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Detailed information for vg0114752997:

Variant ID: vg0114752997 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14752997
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTCCAATTAATTGATAACGAGAAGGAAAAACCCTAAGCATAATGCTGATCCTGCAATTTATCTATGAAAACTTTGGCAGCCTTTTTGATCTGTAAAGA[C/T]
GACGTAGAAGTTGACCGTGCAGTGTTGTTAATTCTGACATTCCTCTCACAGTTTGTTTTCCTATCTCCTATACATCTTAATAGTGTTGTTGAATCTTTCA

Reverse complement sequence

TGAAAGATTCAACAACACTATTAAGATGTATAGGAGATAGGAAAACAAACTGTGAGAGGAATGTCAGAATTAACAACACTGCACGGTCAACTTCTACGTC[G/A]
TCTTTACAGATCAAAAAGGCTGCCAAAGTTTTCATAGATAAATTGCAGGATCAGCATTATGCTTAGGGTTTTTCCTTCTCGTTATCAATTAATTGGACTC

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 94.30% 5.70% 0.00% 0.00% NA
All Indica  2759 92.30% 7.70% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 75.60% 24.40% 0.00% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 5.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0114752997 C -> T LOC_Os01g26000.1 upstream_gene_variant ; 4845.0bp to feature; MODIFIER silent_mutation Average:54.515; most accessible tissue: Callus, score: 85.796 N N N N
vg0114752997 C -> T LOC_Os01g26010.1 downstream_gene_variant ; 2907.0bp to feature; MODIFIER silent_mutation Average:54.515; most accessible tissue: Callus, score: 85.796 N N N N
vg0114752997 C -> T LOC_Os01g26039.1 downstream_gene_variant ; 1776.0bp to feature; MODIFIER silent_mutation Average:54.515; most accessible tissue: Callus, score: 85.796 N N N N
vg0114752997 C -> T LOC_Os01g26020.1 intron_variant ; MODIFIER silent_mutation Average:54.515; most accessible tissue: Callus, score: 85.796 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114752997 5.63E-07 5.72E-08 mr1519 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
vg0114752997 3.53E-08 NA mr1519_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
vg0114752997 2.72E-08 2.75E-11 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