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Detailed information for vg0431086715:

Variant ID: vg0431086715 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31086715
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.08, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAATTCCTATGGAATGGACAATCCTATAGAGATTTTGGAGGAAATTTAGCAAGAGCTTCAATCTCTTGCTAACTTTCCTTTGAGTCTATCTCTCTCAT[C/T]
CAATTCCTGTGTTTTTCCTATGGTTCAATCAAACGGTTATTCCTGTGTTTTTCCTGCGTTTTGCAATCCTCTGTTTTACACTTACATTCCTATCAAAATC

Reverse complement sequence

GATTTTGATAGGAATGTAAGTGTAAAACAGAGGATTGCAAAACGCAGGAAAAACACAGGAATAACCGTTTGATTGAACCATAGGAAAAACACAGGAATTG[G/A]
ATGAGAGAGATAGACTCAAAGGAAAGTTAGCAAGAGATTGAAGCTCTTGCTAAATTTCCTCCAAAATCTCTATAGGATTGTCCATTCCATAGGAATTTCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.60% 17.70% 3.00% 2.71% NA
All Indica  2759 78.90% 12.10% 5.00% 3.95% NA
All Japonica  1512 77.00% 22.80% 0.20% 0.07% NA
Aus  269 69.10% 30.90% 0.00% 0.00% NA
Indica I  595 82.00% 13.10% 4.87% 0.00% NA
Indica II  465 88.60% 6.70% 0.65% 4.09% NA
Indica III  913 68.20% 16.60% 8.98% 6.13% NA
Indica Intermediate  786 83.30% 9.30% 3.05% 4.33% NA
Temperate Japonica  767 72.00% 27.60% 0.39% 0.00% NA
Tropical Japonica  504 96.40% 3.60% 0.00% 0.00% NA
Japonica Intermediate  241 52.30% 47.30% 0.00% 0.41% NA
VI/Aromatic  96 25.00% 59.40% 0.00% 15.62% NA
Intermediate  90 75.60% 20.00% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431086715 C -> DEL N N silent_mutation Average:34.084; most accessible tissue: Zhenshan97 root, score: 55.432 N N N N
vg0431086715 C -> T LOC_Os04g52320.1 upstream_gene_variant ; 2436.0bp to feature; MODIFIER silent_mutation Average:34.084; most accessible tissue: Zhenshan97 root, score: 55.432 N N N N
vg0431086715 C -> T LOC_Os04g52310-LOC_Os04g52320 intergenic_region ; MODIFIER silent_mutation Average:34.084; most accessible tissue: Zhenshan97 root, score: 55.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431086715 4.05E-06 4.05E-06 mr1836 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
vg0431086715 NA 2.79E-07 mr1071_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
vg0431086715 NA 9.50E-07 mr1080_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
vg0431086715 NA 3.36E-08 mr1100_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
vg0431086715 NA 2.27E-07 mr1203_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
vg0431086715 NA 1.09E-08 mr1613_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
vg0431086715 NA 4.15E-08 mr1913_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