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Detailed information for vg0609452459:

Variant ID: vg0609452459 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9452459
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:


GGGTCTCCATGTTGTCGTGGATTAAGAATTAGGCAAAATTTGTTACAGGACACTTAAAGATTGTGTTCTTTACTGTGAGACACTCGAAGATCGTGTGTTT[G/A]
CTCGTGGACACTGTAAAAAAGTGGTAATTAGCTGCTAGACACTCCTCCCATTATTTTATTATTTTCGATGAAAACGGAGAGAGAAACTTTGGTTAAAGAC

Reverse complement sequence

GTCTTTAACCAAAGTTTCTCTCTCCGTTTTCATCGAAAATAATAAAATAATGGGAGGAGTGTCTAGCAGCTAATTACCACTTTTTTACAGTGTCCACGAG[C/T]
AAACACACGATCTTCGAGTGTCTCACAGTAAAGAACACAATCTTTAAGTGTCCTGTAACAAATTTTGCCTAATTCTTAATCCACGACAACATGGAGACCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.70% 15.80% 0.19% 39.29% NA
All Indica  2759 73.80% 10.10% 0.11% 16.02% NA
All Japonica  1512 2.10% 29.60% 0.13% 68.19% NA
Aus  269 1.90% 3.70% 0.74% 93.68% NA
Indica I  595 82.20% 4.90% 0.00% 12.94% NA
Indica II  465 82.40% 1.50% 0.00% 16.13% NA
Indica III  913 61.30% 21.00% 0.33% 17.31% NA
Indica Intermediate  786 76.80% 6.40% 0.00% 16.79% NA
Temperate Japonica  767 1.80% 54.60% 0.13% 43.42% NA
Tropical Japonica  504 2.00% 1.20% 0.20% 96.63% NA
Japonica Intermediate  241 3.30% 9.10% 0.00% 87.55% NA
VI/Aromatic  96 4.20% 3.10% 0.00% 92.71% NA
Intermediate  90 38.90% 11.10% 2.22% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609452459 G -> A LOC_Os06g16470.1 upstream_gene_variant ; 4984.0bp to feature; MODIFIER silent_mutation Average:58.659; most accessible tissue: Callus, score: 68.986 N N N N
vg0609452459 G -> A LOC_Os06g16460-LOC_Os06g16470 intergenic_region ; MODIFIER silent_mutation Average:58.659; most accessible tissue: Callus, score: 68.986 N N N N
vg0609452459 G -> DEL N N silent_mutation Average:58.659; most accessible tissue: Callus, score: 68.986 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609452459 6.00E-06 NA mr1094 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
vg0609452459 5.50E-06 NA mr1096 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
vg0609452459 2.21E-06 NA mr1068_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
vg0609452459 3.08E-07 NA mr1087_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
vg0609452459 6.96E-07 NA mr1090_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
vg0609452459 NA 9.93E-08 mr1090_2 Jap_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
vg0609452459 1.33E-06 NA mr1091_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
vg0609452459 2.65E-06 NA mr1094_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
vg0609452459 NA 2.65E-06 mr1094_2 Jap_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
vg0609452459 5.93E-08 NA mr1096_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
vg0609452459 NA 1.20E-06 mr1096_2 Jap_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
vg0609452459 4.45E-06 NA mr1110_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
vg0609452459 2.63E-06 NA mr1121_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
vg0609452459 NA 1.21E-06 mr1211_2 Jap_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
vg0609452459 NA 1.51E-09 mr1570_2 Jap_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