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Detailed information for vg1008811441:

Variant ID: vg1008811441 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8811441
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: 200. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTGTCAAATCATAGAGCAATTAAGTTTAAAAGATCCGTCTCGCAAATTAGTTACAATCTGTGTAATTAGTTATTTTTTTAGCCTATATTTAATACTT[C/T]
ATATATGTGTTCAAACGTTCAACGGGACAGGGTGAAAATTTTTAAGGTGAGATCTAAATTGGGCCTGAGTAATGGCGACCTCTTAAACTAGTTAGGTGGT

Reverse complement sequence

ACCACCTAACTAGTTTAAGAGGTCGCCATTACTCAGGCCCAATTTAGATCTCACCTTAAAAATTTTCACCCTGTCCCGTTGAACGTTTGAACACATATAT[G/A]
AAGTATTAAATATAGGCTAAAAAAATAACTAATTACACAGATTGTAACTAATTTGCGAGACGGATCTTTTAAACTTAATTGCTCTATGATTTGACAATAT

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 63.60% 36.40% 0.02% 0.00% NA
All Indica  2759 61.90% 38.10% 0.04% 0.00% NA
All Japonica  1512 80.40% 19.60% 0.00% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 88.90% 10.90% 0.17% 0.00% NA
Indica II  465 40.90% 59.10% 0.00% 0.00% NA
Indica III  913 61.00% 39.00% 0.00% 0.00% NA
Indica Intermediate  786 55.00% 45.00% 0.00% 0.00% NA
Temperate Japonica  767 93.90% 6.10% 0.00% 0.00% NA
Tropical Japonica  504 56.30% 43.70% 0.00% 0.00% NA
Japonica Intermediate  241 88.00% 12.00% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg1008811441 C -> T LOC_Os10g17489.1 upstream_gene_variant ; 3801.0bp to feature; MODIFIER silent_mutation Average:43.164; most accessible tissue: Callus, score: 61.069 N N N N
vg1008811441 C -> T LOC_Os10g17470.1 downstream_gene_variant ; 2896.0bp to feature; MODIFIER silent_mutation Average:43.164; most accessible tissue: Callus, score: 61.069 N N N N
vg1008811441 C -> T LOC_Os10g17470-LOC_Os10g17489 intergenic_region ; MODIFIER silent_mutation Average:43.164; most accessible tissue: Callus, score: 61.069 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008811441 5.78E-06 NA mr1027 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
vg1008811441 8.32E-06 8.31E-06 mr1027 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
vg1008811441 NA 1.68E-08 mr1593 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
vg1008811441 NA 3.76E-14 mr1709 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
vg1008811441 NA 2.52E-12 mr1709 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
vg1008811441 1.61E-06 NA mr1027_2 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
vg1008811441 4.65E-06 2.35E-10 mr1027_2 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
vg1008811441 NA 2.22E-08 mr1170_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
vg1008811441 NA 8.46E-07 mr1580_2 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
vg1008811441 NA 7.47E-17 mr1709_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
vg1008811441 NA 2.53E-11 mr1709_2 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
vg1008811441 NA 7.15E-08 mr1817_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
vg1008811441 NA 3.60E-06 mr1825_2 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