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Detailed information for vg0428010540:

Variant ID: vg0428010540 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 28010540
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.12, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TCATAAGAATCAATCTTTTTAAAGAGAAAGGTAGGAGCTTTGTCGATCAAGAAATAAACAAAAACAATAAATTTGATTTCCACGATAATTAGGAAGAGGT[T/C]
ATTTAGACCCTCTTTGTTTGGGCTTAGGTTTATTGGTTTAGATTTTTAAGTTAGCTTATTGGCTTATATGATTTATAAGCTGGTAGATTTAATGTTCTAA

Reverse complement sequence

TTAGAACATTAAATCTACCAGCTTATAAATCATATAAGCCAATAAGCTAACTTAAAAATCTAAACCAATAAACCTAAGCCCAAACAAAGAGGGTCTAAAT[A/G]
ACCTCTTCCTAATTATCGTGGAAATCAAATTTATTGTTTTTGTTTATTTCTTGATCGACAAAGCTCCTACCTTTCTCTTTAAAAAGATTGATTCTTATGA

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 58.60% 41.40% 0.02% 0.00% NA
All Indica  2759 92.80% 7.20% 0.04% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 59.90% 40.10% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 95.70% 4.10% 0.22% 0.00% NA
Indica III  913 88.10% 11.90% 0.00% 0.00% NA
Indica Intermediate  786 93.60% 6.40% 0.00% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 40.00% 60.00% 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
vg0428010540 T -> C LOC_Os04g47170.1 upstream_gene_variant ; 3179.0bp to feature; MODIFIER silent_mutation Average:38.244; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0428010540 T -> C LOC_Os04g47160-LOC_Os04g47170 intergenic_region ; MODIFIER silent_mutation Average:38.244; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0428010540 NA 4.24E-09 mr1663 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
vg0428010540 NA 2.00E-06 mr1137_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
vg0428010540 NA 2.11E-41 mr1145_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
vg0428010540 NA 6.61E-36 mr1181_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
vg0428010540 6.64E-06 NA mr1241_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
vg0428010540 NA 2.75E-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