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Detailed information for vg0113853307:

Variant ID: vg0113853307 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13853307
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAACCAACACAAGATAATGAAAACATAATTATTGAATTCTATTTGTGAATCTCTACCCGAAGTTGGCAAAAAGTTGTATAACCATTGACTCAAGTTTA[C/T]
GACATACATTATTAATTAGCATGATATTCTCATCAGACCTTTGTAATTGGGCACAACACCGGAGCCAATACGTTATACGTTGCCCAGAAAAGTACCTGCA

Reverse complement sequence

TGCAGGTACTTTTCTGGGCAACGTATAACGTATTGGCTCCGGTGTTGTGCCCAATTACAAAGGTCTGATGAGAATATCATGCTAATTAATAATGTATGTC[G/A]
TAAACTTGAGTCAATGGTTATACAACTTTTTGCCAACTTCGGGTAGAGATTCACAAATAGAATTCAATAATTATGTTTTCATTATCTTGTGTTGGTTTTT

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 68.80% 31.10% 0.08% 0.00% NA
All Indica  2759 60.50% 39.30% 0.14% 0.00% NA
All Japonica  1512 97.80% 2.20% 0.00% 0.00% NA
Aus  269 2.60% 97.40% 0.00% 0.00% NA
Indica I  595 67.60% 32.40% 0.00% 0.00% NA
Indica II  465 91.00% 9.00% 0.00% 0.00% NA
Indica III  913 42.40% 57.30% 0.33% 0.00% NA
Indica Intermediate  786 58.30% 41.60% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0113853307 C -> T LOC_Os01g24570.1 upstream_gene_variant ; 4271.0bp to feature; MODIFIER silent_mutation Average:53.228; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0113853307 C -> T LOC_Os01g24590.1 downstream_gene_variant ; 4294.0bp to feature; MODIFIER silent_mutation Average:53.228; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N
vg0113853307 C -> T LOC_Os01g24570-LOC_Os01g24590 intergenic_region ; MODIFIER silent_mutation Average:53.228; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113853307 NA 5.54E-06 Awn_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0113853307 NA 6.70E-06 mr1277_2 Ind_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
vg0113853307 NA 4.14E-09 mr1519_2 Ind_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
vg0113853307 NA 7.47E-06 mr1587_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
vg0113853307 NA 5.86E-06 mr1792_2 Ind_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
vg0113853307 NA 5.24E-06 mr1803_2 Ind_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
vg0113853307 NA 1.02E-06 mr1874_2 Ind_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