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Detailed information for vg0710554467:

Variant ID: vg0710554467 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10554467
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAACTGCAGTATAATAATTCATTTTATTAGTCAAAAATAAAATGATTTCAAATGAAAAATTGTCAACAACAAAGTTGTATAACTTATCAAAATTTACAA[G/T]
TTTTATTTTGGTCATTTTTCTATATAACTTTTTTGAACAATTTAAATTTGAATTAGAAAATATGACAACTTCAAACAATATTTTCAAATATTAAATGATT

Reverse complement sequence

AATCATTTAATATTTGAAAATATTGTTTGAAGTTGTCATATTTTCTAATTCAAATTTAAATTGTTCAAAAAAGTTATATAGAAAAATGACCAAAATAAAA[C/A]
TTGTAAATTTTGATAAGTTATACAACTTTGTTGTTGACAATTTTTCATTTGAAATCATTTTATTTTTGACTAATAAAATGAATTATTATACTGCAGTTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.20% 34.00% 0.53% 1.33% NA
All Indica  2759 96.10% 3.90% 0.00% 0.00% NA
All Japonica  1512 6.20% 88.20% 1.52% 4.17% NA
Aus  269 50.60% 49.40% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 89.90% 10.10% 0.00% 0.00% NA
Temperate Japonica  767 2.00% 86.80% 3.00% 8.21% NA
Tropical Japonica  504 13.70% 86.30% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 63.30% 34.40% 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
vg0710554467 G -> DEL N N silent_mutation Average:17.829; most accessible tissue: Callus, score: 31.5 N N N N
vg0710554467 G -> T LOC_Os07g17840.1 upstream_gene_variant ; 580.0bp to feature; MODIFIER silent_mutation Average:17.829; most accessible tissue: Callus, score: 31.5 N N N N
vg0710554467 G -> T LOC_Os07g17840-LOC_Os07g17850 intergenic_region ; MODIFIER silent_mutation Average:17.829; most accessible tissue: Callus, score: 31.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710554467 NA 7.28E-08 mr1028 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
vg0710554467 NA 5.66E-14 mr1035 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
vg0710554467 1.95E-06 1.95E-06 mr1369 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
vg0710554467 NA 7.65E-07 mr1453 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
vg0710554467 NA 1.31E-12 mr1626 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
vg0710554467 NA 1.17E-08 mr1648 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
vg0710554467 NA 1.38E-07 mr1648 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
vg0710554467 NA 3.25E-08 mr1652 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
vg0710554467 NA 2.10E-08 mr1666 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
vg0710554467 NA 1.65E-07 mr1697 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
vg0710554467 NA 3.87E-07 mr1761 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
vg0710554467 NA 1.87E-10 mr1761_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