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Detailed information for vg0817688257:

Variant ID: vg0817688257 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17688257
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


CACTCAAAGTATTTAAGAGAAGTTTTATCTAGCTCAACACTTACTTTAATTATTAAAAAAATACCTAGAAATTTCTTTTTCACAACAATTTATAATTTAG[C/T]
GGTTTTTAGGGTCTGACAGTTATCCGCATCGTAACCTCTCACTGACAAGCAAGACAAAAACAATGTGAATATATATTTGTGAACAATATGGTAACTGATG

Reverse complement sequence

CATCAGTTACCATATTGTTCACAAATATATATTCACATTGTTTTTGTCTTGCTTGTCAGTGAGAGGTTACGATGCGGATAACTGTCAGACCCTAAAAACC[G/A]
CTAAATTATAAATTGTTGTGAAAAAGAAATTTCTAGGTATTTTTTTAATAATTAAAGTAAGTGTTGAGCTAGATAAAACTTCTCTTAAATACTTTGAGTG

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 83.40% 15.70% 0.06% 0.87% NA
All Indica  2759 88.40% 10.00% 0.04% 1.49% NA
All Japonica  1512 71.80% 28.10% 0.07% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 67.20% 32.80% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 94.30% 1.50% 0.00% 4.16% NA
Indica Intermediate  786 92.20% 7.30% 0.13% 0.38% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 30.60% 69.20% 0.20% 0.00% NA
Japonica Intermediate  241 73.40% 26.60% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 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
vg0817688257 C -> T LOC_Os08g28920.1 upstream_gene_variant ; 2970.0bp to feature; MODIFIER silent_mutation Average:62.507; most accessible tissue: Callus, score: 95.005 N N N N
vg0817688257 C -> T LOC_Os08g28930.1 intron_variant ; MODIFIER silent_mutation Average:62.507; most accessible tissue: Callus, score: 95.005 N N N N
vg0817688257 C -> DEL N N silent_mutation Average:62.507; most accessible tissue: Callus, score: 95.005 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817688257 NA 1.96E-06 mr1627 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
vg0817688257 NA 6.34E-06 mr1184_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
vg0817688257 NA 2.43E-06 mr1329_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
vg0817688257 NA 9.70E-06 mr1337_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
vg0817688257 NA 8.39E-09 mr1364_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
vg0817688257 NA 1.11E-06 mr1373_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
vg0817688257 NA 8.06E-07 mr1397_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
vg0817688257 7.87E-06 2.54E-07 mr1524_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
vg0817688257 NA 8.06E-06 mr1652_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
vg0817688257 8.48E-06 8.47E-06 mr1674_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
vg0817688257 NA 5.83E-06 mr1812_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
vg0817688257 NA 1.07E-06 mr1832_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
vg0817688257 NA 1.23E-06 mr1833_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
vg0817688257 NA 7.42E-07 mr1843_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
vg0817688257 8.43E-07 8.42E-07 mr1847_2 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
vg0817688257 NA 8.69E-07 mr1860_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
vg0817688257 NA 3.32E-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