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Detailed information for vg0810529886:

Variant ID: vg0810529886 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10529886
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGTGCACCGTTCCTGGATCATAATCACCCCCTTATAGACAAGGCATGGACTCCCCAGCGACCCCCGTGGGCTTATCTCCGCCACTTTTCAGTTTGGTGC[C/T]
CCGCAATGAACCATGCTATACAAAAGGTAAAGCCGTTGCCCACGCTGACTTGTGGTTGGCATGGTTAATGTTTCACAACCGAAACTCATGAACCGGTCCT

Reverse complement sequence

AGGACCGGTTCATGAGTTTCGGTTGTGAAACATTAACCATGCCAACCACAAGTCAGCGTGGGCAACGGCTTTACCTTTTGTATAGCATGGTTCATTGCGG[G/A]
GCACCAAACTGAAAAGTGGCGGAGATAAGCCCACGGGGGTCGCTGGGGAGTCCATGCCTTGTCTATAAGGGGGTGATTATGATCCAGGAACGGTGCACTG

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 98.20% 1.20% 0.57% 0.00% NA
All Indica  2759 97.00% 2.00% 0.98% 0.00% NA
All Japonica  1512 99.90% 0.10% 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 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 91.80% 5.60% 2.63% 0.00% NA
Indica Intermediate  786 99.10% 0.60% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0810529886 C -> T LOC_Os08g17180.1 downstream_gene_variant ; 855.0bp to feature; MODIFIER silent_mutation Average:16.666; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0810529886 C -> T LOC_Os08g17180-LOC_Os08g17210 intergenic_region ; MODIFIER silent_mutation Average:16.666; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810529886 3.51E-06 NA mr1260_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
vg0810529886 5.90E-07 4.20E-06 mr1260_2 Ind_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