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Detailed information for vg0420998565:

Variant ID: vg0420998565 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20998565
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAATTTATACAAGTATTTGTAAAATCAAGGAGTTGATTTAGATTTTATGATGAAAATATTGGTGGTTTGCTAATGTTAATTTGGAGATTTTATAGATG[G/A]
TTGATTTTGTGAAGTGTACAGTTTCGATTGACCCTGGCGGTCAGACCGGTCGTGTGCCGCCAGTCAGACCGCAGGTGTTGCGGCGGTCAGACCGGTTGGC

Reverse complement sequence

GCCAACCGGTCTGACCGCCGCAACACCTGCGGTCTGACTGGCGGCACACGACCGGTCTGACCGCCAGGGTCAATCGAAACTGTACACTTCACAAAATCAA[C/T]
CATCTATAAAATCTCCAAATTAACATTAGCAAACCACCAATATTTTCATCATAAAATCTAAATCAACTCCTTGATTTTACAAATACTTGTATAAATTAAT

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 92.40% 7.50% 0.04% 0.00% NA
All Indica  2759 94.80% 5.10% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 27.50% 72.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 91.10% 8.70% 0.22% 0.00% NA
Indica Intermediate  786 93.10% 6.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 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
vg0420998565 G -> A LOC_Os04g34720.1 upstream_gene_variant ; 3157.0bp to feature; MODIFIER silent_mutation Average:24.984; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N
vg0420998565 G -> A LOC_Os04g34720.2 upstream_gene_variant ; 3157.0bp to feature; MODIFIER silent_mutation Average:24.984; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N
vg0420998565 G -> A LOC_Os04g34699.1 downstream_gene_variant ; 3543.0bp to feature; MODIFIER silent_mutation Average:24.984; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N
vg0420998565 G -> A LOC_Os04g34699-LOC_Os04g34720 intergenic_region ; MODIFIER silent_mutation Average:24.984; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420998565 2.26E-06 NA mr1114 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
vg0420998565 8.30E-08 NA mr1123 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
vg0420998565 NA 6.76E-06 mr1230 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
vg0420998565 1.54E-06 NA mr1242 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
vg0420998565 5.03E-06 NA mr1247 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
vg0420998565 1.82E-06 NA mr1496 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
vg0420998565 1.26E-06 NA mr1114_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
vg0420998565 7.33E-06 NA mr1117_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
vg0420998565 4.65E-06 NA mr1119_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
vg0420998565 1.27E-07 NA mr1123_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
vg0420998565 6.82E-08 NA mr1242_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
vg0420998565 9.09E-06 NA mr1247_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
vg0420998565 4.01E-07 NA mr1496_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