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Detailed information for vg1117464587:

Variant ID: vg1117464587 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17464587
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TAAAGTTGTTTTTAAAAAAATCATATTAATCCATTAAAATAGTAAATACTTAATTAATCATAAGAAAATATGTCGTTCCATTTTACGTGCCGAACAACTC[C/T]
GTACACCAATCTGAAGCATAGAACATTGGAGACAAGTCGGAGTAATAAGAGAAGTATATAAGAGGATATGTGGATAAAAGGAGAGAGGAAATAGGTGATT

Reverse complement sequence

AATCACCTATTTCCTCTCTCCTTTTATCCACATATCCTCTTATATACTTCTCTTATTACTCCGACTTGTCTCCAATGTTCTATGCTTCAGATTGGTGTAC[G/A]
GAGTTGTTCGGCACGTAAAATGGAACGACATATTTTCTTATGATTAATTAAGTATTTACTATTTTAATGGATTAATATGATTTTTTTAAAAACAACTTTA

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 86.90% 10.50% 0.15% 2.48% NA
All Indica  2759 82.60% 17.30% 0.07% 0.00% NA
All Japonica  1512 91.70% 0.40% 0.33% 7.61% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 77.50% 22.40% 0.17% 0.00% NA
Indica II  465 77.20% 22.80% 0.00% 0.00% NA
Indica III  913 85.90% 14.10% 0.00% 0.00% NA
Indica Intermediate  786 86.00% 13.90% 0.13% 0.00% NA
Temperate Japonica  767 84.10% 0.30% 0.65% 14.99% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 84.40% 13.30% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117464587 C -> T LOC_Os11g30020.1 upstream_gene_variant ; 472.0bp to feature; MODIFIER silent_mutation Average:44.294; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1117464587 C -> T LOC_Os11g30020-LOC_Os11g30030 intergenic_region ; MODIFIER silent_mutation Average:44.294; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg1117464587 C -> DEL N N silent_mutation Average:44.294; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117464587 2.65E-06 2.65E-06 mr1019 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
vg1117464587 NA 9.57E-06 mr1038 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
vg1117464587 NA 4.54E-08 mr1053 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
vg1117464587 NA 3.23E-06 mr1060 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
vg1117464587 NA 4.65E-06 mr1060 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
vg1117464587 NA 6.68E-06 mr1287 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
vg1117464587 2.29E-06 NA mr1303 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
vg1117464587 6.81E-07 6.80E-07 mr1303 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
vg1117464587 NA 6.36E-06 mr1372 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
vg1117464587 NA 2.96E-06 mr1432 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
vg1117464587 NA 9.86E-06 mr1854 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
vg1117464587 NA 5.10E-06 mr1941 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
vg1117464587 NA 4.21E-07 mr1951 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