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Detailed information for vg0713263559:

Variant ID: vg0713263559 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 13263559
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.02, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


GCAATTATTCCATGTATCTAAAGGTATTGGGCAAATGGACCAGGACTTTGCCCATAAGGAATATGTCTCCCATAATATTCTCCTCCTCGATCTGATCTCA[C/G]
TACCTTAATTTTTGCATTATGCTGATTTTCAACCTCAGCTTTGAATATCTTAAACTTATCGAGTGATTCAGATCTATCTTTAATGGGAAAAACATATCCA

Reverse complement sequence

TGGATATGTTTTTCCCATTAAAGATAGATCTGAATCACTCGATAAGTTTAAGATATTCAAAGCTGAGGTTGAAAATCAGCATAATGCAAAAATTAAGGTA[G/C]
TGAGATCAGATCGAGGAGGAGAATATTATGGGAGACATATTCCTTATGGGCAAAGTCCTGGTCCATTTGCCCAATACCTTTAGATACATGGAATAATTGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.40% 6.30% 17.60% 9.73% NA
All Indica  2759 49.40% 9.90% 27.47% 13.30% NA
All Japonica  1512 95.50% 0.20% 0.99% 3.31% NA
Aus  269 66.90% 6.70% 12.64% 13.75% NA
Indica I  595 56.80% 1.00% 22.18% 20.00% NA
Indica II  465 44.90% 2.60% 21.51% 30.97% NA
Indica III  913 48.20% 18.00% 31.65% 2.19% NA
Indica Intermediate  786 47.70% 11.50% 30.15% 10.69% NA
Temperate Japonica  767 95.20% 0.10% 0.91% 3.78% NA
Tropical Japonica  504 99.20% 0.00% 0.40% 0.40% NA
Japonica Intermediate  241 88.80% 0.80% 2.49% 7.88% NA
VI/Aromatic  96 85.40% 1.00% 13.54% 0.00% NA
Intermediate  90 77.80% 2.20% 13.33% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0713263559 C -> DEL N N silent_mutation Average:18.698; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0713263559 C -> G LOC_Os07g23480.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:18.698; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0713263559 C -> G LOC_Os07g23470.1 upstream_gene_variant ; 4889.0bp to feature; MODIFIER silent_mutation Average:18.698; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0713263559 NA 9.60E-06 mr1063 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
vg0713263559 NA 5.30E-19 mr1133 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
vg0713263559 NA 1.88E-14 mr1133 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
vg0713263559 7.52E-06 NA mr1540 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
vg0713263559 9.78E-06 9.78E-06 mr1540 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
vg0713263559 3.35E-07 4.38E-10 mr1662 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
vg0713263559 3.49E-07 1.43E-10 mr1662 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
vg0713263559 8.13E-06 2.66E-12 mr1667 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
vg0713263559 NA 7.93E-10 mr1667 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
vg0713263559 NA 9.80E-06 mr1732 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
vg0713263559 4.93E-08 1.55E-22 mr1133_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
vg0713263559 5.60E-07 9.31E-17 mr1133_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
vg0713263559 NA 7.28E-06 mr1662_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
vg0713263559 NA 4.66E-12 mr1667_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
vg0713263559 NA 2.98E-10 mr1667_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