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Detailed information for vg0138161446:

Variant ID: vg0138161446 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38161446
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATAAAGACTCAAAGGATTTTTCCATGAGGTTCTACCTCTTGTTAAAATTCCTCCAAAACTTGAAATTCATAGGGTTCATTTCTTTGATTCAAAGGGCTT[T/C]
GTAGGAAAAATTCCTATAGGAATGAAATCCTCTAAGGGCCCCTTTGAATCAAAGGATTTATGTAGGAATTTCATAAATTCAAATTCTATAGAAAATTTTC

Reverse complement sequence

GAAAATTTTCTATAGAATTTGAATTTATGAAATTCCTACATAAATCCTTTGATTCAAAGGGGCCCTTAGAGGATTTCATTCCTATAGGAATTTTTCCTAC[A/G]
AAGCCCTTTGAATCAAAGAAATGAACCCTATGAATTTCAAGTTTTGGAGGAATTTTAACAAGAGGTAGAACCTCATGGAAAAATCCTTTGAGTCTTTATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 5.90% 0.02% 0.00% NA
All Indica  2759 97.20% 2.80% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 29.70% 70.30% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.30% 3.70% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.60% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0138161446 T -> C LOC_Os01g65730.1 upstream_gene_variant ; 1661.0bp to feature; MODIFIER silent_mutation Average:24.846; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0138161446 T -> C LOC_Os01g65740.1 upstream_gene_variant ; 3091.0bp to feature; MODIFIER silent_mutation Average:24.846; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0138161446 T -> C LOC_Os01g65720.1 downstream_gene_variant ; 4335.0bp to feature; MODIFIER silent_mutation Average:24.846; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N
vg0138161446 T -> C LOC_Os01g65730-LOC_Os01g65740 intergenic_region ; MODIFIER silent_mutation Average:24.846; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138161446 NA 1.69E-06 mr1004 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
vg0138161446 NA 7.21E-07 mr1126 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
vg0138161446 3.41E-07 NA mr1134 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
vg0138161446 3.59E-06 NA mr1135 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
vg0138161446 NA 1.47E-06 mr1286 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
vg0138161446 NA 8.65E-09 mr1348 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
vg0138161446 NA 4.86E-07 mr1415 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
vg0138161446 5.51E-09 NA mr1504 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
vg0138161446 NA 4.86E-07 mr1567 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
vg0138161446 NA 5.80E-06 mr1569 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
vg0138161446 NA 9.85E-09 mr1608 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
vg0138161446 NA 4.56E-06 mr1665 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
vg0138161446 NA 4.10E-07 mr1764 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
vg0138161446 NA 8.59E-06 mr1774 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