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Detailed information for vg0811482287:

Variant ID: vg0811482287 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 11482287
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ATACAAGTAAATAGAATCATCAATTTAGATTAACTAGGATATATGATAACCAGTAGCTGCAAAAGATAGATTAGAACATCTAAAACGACATCCTAATCCG[C/T]
CAATGCAAACCACTGTGACATGCCATACCTCTTGCCGGAAAATCGAAGCCGATGCCCCAACTTGAAGCAAGAACTCGTCGAGAAAGTCGAAAAGTAAAAA

Reverse complement sequence

TTTTTACTTTTCGACTTTCTCGACGAGTTCTTGCTTCAAGTTGGGGCATCGGCTTCGATTTTCCGGCAAGAGGTATGGCATGTCACAGTGGTTTGCATTG[G/A]
CGGATTAGGATGTCGTTTTAGATGTTCTAATCTATCTTTTGCAGCTACTGGTTATCATATATCCTAGTTAATCTAAATTGATGATTCTATTTACTTGTAT

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 90.80% 7.30% 1.86% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 71.60% 22.70% 5.69% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 50.80% 38.30% 10.82% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 79.70% 19.10% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0811482287 C -> T LOC_Os08g19200.1 upstream_gene_variant ; 4718.0bp to feature; MODIFIER silent_mutation Average:43.235; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0811482287 C -> T LOC_Os08g19210.1 upstream_gene_variant ; 5000.0bp to feature; MODIFIER silent_mutation Average:43.235; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0811482287 C -> T LOC_Os08g19200-LOC_Os08g19210 intergenic_region ; MODIFIER silent_mutation Average:43.235; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0811482287 3.77E-06 NA mr1071 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
vg0811482287 NA 7.38E-07 mr1129 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
vg0811482287 2.63E-06 NA mr1137 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
vg0811482287 9.57E-08 NA mr1140 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
vg0811482287 NA 1.70E-06 mr1252 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
vg0811482287 NA 9.43E-06 mr1277 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
vg0811482287 2.97E-07 NA mr1618 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
vg0811482287 NA 2.28E-06 mr1708 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