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Detailed information for vg0427140714:

Variant ID: vg0427140714 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 27140714
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


TCGAAATAAAAATAAAATACAATCTAAAATTAGAAAAGGAAAGGATAGTCCAAGTAGGAATACAATTTAAAAATAGCTGAAATTCGGAATTAAACATAAG[T/C]
AATATTGAAAGAAGTTTCCATATAAGAACCCAATACGAGATTAATACAAATTCGAAATAAAAATAAAATAAAATCTAAAATTAGAAAAGAAAATAGAGTC

Reverse complement sequence

GACTCTATTTTCTTTTCTAATTTTAGATTTTATTTTATTTTTATTTCGAATTTGTATTAATCTCGTATTGGGTTCTTATATGGAAACTTCTTTCAATATT[A/G]
CTTATGTTTAATTCCGAATTTCAGCTATTTTTAAATTGTATTCCTACTTGGACTATCCTTTCCTTTTCTAATTTTAGATTGTATTTTATTTTTATTTCGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.10% 38.60% 0.30% 0.00% NA
All Indica  2759 38.70% 60.80% 0.51% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 56.50% 43.50% 0.00% 0.00% NA
Indica I  595 21.80% 77.30% 0.84% 0.00% NA
Indica II  465 11.40% 88.20% 0.43% 0.00% NA
Indica III  913 57.20% 42.70% 0.11% 0.00% NA
Indica Intermediate  786 46.20% 53.10% 0.76% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0427140714 T -> C LOC_Os04g45834.2 downstream_gene_variant ; 1530.0bp to feature; MODIFIER silent_mutation Average:30.06; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N
vg0427140714 T -> C LOC_Os04g45834.1 intron_variant ; MODIFIER silent_mutation Average:30.06; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N
vg0427140714 T -> C LOC_Os04g45834.3 intron_variant ; MODIFIER silent_mutation Average:30.06; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0427140714 NA 1.25E-08 mr1212_2 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
vg0427140714 NA 6.09E-09 mr1379_2 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
vg0427140714 NA 5.93E-06 mr1536_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
vg0427140714 NA 1.97E-06 mr1559_2 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
vg0427140714 6.73E-07 6.73E-07 mr1574_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
vg0427140714 5.12E-06 NA mr1661_2 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
vg0427140714 6.05E-06 6.05E-06 mr1693_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
vg0427140714 1.14E-06 3.36E-06 mr1762_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
vg0427140714 NA 5.14E-06 mr1762_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
vg0427140714 NA 1.77E-07 mr1804_2 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
vg0427140714 NA 2.78E-07 mr1819_2 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
vg0427140714 NA 1.39E-06 mr1915_2 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