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Detailed information for vg0613793879:

Variant ID: vg0613793879 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13793879
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAGGGCCTTAGGCATATTGGTCTAGTAGAGTAGGAAAAGACTGTGGGGAAGCTCCAAAAGGAGTGCCCCAAATGGTGGAGTTCTCTCCAGGGGAGTTCT[G/A]
GAGATGTCGAAACTCTTTCGGATCTTGTACCTCAATTGATGCTTCTTTTATATAAGTAAGTATTCGTGATTTCCTTTGGTATTTATTTTTTTAAATAAGA

Reverse complement sequence

TCTTATTTAAAAAAATAAATACCAAAGGAAATCACGAATACTTACTTATATAAAAGAAGCATCAATTGAGGTACAAGATCCGAAAGAGTTTCGACATCTC[C/T]
AGAACTCCCCTGGAGAGAACTCCACCATTTGGGGCACTCCTTTTGGAGCTTCCCCACAGTCTTTTCCTACTCTACTAGACCAATATGCCTAAGGCCCTGT

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 92.40% 7.30% 0.23% 0.00% NA
All Indica  2759 99.30% 0.60% 0.07% 0.00% NA
All Japonica  1512 77.80% 21.60% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.40% 0.13% 0.00% NA
Temperate Japonica  767 96.90% 2.90% 0.26% 0.00% NA
Tropical Japonica  504 57.50% 41.70% 0.79% 0.00% NA
Japonica Intermediate  241 59.30% 39.40% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0613793879 G -> A LOC_Os06g23640-LOC_Os06g23650 intergenic_region ; MODIFIER silent_mutation Average:45.933; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613793879 NA 3.16E-06 mr1205 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
vg0613793879 NA 2.00E-06 mr1229 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
vg0613793879 NA 4.07E-07 mr1229 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
vg0613793879 1.70E-06 1.70E-06 mr1597 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
vg0613793879 NA 2.06E-07 mr1880 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
vg0613793879 NA 1.90E-09 mr1880 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
vg0613793879 NA 6.30E-08 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