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Detailed information for vg0403206873:

Variant ID: vg0403206873 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3206873
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


TACTGCTGCATCTGCTGCATCATGGCTGCCATCATCTGAGTCTGATGTGCCATAACTTGGGCCAGTGTCGGATTTTCGGGAAGTGGTGGCGGACCATTGC[C/T]
GGAATCACTGCTGGGGTGCACACCATCGGCGCGTTCTTCACCGTTGCTGCCCTCGCCTGTCGTGCGGGTGCCAGTCCTGGTGTAGACCATCTGGAGGAAG

Reverse complement sequence

CTTCCTCCAGATGGTCTACACCAGGACTGGCACCCGCACGACAGGCGAGGGCAGCAACGGTGAAGAACGCGCCGATGGTGTGCACCCCAGCAGTGATTCC[G/A]
GCAATGGTCCGCCACCACTTCCCGAAAATCCGACACTGGCCCAAGTTATGGCACATCAGACTCAGATGATGGCAGCCATGATGCAGCAGATGCAGCAGTA

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 82.70% 13.60% 2.88% 0.78% NA
All Indica  2759 73.60% 22.60% 3.26% 0.54% NA
All Japonica  1512 94.80% 0.90% 2.84% 1.46% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 52.40% 44.40% 3.03% 0.17% NA
Indica II  465 81.30% 13.10% 4.73% 0.86% NA
Indica III  913 84.30% 13.70% 1.64% 0.33% NA
Indica Intermediate  786 72.60% 22.00% 4.45% 0.89% NA
Temperate Japonica  767 98.00% 0.70% 1.17% 0.13% NA
Tropical Japonica  504 90.70% 0.40% 5.36% 3.57% NA
Japonica Intermediate  241 93.40% 2.50% 2.90% 1.24% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg0403206873 C -> DEL N N silent_mutation Average:25.055; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0403206873 C -> T LOC_Os04g06144.1 upstream_gene_variant ; 792.0bp to feature; MODIFIER silent_mutation Average:25.055; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0403206873 C -> T LOC_Os04g06160.1 downstream_gene_variant ; 339.0bp to feature; MODIFIER silent_mutation Average:25.055; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0403206873 C -> T LOC_Os04g06144-LOC_Os04g06160 intergenic_region ; MODIFIER silent_mutation Average:25.055; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403206873 2.02E-08 3.05E-40 mr1026 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
vg0403206873 2.21E-09 6.63E-24 mr1026 Ind_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
vg0403206873 NA 7.50E-07 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
vg0403206873 NA 3.94E-06 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
vg0403206873 NA 3.27E-18 mr1118 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
vg0403206873 2.98E-07 2.82E-20 mr1118 Ind_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
vg0403206873 NA 1.41E-06 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
vg0403206873 2.31E-07 6.31E-37 mr1161 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
vg0403206873 2.08E-08 9.09E-22 mr1161 Ind_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
vg0403206873 NA 8.20E-06 mr1242 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
vg0403206873 NA 3.76E-06 mr1261 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
vg0403206873 NA 8.66E-23 mr1495 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
vg0403206873 1.81E-06 3.18E-23 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
vg0403206873 NA 1.30E-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
vg0403206873 NA 6.29E-09 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
vg0403206873 NA 3.75E-06 mr1113_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
vg0403206873 NA 1.03E-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
vg0403206873 NA 4.03E-21 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
vg0403206873 NA 4.33E-24 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
vg0403206873 NA 2.65E-09 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
vg0403206873 4.77E-06 3.79E-35 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
vg0403206873 NA 7.57E-19 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
vg0403206873 NA 8.24E-07 mr1212_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
vg0403206873 NA 4.95E-08 mr1233_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
vg0403206873 NA 1.83E-07 mr1247_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
vg0403206873 NA 7.47E-29 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
vg0403206873 NA 9.62E-25 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
vg0403206873 NA 2.94E-09 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
vg0403206873 NA 4.54E-12 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
vg0403206873 NA 5.73E-08 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