\

Search for Variation information by Variation ID:

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

Detailed information for vg1019343930:

Variant ID: vg1019343930 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19343930
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GATCTACTTAGTACAACAATTCCAATATACCTGGTGGAACATCGTGTAACATTTAAAAATAATTCAATAATTAGGTAAAAAAAATTTCGTCGGAATATAT[C/T]
CATGTGTGGTCTTGTTTTGAAGATTTAATTGCAACGAATTTAATGATGTAATCGGATCATAATTTAAATAAGTAATTTAAGAGAAAAATCAGTTTAAAAT

Reverse complement sequence

ATTTTAAACTGATTTTTCTCTTAAATTACTTATTTAAATTATGATCCGATTACATCATTAAATTCGTTGCAATTAAATCTTCAAAACAAGACCACACATG[G/A]
ATATATTCCGACGAAATTTTTTTTACCTAATTATTGAATTATTTTTAAATGTTACACGATGTTCCACCAGGTATATTGGAATTGTTGTACTAAGTAGATC

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 59.30% 15.50% 0.80% 24.42% NA
All Indica  2759 45.40% 14.00% 1.20% 39.40% NA
All Japonica  1512 95.20% 1.80% 0.07% 2.91% NA
Aus  269 8.60% 89.60% 0.37% 1.49% NA
Indica I  595 76.30% 0.00% 1.01% 22.69% NA
Indica II  465 21.90% 44.70% 0.86% 32.47% NA
Indica III  913 36.70% 3.30% 1.64% 58.38% NA
Indica Intermediate  786 46.10% 18.80% 1.02% 34.10% NA
Temperate Japonica  767 97.80% 1.80% 0.13% 0.26% NA
Tropical Japonica  504 91.90% 0.40% 0.00% 7.74% NA
Japonica Intermediate  241 94.20% 4.60% 0.00% 1.24% NA
VI/Aromatic  96 36.50% 60.40% 2.08% 1.04% NA
Intermediate  90 55.60% 23.30% 1.11% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1019343930 C -> T LOC_Os10g36180.1 upstream_gene_variant ; 2404.0bp to feature; MODIFIER silent_mutation Average:41.571; most accessible tissue: Callus, score: 96.286 N N N N
vg1019343930 C -> T LOC_Os10g36170-LOC_Os10g36180 intergenic_region ; MODIFIER silent_mutation Average:41.571; most accessible tissue: Callus, score: 96.286 N N N N
vg1019343930 C -> DEL N N silent_mutation Average:41.571; most accessible tissue: Callus, score: 96.286 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019343930 NA 5.94E-06 mr1038 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
vg1019343930 NA 3.56E-08 mr1180 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
vg1019343930 NA 1.26E-12 mr1231 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
vg1019343930 NA 2.14E-13 mr1232 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
vg1019343930 NA 2.04E-07 mr1262 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
vg1019343930 NA 4.12E-07 mr1319 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
vg1019343930 NA 3.10E-06 mr1373 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
vg1019343930 NA 1.07E-20 mr1557 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
vg1019343930 NA 1.05E-06 mr1633 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
vg1019343930 NA 4.02E-09 mr1659 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
vg1019343930 NA 1.17E-07 mr1735 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
vg1019343930 NA 1.51E-06 mr1906 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
vg1019343930 NA 2.68E-14 mr1909 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
vg1019343930 NA 3.76E-13 mr1921 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
vg1019343930 NA 2.15E-09 mr1232_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