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Detailed information for vg0613478814:

Variant ID: vg0613478814 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13478814
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTATTACAACATTTTATTTAAATTTAATAAGTATTGAAAAATTACTTAGAATTCATAAAAACAATCCATAATATCTCTAGTACTTTTAATAAAAAAAGGT[G/A]
ACTATAAAACTTTCTATATTAATTAATTGGAAAAAAAGCTACATATTTAGTTGGCACTACGAGACCATAAGCAGTAGCCATGATATCAGGGCGTAGGTGC

Reverse complement sequence

GCACCTACGCCCTGATATCATGGCTACTGCTTATGGTCTCGTAGTGCCAACTAAATATGTAGCTTTTTTTCCAATTAATTAATATAGAAAGTTTTATAGT[C/T]
ACCTTTTTTTATTAAAAGTACTAGAGATATTATGGATTGTTTTTATGAATTCTAAGTAATTTTTCAATACTTATTAAATTTAAATAAAATGTTGTAATAG

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 90.60% 8.90% 0.51% 0.00% NA
All Indica  2759 98.40% 1.50% 0.07% 0.00% NA
All Japonica  1512 74.40% 24.40% 1.19% 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 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.20% 0.13% 0.00% NA
Temperate Japonica  767 96.20% 2.90% 0.91% 0.00% NA
Tropical Japonica  504 39.90% 58.50% 1.59% 0.00% NA
Japonica Intermediate  241 77.20% 21.60% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 10.00% 4.44% 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
vg0613478814 G -> A LOC_Os06g23114.1 intron_variant ; MODIFIER silent_mutation Average:46.133; most accessible tissue: Minghui63 root, score: 65.279 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613478814 1.56E-08 NA mr1033 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
vg0613478814 3.02E-07 8.33E-29 mr1301 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
vg0613478814 NA 5.89E-14 mr1301 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
vg0613478814 4.80E-06 3.22E-18 mr1410 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
vg0613478814 NA 2.69E-08 mr1593 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
vg0613478814 NA 9.21E-11 mr1993 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
vg0613478814 NA 8.86E-08 mr1993 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
vg0613478814 4.15E-13 NA mr1033_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
vg0613478814 1.92E-06 5.96E-29 mr1301_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
vg0613478814 NA 3.61E-09 mr1354_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
vg0613478814 NA 3.83E-19 mr1410_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
vg0613478814 NA 2.52E-11 mr1593_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
vg0613478814 NA 7.63E-13 mr1993_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