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Detailed information for vg0116932562:

Variant ID: vg0116932562 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16932562
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGCAACCAAACTAAATCACCCGGTTCAAGCTTAACCTCTTGCCTACCTTTACTACCAACAATTCTATACTTTTCAGTCATCTTTTCAATGTTGAGCTT[G/T]
GTTGACTCATGCATTTTCAAAATAAATTCAGCGCGTGCCTTAGCATCATGATGAACCCTCTCACTAGTAGGTAAAGGCAAAATATCAATTGGAGCACGAG

Reverse complement sequence

CTCGTGCTCCAATTGATATTTTGCCTTTACCTACTAGTGAGAGGGTTCATCATGATGCTAAGGCACGCGCTGAATTTATTTTGAAAATGCATGAGTCAAC[C/A]
AAGCTCAACATTGAAAAGATGACTGAAAAGTATAGAATTGTTGGTAGTAAAGGTAGGCAAGAGGTTAAGCTTGAACCGGGTGATTTAGTTTGGTTGCACT

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 52.90% 2.20% 16.36% 28.59% NA
All Indica  2759 25.00% 3.30% 24.72% 46.97% NA
All Japonica  1512 99.10% 0.00% 0.26% 0.60% NA
Aus  269 53.20% 4.50% 29.37% 13.01% NA
Indica I  595 29.90% 5.90% 19.16% 45.04% NA
Indica II  465 28.80% 1.30% 15.27% 54.62% NA
Indica III  913 14.00% 3.10% 33.73% 49.18% NA
Indica Intermediate  786 31.70% 2.90% 24.05% 41.35% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 0.00% 0.60% 1.79% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 80.00% 0.00% 8.89% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0116932562 G -> T LOC_Os01g30970.1 downstream_gene_variant ; 2842.0bp to feature; MODIFIER silent_mutation Average:6.553; most accessible tissue: Callus, score: 19.307 N N N N
vg0116932562 G -> T LOC_Os01g30980.1 intron_variant ; MODIFIER silent_mutation Average:6.553; most accessible tissue: Callus, score: 19.307 N N N N
vg0116932562 G -> DEL N N silent_mutation Average:6.553; most accessible tissue: Callus, score: 19.307 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116932562 NA 3.87E-06 mr1215 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
vg0116932562 NA 6.34E-06 mr1378 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
vg0116932562 NA 4.33E-07 mr1511 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
vg0116932562 NA 7.82E-06 mr1534 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
vg0116932562 NA 3.97E-10 mr1707 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
vg0116932562 1.58E-06 1.22E-11 mr1728 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
vg0116932562 NA 1.41E-07 mr1728 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
vg0116932562 NA 4.09E-11 mr1860 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
vg0116932562 NA 2.77E-06 mr1860 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
vg0116932562 NA 5.22E-07 mr1881 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
vg0116932562 NA 2.14E-09 mr1707_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
vg0116932562 NA 4.27E-06 mr1707_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
vg0116932562 NA 1.29E-11 mr1728_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
vg0116932562 NA 4.98E-06 mr1728_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
vg0116932562 NA 1.04E-09 mr1860_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
vg0116932562 NA 3.56E-06 mr1860_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