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Detailed information for vg1013981083:

Variant ID: vg1013981083 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13981083
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCCTAGATGCGGAGCTAACAAATCTCTCCATGGAATTTAGGACATCCATTTGGTTTTCTTCAGAGAAGATTTGCAACTGAGAAACTTAATGCACCTTG[G/A]
TTATTTATGTGCCAACTCCAACCACCATGGCCAAAAACTTACTACTAGTTGTTAGTGGCACATGCTTTATCTTTTTTCTTTCATGAACATACTACCACTT

Reverse complement sequence

AAGTGGTAGTATGTTCATGAAAGAAAAAAGATAAAGCATGTGCCACTAACAACTAGTAGTAAGTTTTTGGCCATGGTGGTTGGAGTTGGCACATAAATAA[C/T]
CAAGGTGCATTAAGTTTCTCAGTTGCAAATCTTCTCTGAAGAAAACCAAATGGATGTCCTAAATTCCATGGAGAGATTTGTTAGCTCCGCATCTAGGGGT

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 97.20% 2.60% 0.25% 0.00% NA
All Indica  2759 95.30% 4.20% 0.43% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 93.10% 6.50% 0.43% 0.00% NA
Indica III  913 95.10% 4.80% 0.11% 0.00% NA
Indica Intermediate  786 93.50% 5.50% 1.02% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg1013981083 G -> A LOC_Os10g26750.1 upstream_gene_variant ; 1621.0bp to feature; MODIFIER silent_mutation Average:33.199; most accessible tissue: Zhenshan97 young leaf, score: 62.534 N N N N
vg1013981083 G -> A LOC_Os10g26750-LOC_Os10g26760 intergenic_region ; MODIFIER silent_mutation Average:33.199; most accessible tissue: Zhenshan97 young leaf, score: 62.534 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013981083 3.16E-06 3.16E-06 mr1470 Ind_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
vg1013981083 NA 6.06E-06 mr1668 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
vg1013981083 NA 8.28E-06 mr1669 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
vg1013981083 NA 2.18E-07 mr1958 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