Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1009475111:

Variant ID: vg1009475111 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9475111
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTTTTTAACGGCCTGTTTGGCGAGAGAAGGGAAGAGGAATGGGAGTTTGAAGGAGGGAGTTGATGGTGGGATTGATCATGGGAGTTACTTTTTTACT[C/T]
CCCATCCCTTGTTTGGTTTCACATCGAATTCCCTCCAAGTCTCATGAATTAACAGGCCTTCTCTAGGTAAGAGATTGGTGGGAATTGGACCCCTTAATTC

Reverse complement sequence

GAATTAAGGGGTCCAATTCCCACCAATCTCTTACCTAGAGAAGGCCTGTTAATTCATGAGACTTGGAGGGAATTCGATGTGAAACCAAACAAGGGATGGG[G/A]
AGTAAAAAAGTAACTCCCATGATCAATCCCACCATCAACTCCCTCCTTCAAACTCCCATTCCTCTTCCCTTCTCTCGCCAAACAGGCCGTTAAAAAATTT

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 30.60% 22.40% 0.83% 46.19% NA
All Indica  2759 34.70% 2.40% 1.34% 61.58% NA
All Japonica  1512 10.30% 63.70% 0.00% 25.99% NA
Aus  269 97.00% 0.40% 0.00% 2.60% NA
Indica I  595 72.30% 1.30% 1.51% 24.87% NA
Indica II  465 17.60% 2.80% 2.15% 77.42% NA
Indica III  913 18.20% 2.40% 0.44% 78.97% NA
Indica Intermediate  786 35.60% 2.80% 1.78% 59.80% NA
Temperate Japonica  767 1.80% 82.70% 0.00% 15.51% NA
Tropical Japonica  504 23.40% 43.80% 0.00% 32.74% NA
Japonica Intermediate  241 10.00% 44.80% 0.00% 45.23% NA
VI/Aromatic  96 43.80% 0.00% 0.00% 56.25% NA
Intermediate  90 33.30% 31.10% 2.22% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1009475111 C -> T LOC_Os10g18660-LOC_Os10g18670 intergenic_region ; MODIFIER silent_mutation Average:38.045; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N
vg1009475111 C -> DEL N N silent_mutation Average:38.045; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009475111 NA 3.93E-06 mr1096 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
vg1009475111 1.58E-06 NA mr1128 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
vg1009475111 NA 7.18E-07 mr1662 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
vg1009475111 NA 3.48E-06 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
vg1009475111 NA 1.62E-10 mr1118_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
vg1009475111 NA 1.65E-11 mr1161_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
vg1009475111 NA 5.77E-12 mr1495_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
vg1009475111 NA 1.69E-06 mr1662_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