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Detailed information for vg0113517997:

Variant ID: vg0113517997 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13517997
Reference Allele: GAlternative Allele: C,A
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, C: 0.06, A: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TCACTGCTGGATTTTTCCAAACGGCCACAGCAGATTTTTGCATGCGGGCCTCTCGTCCGTCTGTAATCAGGTGTCTGTGAAAATCATCATTTTTTCATAT[G/C,A]
GGTATATTGCATGTGAAAACGGACGGTCATCTAAACCAAATGCATGCGAAAATAGTTTTGACCAAAAAACTAAAATTCGTGGGAGAGGGCAGCCGCCGCC

Reverse complement sequence

GGCGGCGGCTGCCCTCTCCCACGAATTTTAGTTTTTTGGTCAAAACTATTTTCGCATGCATTTGGTTTAGATGACCGTCCGTTTTCACATGCAATATACC[C/G,T]
ATATGAAAAAATGATGATTTTCACAGACACCTGATTACAGACGGACGAGAGGCCCGCATGCAAAAATCTGCTGTGGCCGTTTGGAAAAATCCAGCAGTGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.00% 23.80% 0.19% 0.00% A: 0.02%
All Indica  2759 68.70% 31.00% 0.25% 0.00% A: 0.04%
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 9.30% 90.30% 0.37% 0.00% NA
Indica I  595 63.90% 35.80% 0.34% 0.00% NA
Indica II  465 74.40% 25.60% 0.00% 0.00% NA
Indica III  913 69.20% 30.40% 0.22% 0.00% A: 0.11%
Indica Intermediate  786 68.30% 31.30% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 74.40% 24.40% 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
vg0113517997 G -> A LOC_Os01g24010.1 intron_variant ; MODIFIER silent_mutation Average:71.694; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg0113517997 G -> C LOC_Os01g24010.1 intron_variant ; MODIFIER silent_mutation Average:71.694; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113517997 NA 1.44E-07 mr1654 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
vg0113517997 NA 1.27E-06 mr1654 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
vg0113517997 NA 5.03E-13 mr1193_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
vg0113517997 NA 1.69E-08 mr1378_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
vg0113517997 NA 1.41E-13 mr1654_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
vg0113517997 NA 4.11E-11 mr1654_2 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