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Detailed information for vg0207527515:

Variant ID: vg0207527515 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7527515
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATACTTGTAAGTAATAGACCGATTGTATTAGAATGTCGTATTTGTTATATAGCAAACTATAGGCATGTGGATCTAGGCCTGCCACTCGGTATTCATTAC[C/T]
CATCCGATATCCATACCCACATTATTTATGTAGGGTATAGGTAAACAAATTTACCCATTTAAAATTTGGATTTGTGGAGTGTATTACCTATTTTACCCAC

Reverse complement sequence

GTGGGTAAAATAGGTAATACACTCCACAAATCCAAATTTTAAATGGGTAAATTTGTTTACCTATACCCTACATAAATAATGTGGGTATGGATATCGGATG[G/A]
GTAATGAATACCGAGTGGCAGGCCTAGATCCACATGCCTATAGTTTGCTATATAACAAATACGACATTCTAATACAATCGGTCTATTACTTACAAGTATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 2.80% 0.78% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 89.20% 8.40% 2.38% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 98.60% 0.00% 1.43% 0.00% NA
Tropical Japonica  504 72.00% 24.80% 3.17% 0.00% NA
Japonica Intermediate  241 95.40% 0.80% 3.73% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0207527515 C -> T LOC_Os02g13880.1 upstream_gene_variant ; 2952.0bp to feature; MODIFIER silent_mutation Average:53.73; most accessible tissue: Callus, score: 84.193 N N N N
vg0207527515 C -> T LOC_Os02g13880-LOC_Os02g13890 intergenic_region ; MODIFIER silent_mutation Average:53.73; most accessible tissue: Callus, score: 84.193 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207527515 NA 5.79E-07 mr1125 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
vg0207527515 7.13E-06 1.52E-06 mr1188 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
vg0207527515 NA 7.17E-06 mr1448 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
vg0207527515 4.54E-06 2.93E-09 mr1125_2 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
vg0207527515 NA 9.83E-07 mr1188_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