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Detailed information for vg0109515272:

Variant ID: vg0109515272 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9515272
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCAGTTATTAAAATTTGGCAGCAAATTAAATGTAGTCACTTTTTTTATAACTTTACTAAAATTTGGTAAGGTTGAAAATGGCTTCAAAGTGAATAGGCC[T/C]
ATAGAGACACATAGATCGTTATTAGAGAGAGAGAGAGGGGGGGATTATATACGTAGATAATAAGCGAATGCAACAAGCTGATGTGTGGTGCTATCCTAGA

Reverse complement sequence

TCTAGGATAGCACCACACATCAGCTTGTTGCATTCGCTTATTATCTACGTATATAATCCCCCCCTCTCTCTCTCTCTAATAACGATCTATGTGTCTCTAT[A/G]
GGCCTATTCACTTTGAAGCCATTTTCAACCTTACCAAATTTTAGTAAAGTTATAAAAAAAGTGACTACATTTAATTTGCTGCCAAATTTTAATAACTGGA

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 81.80% 17.90% 0.06% 0.28% NA
All Indica  2759 98.90% 0.50% 0.07% 0.43% NA
All Japonica  1512 46.20% 53.80% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.00% 0.37% NA
Indica I  595 98.50% 0.70% 0.00% 0.84% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.20% 0.00% 0.22% NA
Indica Intermediate  786 98.10% 1.00% 0.25% 0.64% NA
Temperate Japonica  767 17.10% 82.90% 0.00% 0.00% NA
Tropical Japonica  504 80.20% 19.80% 0.00% 0.00% NA
Japonica Intermediate  241 68.00% 32.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 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
vg0109515272 T -> DEL N N silent_mutation Average:61.064; most accessible tissue: Callus, score: 81.251 N N N N
vg0109515272 T -> C LOC_Os01g16750.1 downstream_gene_variant ; 170.0bp to feature; MODIFIER silent_mutation Average:61.064; most accessible tissue: Callus, score: 81.251 N N N N
vg0109515272 T -> C LOC_Os01g16750-LOC_Os01g16770 intergenic_region ; MODIFIER silent_mutation Average:61.064; most accessible tissue: Callus, score: 81.251 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109515272 NA 1.97E-32 mr1137 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
vg0109515272 NA 3.42E-08 mr1229 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
vg0109515272 2.90E-06 8.51E-40 mr1486 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
vg0109515272 NA 9.08E-11 mr1486 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
vg0109515272 NA 3.95E-06 mr1530 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
vg0109515272 NA 4.45E-22 mr1548 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
vg0109515272 NA 9.92E-08 mr1548 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
vg0109515272 NA 3.60E-06 mr1576 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
vg0109515272 NA 2.77E-28 mr1617 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
vg0109515272 NA 1.30E-12 mr1741 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
vg0109515272 NA 7.41E-08 mr1815 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
vg0109515272 NA 7.47E-06 mr1871 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
vg0109515272 NA 1.31E-09 mr1486_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
vg0109515272 NA 2.88E-11 mr1722_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