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Detailed information for vg0815709042:

Variant ID: vg0815709042 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15709042
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCTTACCTATAATTAGCATACATGCATAGATAGGAAGTTCAAGCCACATATAATAAGGAGTTCAAGTCTCGTACATAATAGCAAATTTAAGTCTTATA[C/T]
ATTGTAGCAAATTTTAGTCTTGCACATTGTCTTGACGGGAGAGACGGGAGTTCCGGGCGTGGGACTGGAAGGAGGAGGTGCAGCAGCTCAGCCACGAGTA

Reverse complement sequence

TACTCGTGGCTGAGCTGCTGCACCTCCTCCTTCCAGTCCCACGCCCGGAACTCCCGTCTCTCCCGTCAAGACAATGTGCAAGACTAAAATTTGCTACAAT[G/A]
TATAAGACTTAAATTTGCTATTATGTACGAGACTTGAACTCCTTATTATATGTGGCTTGAACTTCCTATCTATGCATGTATGCTAATTATAGGTAAGGCC

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 91.10% 8.90% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 82.70% 17.30% 0.00% 0.00% NA
Aus  269 67.30% 32.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 96.60% 3.40% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 73.00% 27.00% 0.00% 0.00% NA
Japonica Intermediate  241 51.90% 48.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0815709042 C -> T LOC_Os08g25820.1 upstream_gene_variant ; 1748.0bp to feature; MODIFIER silent_mutation Average:73.61; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0815709042 C -> T LOC_Os08g25820.2 upstream_gene_variant ; 1739.0bp to feature; MODIFIER silent_mutation Average:73.61; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0815709042 C -> T LOC_Os08g25799-LOC_Os08g25820 intergenic_region ; MODIFIER silent_mutation Average:73.61; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815709042 NA 4.11E-07 mr1519 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
vg0815709042 NA 4.48E-06 mr1064_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
vg0815709042 NA 6.05E-09 mr1519_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