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Detailed information for vg0614471183:

Variant ID: vg0614471183 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14471183
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


AAATAGCCACAAACCGTCCTTGTGTTCCCCTTGCACGTCTGCATCGTTGGTGTGGCTTGTTGAGTACGGTGGTTGTACTCAGCCTTGCTATTATTCCCCC[A/T]
TTTCAGAAGTGTAGTGCTTCTGAGCTGAAGACGAAGTTAGAAGACCAAGGCTCAGACCCCAGTTGAGTTTTGCCTGTGGAGTGAAGCTAGGATCGCCTTT

Reverse complement sequence

AAAGGCGATCCTAGCTTCACTCCACAGGCAAAACTCAACTGGGGTCTGAGCCTTGGTCTTCTAACTTCGTCTTCAGCTCAGAAGCACTACACTTCTGAAA[T/A]
GGGGGAATAATAGCAAGGCTGAGTACAACCACCGTACTCAACAAGCCACACCAACGATGCAGACGTGCAAGGGGAACACAAGGACGGTTTGTGGCTATTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 19.00% 12.20% 23.55% 45.26% NA
All Indica  2759 2.00% 1.40% 30.19% 66.47% NA
All Japonica  1512 54.90% 34.40% 4.89% 5.82% NA
Aus  269 0.00% 1.10% 45.72% 53.16% NA
Indica I  595 3.70% 0.20% 20.00% 76.13% NA
Indica II  465 1.30% 1.10% 33.76% 63.87% NA
Indica III  913 0.50% 0.70% 32.64% 66.16% NA
Indica Intermediate  786 2.70% 3.30% 32.95% 61.07% NA
Temperate Japonica  767 89.60% 5.20% 2.61% 2.61% NA
Tropical Japonica  504 6.70% 74.20% 8.73% 10.32% NA
Japonica Intermediate  241 45.20% 44.00% 4.15% 6.64% NA
VI/Aromatic  96 1.00% 0.00% 56.25% 42.71% NA
Intermediate  90 14.40% 16.70% 32.22% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614471183 A -> T LOC_Os06g24640.1 upstream_gene_variant ; 2200.0bp to feature; MODIFIER silent_mutation Average:7.11; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg0614471183 A -> T LOC_Os06g24650.1 upstream_gene_variant ; 3097.0bp to feature; MODIFIER silent_mutation Average:7.11; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg0614471183 A -> T LOC_Os06g24640-LOC_Os06g24650 intergenic_region ; MODIFIER silent_mutation Average:7.11; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg0614471183 A -> DEL N N silent_mutation Average:7.11; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614471183 NA 6.45E-10 mr1648 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
vg0614471183 NA 5.16E-06 mr1648 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
vg0614471183 NA 3.89E-09 mr1354_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
vg0614471183 NA 1.14E-07 mr1363_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
vg0614471183 NA 3.77E-06 mr1363_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
vg0614471183 NA 6.07E-08 mr1369_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
vg0614471183 NA 1.61E-06 mr1418_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
vg0614471183 NA 7.08E-09 mr1453_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
vg0614471183 NA 1.39E-07 mr1502_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
vg0614471183 NA 4.82E-07 mr1509_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
vg0614471183 NA 2.47E-08 mr1543_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
vg0614471183 NA 2.29E-06 mr1544_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
vg0614471183 7.69E-06 NA mr1546_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
vg0614471183 4.29E-06 NA mr1546_2 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
vg0614471183 NA 5.20E-09 mr1578_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
vg0614471183 NA 3.15E-07 mr1582_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
vg0614471183 NA 7.24E-06 mr1695_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
vg0614471183 1.05E-06 NA mr1712_2 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
vg0614471183 NA 3.01E-08 mr1786_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
vg0614471183 NA 6.22E-06 mr1786_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
vg0614471183 NA 1.43E-09 mr1952_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