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Detailed information for vg0404016698:

Variant ID: vg0404016698 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4016698
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, T: 0.00, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTACTCTAAGGTTTTAATATGTGGAGCTCGGCAGGGATCAAACATGGAATACATGCATTCACATTTATTACTAAGTCAAAAGCTTAGACTAAAGCAGA[A/T]
AACTAAACATACTCAAGATCAAGATCATGCAATGTGTGTGTGATATATGGTGGAAATGGTTTATGAAGGAAAATAAAGAAAATGCTTCTCCTTTGTGCCT

Reverse complement sequence

AGGCACAAAGGAGAAGCATTTTCTTTATTTTCCTTCATAAACCATTTCCACCATATATCACACACACATTGCATGATCTTGATCTTGAGTATGTTTAGTT[T/A]
TCTGCTTTAGTCTAAGCTTTTGACTTAGTAATAAATGTGAATGCATGTATTCCATGTTTGATCCCTGCCGAGCTCCACATATTAAAACCTTAGAGTAGGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.30% 1.10% 1.04% 39.61% NA
All Indica  2759 35.90% 1.80% 1.52% 60.78% NA
All Japonica  1512 95.20% 0.00% 0.26% 4.56% NA
Aus  269 63.20% 0.00% 0.74% 36.06% NA
Indica I  595 53.60% 0.00% 1.51% 44.87% NA
Indica II  465 48.80% 5.20% 2.37% 43.66% NA
Indica III  913 15.20% 1.20% 1.86% 81.71% NA
Indica Intermediate  786 38.80% 1.90% 0.64% 58.65% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 88.50% 0.00% 0.60% 10.91% NA
Japonica Intermediate  241 94.20% 0.00% 0.41% 5.39% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 68.90% 0.00% 1.11% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0404016698 A -> DEL N N silent_mutation Average:19.862; most accessible tissue: Zhenshan97 young leaf, score: 44.598 N N N N
vg0404016698 A -> T LOC_Os04g07540.1 downstream_gene_variant ; 4153.0bp to feature; MODIFIER silent_mutation Average:19.862; most accessible tissue: Zhenshan97 young leaf, score: 44.598 N N N N
vg0404016698 A -> T LOC_Os04g07550.1 downstream_gene_variant ; 2276.0bp to feature; MODIFIER silent_mutation Average:19.862; most accessible tissue: Zhenshan97 young leaf, score: 44.598 N N N N
vg0404016698 A -> T LOC_Os04g07560.1 downstream_gene_variant ; 4039.0bp to feature; MODIFIER silent_mutation Average:19.862; most accessible tissue: Zhenshan97 young leaf, score: 44.598 N N N N
vg0404016698 A -> T LOC_Os04g07540-LOC_Os04g07550 intergenic_region ; MODIFIER silent_mutation Average:19.862; most accessible tissue: Zhenshan97 young leaf, score: 44.598 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404016698 NA 1.62E-08 mr1109 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
vg0404016698 3.94E-06 NA mr1129 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
vg0404016698 5.50E-06 1.39E-09 mr1129 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
vg0404016698 NA 4.51E-06 mr1251 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
vg0404016698 NA 8.78E-19 mr1255 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
vg0404016698 NA 9.03E-08 mr1255 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
vg0404016698 NA 3.88E-08 mr1257 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
vg0404016698 NA 1.54E-07 mr1423 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
vg0404016698 8.14E-07 NA mr1435 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
vg0404016698 4.06E-07 3.88E-08 mr1435 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
vg0404016698 NA 3.44E-10 mr1109_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
vg0404016698 4.17E-06 7.02E-11 mr1129_2 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
vg0404016698 NA 2.74E-07 mr1236_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
vg0404016698 NA 4.01E-08 mr1236_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
vg0404016698 7.24E-06 2.43E-08 mr1251_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
vg0404016698 NA 2.49E-06 mr1253_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
vg0404016698 NA 1.94E-20 mr1255_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
vg0404016698 NA 6.92E-09 mr1255_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
vg0404016698 NA 2.32E-10 mr1257_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
vg0404016698 NA 8.49E-07 mr1423_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
vg0404016698 7.46E-06 2.63E-08 mr1435_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
vg0404016698 6.10E-06 4.64E-08 mr1599_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