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Detailed information for vg0315011642:

Variant ID: vg0315011642 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15011642
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATATAAATCACACTTAAAGTATTATGAGTAATAAAACAACTCATAACAAAATAAATTACAATTACGTAAATTTTTTGAATAAGACAAATGGTCAAACAT[G/A]
TGAGAAAAAGTCAACGGCGTCATCTATTAAAAAAACGGAGGTAGTATGTTATTCCCTTTTCTGCATCCATGATAGATATTGCCTCTGGTTTTAAATGGAC

Reverse complement sequence

GTCCATTTAAAACCAGAGGCAATATCTATCATGGATGCAGAAAAGGGAATAACATACTACCTCCGTTTTTTTAATAGATGACGCCGTTGACTTTTTCTCA[C/T]
ATGTTTGACCATTTGTCTTATTCAAAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGTTTTATTACTCATAATACTTTAAGTGTGATTTATATT

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 97.60% 2.40% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.90% 7.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 80.40% 19.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0315011642 G -> A LOC_Os03g26240.1 upstream_gene_variant ; 2189.0bp to feature; MODIFIER silent_mutation Average:40.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0315011642 G -> A LOC_Os03g26260.1 upstream_gene_variant ; 4164.0bp to feature; MODIFIER silent_mutation Average:40.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0315011642 G -> A LOC_Os03g26229.1 downstream_gene_variant ; 3382.0bp to feature; MODIFIER silent_mutation Average:40.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0315011642 G -> A LOC_Os03g26250.1 intron_variant ; MODIFIER silent_mutation Average:40.43; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315011642 NA 1.85E-06 mr1073 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
vg0315011642 NA 1.52E-07 mr1217 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
vg0315011642 NA 1.72E-08 mr1852 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
vg0315011642 NA 9.05E-06 mr1786_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