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Detailed information for vg0715863524:

Variant ID: vg0715863524 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15863524
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTTTGCCTGTTCGGCAAGAGATATTAGTAATACACACTTAGAGCCTATTTGATTCCCCTATCAAAATTTTACACCGTCACATCAAACGTTTGAACACAT[A/G]
CATAAAGTATTAAATATAAACGAAAAAATATCTAGTTATATAGATTATGTGTAAATTGCAAGATGAATCTTTTAAGCCTAATTGCACCATGATTTATCAA

Reverse complement sequence

TTGATAAATCATGGTGCAATTAGGCTTAAAAGATTCATCTTGCAATTTACACATAATCTATATAACTAGATATTTTTTCGTTTATATTTAATACTTTATG[T/C]
ATGTGTTCAAACGTTTGATGTGACGGTGTAAAATTTTGATAGGGGAATCAAATAGGCTCTAAGTGTGTATTACTAATATCTCTTGCCGAACAGGCAAACG

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 76.80% 22.90% 0.32% 0.00% NA
All Indica  2759 96.50% 3.20% 0.29% 0.00% NA
All Japonica  1512 48.30% 51.70% 0.00% 0.00% NA
Aus  269 25.70% 71.70% 2.60% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 91.30% 8.00% 0.64% 0.00% NA
Temperate Japonica  767 27.00% 73.00% 0.00% 0.00% NA
Tropical Japonica  504 71.00% 29.00% 0.00% 0.00% NA
Japonica Intermediate  241 68.90% 31.10% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0715863524 A -> G LOC_Os07g27290.1 downstream_gene_variant ; 553.0bp to feature; MODIFIER silent_mutation Average:32.886; most accessible tissue: Callus, score: 48.912 N N N N
vg0715863524 A -> G LOC_Os07g27290-LOC_Os07g27300 intergenic_region ; MODIFIER silent_mutation Average:32.886; most accessible tissue: Callus, score: 48.912 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715863524 NA 8.35E-07 mr1157 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
vg0715863524 NA 3.97E-07 mr1206 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
vg0715863524 NA 5.29E-10 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
vg0715863524 NA 2.92E-06 mr1621 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
vg0715863524 NA 1.91E-11 mr1763 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
vg0715863524 NA 4.99E-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
vg0715863524 NA 8.00E-06 mr1937 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