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Detailed information for vg0700266518:

Variant ID: vg0700266518 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 266518
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: 117. )

Flanking Sequence (100 bp) in Reference Genome:


GGATAGTATAGGGGGACGAAAATATTGCGTAACGTGGGATAATTGTATTGAGCCTCAGGGGGGCAAAATATATAATAGTACATGGGGAGGAAATAAGGAA[G/A]
GATTACAGATATGGAAGAAATCCACACAAATCAATCAAATCCTAATATGACTCTAACTACCATATACTTTAACATTTTTTAACACCCCCATCTGCTCCTA

Reverse complement sequence

TAGGAGCAGATGGGGGTGTTAAAAAATGTTAAAGTATATGGTAGTTAGAGTCATATTAGGATTTGATTGATTTGTGTGGATTTCTTCCATATCTGTAATC[C/T]
TTCCTTATTTCCTCCCCATGTACTATTATATATTTTGCCCCCCTGAGGCTCAATACAATTATCCCACGTTACGCAATATTTTCGTCCCCCTATACTATCC

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 63.60% 35.90% 0.42% 0.06% NA
All Indica  2759 41.10% 58.30% 0.51% 0.11% NA
All Japonica  1512 97.80% 2.10% 0.20% 0.00% NA
Aus  269 88.10% 11.90% 0.00% 0.00% NA
Indica I  595 57.10% 42.20% 0.67% 0.00% NA
Indica II  465 52.90% 46.50% 0.43% 0.22% NA
Indica III  913 30.10% 69.70% 0.22% 0.00% NA
Indica Intermediate  786 34.60% 64.40% 0.76% 0.25% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 94.80% 5.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 74.40% 23.30% 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
vg0700266518 G -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700266518 G -> A LOC_Os07g01410.1 downstream_gene_variant ; 3774.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700266518 G -> A LOC_Os07g01420.1 downstream_gene_variant ; 868.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700266518 G -> A LOC_Os07g01420-LOC_Os07g01430 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0700266518 3.96E-08 NA mr1158 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
vg0700266518 5.28E-08 1.74E-10 mr1158 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
vg0700266518 NA 1.95E-07 mr1168 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
vg0700266518 NA 1.85E-11 mr1316 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
vg0700266518 NA 1.99E-07 mr1316 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
vg0700266518 NA 1.58E-06 mr1352 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
vg0700266518 1.15E-08 NA mr1383 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
vg0700266518 3.20E-07 5.10E-10 mr1383 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
vg0700266518 NA 4.55E-07 mr1158_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
vg0700266518 NA 6.61E-09 mr1158_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
vg0700266518 NA 6.79E-08 mr1168_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
vg0700266518 NA 4.72E-07 mr1925_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