAAAATCATGATTAATATTTTATTGTTATTAGATGATAAAACATGAATAATACTTACTTATGCTTTTTAATT

Reverse complement sequence

AATTAAAAAGCATAAGTAAGTATTATTCATGTTTTATCATCTAATAACAATAAAATATTAATCATGATTTTTTTTTAAATAAGACCGACAATTAAAGTTA[G/A]
ACACGGAAACTCATGGCTGCGCTTAAAATAGGACAAAGTAAGTATTAAAAAATCTGAAGCTCTACATTCGGAAGCTTGTGAATGCGAAAGTAATCCAAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.70% 31.00% 0.25% 0.00% NA
All Indica  2759 95.80% 3.90% 0.29% 0.00% NA
All Japonica  1512 22.60% 77.30% 0.07% 0.00% NA
Aus  269 53.20% 46.50% 0.37% 0.00% NA
Indica I  595 93.90% 5.70% 0.34% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 94.70% 5.10% 0.11% 0.00% NA
Indica Intermediate  786 97.10% 2.40% 0.51% 0.00% NA
Temperate Japonica  767 14.30% 85.70% 0.00% 0.00% NA
Tropical Japonica  504 37.70% 62.30% 0.00% 0.00% NA
Japonica Intermediate  241 17.40% 82.20% 0.41% 0.00% NA
VI/Aromatic  96 67.70% 31.20% 1.04% 0.00% NA
Intermediate  90 61.10% 37.80% 1.11% 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
vg0432977710 C -> T LOC_Os04g55450.1 upstream_gene_variant ; 2186.0bp to feature; MODIFIER silent_mutation Average:46.048; most accessible tissue: Callus, score: 90.618 N N N N
vg0432977710 C -> T LOC_Os04g55440.1 downstream_gene_variant ; 18.0bp to feature; MODIFIER silent_mutation Average:46.048; most accessible tissue: Callus, score: 90.618 N N N N
vg0432977710 C -> T LOC_Os04g55440-LOC_Os04g55450 intergenic_region ; MODIFIER silent_mutation Average:46.048; most accessible tissue: Callus, score: 90.618 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432977710 NA 1.36E-06 mr1045_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
vg0432977710 NA 5.54E-08 mr1063_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
vg0432977710 4.59E-06 8.20E-10 mr1072_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
vg0432977710 NA 1.19E-07 mr1075_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
vg0432977710 NA 2.23E-07 mr1077_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
vg0432977710 NA 1.21E-07 mr1097_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
vg0432977710 NA 7.47E-06 mr1252_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
vg0432977710 6.49E-07 6.02E-10 mr1295_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
vg0432977710 NA 1.78E-06 mr1441_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
vg0432977710 NA 6.17E-06 mr1567_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
vg0432977710 NA 4.45E-06 mr1617_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
vg0432977710 NA 9.06E-08 mr1783_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
vg0432977710 NA 1.65E-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