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Detailed information for vg1008183244:

Variant ID: vg1008183244 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8183244
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGCTCTCTCATATTCTCTCAAGTTCAGTATAGTAGTCTTAAGCTAATGGAGTAGGAATAGAATAGAAATCAGAGTCCGGAAGCCTTCGGAAGAGTTCA[G/A]
GTATGGCTCTAGTAGCTTTCCTTTTCTCTTTTGTAAGCTCTGTACTTTTATTAGAATACTCTTTATACATTTATGGTATTGAAATACTTTCCGAGTATAT

Reverse complement sequence

ATATACTCGGAAAGTATTTCAATACCATAAATGTATAAAGAGTATTCTAATAAAAGTACAGAGCTTACAAAAGAGAAAAGGAAAGCTACTAGAGCCATAC[C/T]
TGAACTCTTCCGAAGGCTTCCGGACTCTGATTTCTATTCTATTCCTACTCCATTAGCTTAAGACTACTATACTGAACTTGAGAGAATATGAGAGAGCTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.20% 24.00% 0.36% 3.43% NA
All Indica  2759 64.80% 35.10% 0.04% 0.11% NA
All Japonica  1512 80.30% 9.30% 0.20% 10.19% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 13.60% 86.20% 0.17% 0.00% NA
Indica II  465 83.90% 15.90% 0.00% 0.22% NA
Indica III  913 84.70% 15.30% 0.00% 0.00% NA
Indica Intermediate  786 69.10% 30.70% 0.00% 0.25% NA
Temperate Japonica  767 78.50% 1.60% 0.26% 19.69% NA
Tropical Japonica  504 76.20% 23.60% 0.20% 0.00% NA
Japonica Intermediate  241 94.60% 4.10% 0.00% 1.24% NA
VI/Aromatic  96 80.20% 7.30% 12.50% 0.00% NA
Intermediate  90 74.40% 18.90% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1008183244 G -> A LOC_Os10g16410.1 downstream_gene_variant ; 2309.0bp to feature; MODIFIER silent_mutation Average:44.529; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1008183244 G -> A LOC_Os10g16410-LOC_Os10g16430 intergenic_region ; MODIFIER silent_mutation Average:44.529; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1008183244 G -> DEL N N silent_mutation Average:44.529; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008183244 NA 1.23E-33 mr1026 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
vg1008183244 2.04E-06 3.23E-20 mr1026 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
vg1008183244 NA 4.87E-08 mr1113 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
vg1008183244 NA 6.27E-08 mr1114 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
vg1008183244 8.43E-06 2.95E-07 mr1116 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
vg1008183244 6.87E-09 8.23E-21 mr1118 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
vg1008183244 NA 7.97E-07 mr1120 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
vg1008183244 5.55E-06 1.21E-18 mr1161 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
vg1008183244 7.45E-11 1.51E-26 mr1495 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
vg1008183244 NA 1.48E-09 mr1496 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
vg1008183244 NA 7.72E-07 mr1789 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
vg1008183244 5.06E-06 8.21E-12 mr1794 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
vg1008183244 NA 7.30E-06 mr1936 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
vg1008183244 NA 6.23E-06 mr1114_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
vg1008183244 NA 3.42E-17 mr1118_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
vg1008183244 6.15E-10 1.01E-27 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
vg1008183244 NA 5.60E-08 mr1120_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
vg1008183244 NA 4.79E-08 mr1123_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
vg1008183244 7.43E-09 1.94E-36 mr1161_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
vg1008183244 1.15E-08 1.12E-21 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
vg1008183244 6.08E-07 1.80E-24 mr1495_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
vg1008183244 1.26E-11 3.65E-31 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
vg1008183244 NA 1.23E-10 mr1496_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
vg1008183244 NA 3.50E-07 mr1531_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
vg1008183244 5.41E-07 NA mr1580_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
vg1008183244 NA 5.65E-15 mr1794_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
vg1008183244 3.13E-07 NA mr1825_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
vg1008183244 NA 1.07E-11 mr1936_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