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Detailed information for vg0229460554:

Variant ID: vg0229460554 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29460554
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTAATTTCATTGAAGACATAAGTGCATGTCCTGCCAACCTGAAGTGGTGTTAATGAAATTTGCGGGCGAAAAAAAAAGGTACAGCAGCATAACATATCA[C/T]
ATTTCACATGCTGTAGCAACATCAGCAGATGCAGCACCTCATCAGATATTGCATCCTCAGCAGAATCAGACACATGATCAGAGTGTTGCTCGGATTGAGG

Reverse complement sequence

CCTCAATCCGAGCAACACTCTGATCATGTGTCTGATTCTGCTGAGGATGCAATATCTGATGAGGTGCTGCATCTGCTGATGTTGCTACAGCATGTGAAAT[G/A]
TGATATGTTATGCTGCTGTACCTTTTTTTTTCGCCCGCAAATTTCATTAACACCACTTCAGGTTGGCAGGACATGCACTTATGTCTTCAATGAAATTAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 2.60% 0.59% 0.00% NA
All Indica  2759 94.50% 4.50% 0.98% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 84.50% 12.30% 3.23% 0.00% NA
Indica III  913 93.80% 5.80% 0.44% 0.00% NA
Indica Intermediate  786 97.50% 1.90% 0.64% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0229460554 C -> T LOC_Os02g48116.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:73.893; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0229460554 C -> T LOC_Os02g48116.1 5_prime_UTR_variant ; 377.0bp to feature; MODIFIER silent_mutation Average:73.893; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0229460554 C -> T LOC_Os02g48110.1 downstream_gene_variant ; 2686.0bp to feature; MODIFIER silent_mutation Average:73.893; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0229460554 C -> T LOC_Os02g48122.1 downstream_gene_variant ; 3273.0bp to feature; MODIFIER silent_mutation Average:73.893; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229460554 NA 3.17E-06 mr1122 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
vg0229460554 NA 6.49E-07 mr1188 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
vg0229460554 NA 2.01E-15 mr1498 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
vg0229460554 NA 1.59E-14 mr1769 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
vg0229460554 NA 4.35E-08 mr1903 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
vg0229460554 NA 6.24E-08 mr1925 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
vg0229460554 NA 1.04E-10 mr1951 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
vg0229460554 NA 7.39E-08 mr1188_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
vg0229460554 NA 1.09E-07 mr1310_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
vg0229460554 NA 1.18E-13 mr1498_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
vg0229460554 NA 1.48E-17 mr1769_2 Ind_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
vg0229460554 NA 3.35E-09 mr1925_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
vg0229460554 NA 1.28E-11 mr1951_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