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Detailed information for vg0913668910:

Variant ID: vg0913668910 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 13668910
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTCAGAACTTCTGGAAGAACCCCACAATAGAGGTTATTCCTTTTTTCCCTTTAGCTCTTTCTGCTGGTTTGAAGTTAGAACTGCCATATTATGATCGT[G/A]
GAGTACAATGGAAAGTCTATTGTTTTGGTGGTGTATGTGCATTCCAGCTCATAACTTTAGGATATGCATGACTGCTTGTAGCAGGTGCTATATGTATGTT

Reverse complement sequence

AACATACATATAGCACCTGCTACAAGCAGTCATGCATATCCTAAAGTTATGAGCTGGAATGCACATACACCACCAAAACAATAGACTTTCCATTGTACTC[C/T]
ACGATCATAATATGGCAGTTCTAACTTCAAACCAGCAGAAAGAGCTAAAGGGAAAAAAGGAATAACCTCTATTGTGGGGTTCTTCCAGAAGTTCTGACCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.20% 1.40% 0.36% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.70% 4.30% 0.99% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 88.10% 10.50% 1.39% 0.00% NA
Japonica Intermediate  241 92.10% 5.00% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0913668910 G -> A LOC_Os09g23120.1 upstream_gene_variant ; 4073.0bp to feature; MODIFIER silent_mutation Average:63.141; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N
vg0913668910 G -> A LOC_Os09g23110.1 intron_variant ; MODIFIER silent_mutation Average:63.141; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0913668910 NA 5.88E-06 mr1099_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
vg0913668910 NA 3.87E-07 mr1222_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
vg0913668910 NA 4.94E-07 mr1911_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
vg0913668910 6.15E-07 1.20E-10 mr1929_2 Jap_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