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Detailed information for vg0405481249:

Variant ID: vg0405481249 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5481249
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTAACTCTTAGAAATTTTTCAACACATTCTAATCGTACTTCATTTTTTTTAGCATTGACAAGTCGCTCCGAACACATATATAGATGTTTATTATTTCT[G/A,T]
TAACACTAATAAAGCGTTATGGCTTATAATAGTATCCGATTGATCCAGACAATTTTCGTAAACAGAATACATCGATTCGGTAGTGTTGGATAATGTTGAA

Reverse complement sequence

TTCAACATTATCCAACACTACCGAATCGATGTATTCTGTTTACGAAAATTGTCTGGATCAATCGGATACTATTATAAGCCATAACGCTTTATTAGTGTTA[C/T,A]
AGAAATAATAAACATCTATATATGTGTTCGGAGCGACTTGTCAATGCTAAAAAAAATGAAGTACGATTAGAATGTGTTGAAAAATTTCTAAGAGTTAAAT

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 89.40% 10.20% 0.08% 0.00% T: 0.36%
All Indica  2759 98.80% 1.10% 0.07% 0.00% NA
All Japonica  1512 70.50% 28.40% 0.13% 0.00% T: 0.93%
Aus  269 99.60% 0.00% 0.00% 0.00% T: 0.37%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.30% 2.60% 0.11% 0.00% NA
Indica Intermediate  786 99.40% 0.50% 0.13% 0.00% NA
Temperate Japonica  767 66.10% 33.00% 0.00% 0.00% T: 0.91%
Tropical Japonica  504 70.80% 28.20% 0.20% 0.00% T: 0.79%
Japonica Intermediate  241 83.80% 14.50% 0.41% 0.00% T: 1.24%
VI/Aromatic  96 90.60% 8.30% 0.00% 0.00% T: 1.04%
Intermediate  90 85.60% 13.30% 0.00% 0.00% T: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405481249 G -> A LOC_Os04g10140.1 upstream_gene_variant ; 1531.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> A LOC_Os04g10160.1 upstream_gene_variant ; 3519.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> A LOC_Os04g10150.1 downstream_gene_variant ; 2192.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> A LOC_Os04g10140-LOC_Os04g10150 intergenic_region ; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> T LOC_Os04g10140.1 upstream_gene_variant ; 1531.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> T LOC_Os04g10160.1 upstream_gene_variant ; 3519.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> T LOC_Os04g10150.1 downstream_gene_variant ; 2192.0bp to feature; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N
vg0405481249 G -> T LOC_Os04g10140-LOC_Os04g10150 intergenic_region ; MODIFIER silent_mutation Average:57.906; most accessible tissue: Callus, score: 84.387 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405481249 8.56E-07 NA mr1035 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
vg0405481249 NA 6.04E-08 mr1035 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
vg0405481249 8.20E-09 NA mr1062 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
vg0405481249 3.64E-06 5.98E-10 mr1062 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
vg0405481249 6.57E-10 2.98E-10 mr1525 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
vg0405481249 9.57E-09 9.56E-09 mr1525 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
vg0405481249 5.63E-08 NA mr1626 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
vg0405481249 2.00E-06 1.56E-09 mr1626 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
vg0405481249 9.62E-06 NA mr1631 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
vg0405481249 1.11E-06 1.11E-06 mr1631 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
vg0405481249 6.43E-12 NA mr1035_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
vg0405481249 6.45E-08 2.57E-11 mr1035_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
vg0405481249 8.14E-14 NA mr1062_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
vg0405481249 1.87E-09 4.57E-13 mr1062_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
vg0405481249 6.66E-13 6.70E-13 mr1525_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
vg0405481249 1.83E-10 1.83E-10 mr1525_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
vg0405481249 5.33E-13 NA mr1631_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
vg0405481249 1.39E-08 8.18E-14 mr1631_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