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Detailed information for vg0605381468:

Variant ID: vg0605381468 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5381468
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


AAATACAGGACAAGCATACAACACCCCTAAGGAATGGGTCTTCTAAACGACGCCTCCAAGGAGGAAACGACGCCAATAGCACCGCCGCCGCCCGTCCTAG[G/T]
ACAGGACATGGTTTTCACCTGAAGAACTCACTGAGAGAGGAAAGAAAATACAGCAACGCCCCAAGGGAAAAACGGCGCCCGCAGGCATCGCCGTTGCCAG

Reverse complement sequence

CTGGCAACGGCGATGCCTGCGGGCGCCGTTTTTCCCTTGGGGCGTTGCTGTATTTTCTTTCCTCTCTCAGTGAGTTCTTCAGGTGAAAACCATGTCCTGT[C/A]
CTAGGACGGGCGGCGGCGGTGCTATTGGCGTCGTTTCCTCCTTGGAGGCGTCGTTTAGAAGACCCATTCCTTAGGGGTGTTGTATGCTTGTCCTGTATTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 1.70% 0.11% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 94.80% 5.00% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 90.00% 9.50% 0.52% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0605381468 G -> T LOC_Os06g10460.1 upstream_gene_variant ; 4932.0bp to feature; MODIFIER silent_mutation Average:64.336; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N
vg0605381468 G -> T LOC_Os06g10450.1 downstream_gene_variant ; 4686.0bp to feature; MODIFIER silent_mutation Average:64.336; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N
vg0605381468 G -> T LOC_Os06g10450-LOC_Os06g10460 intergenic_region ; MODIFIER silent_mutation Average:64.336; most accessible tissue: Minghui63 panicle, score: 84.005 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605381468 NA 2.60E-06 mr1072 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
vg0605381468 NA 6.45E-06 mr1161 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
vg0605381468 NA 2.43E-06 mr1183 Jap_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
vg0605381468 7.76E-07 5.24E-07 mr1318 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
vg0605381468 NA 6.65E-06 mr1503 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
vg0605381468 NA 7.27E-06 mr1763 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
vg0605381468 NA 3.05E-06 mr1775 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