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Detailed information for vg0224699387:

Variant ID: vg0224699387 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 24699387
Reference Allele: TAlternative Allele: C,TG
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


AACGCTGCCGTCAGCGCCCGATTTTAACCTCCTCCCATCGGGCGCCTGAGCGGGAGTCAAACCTGAGGTTTTTTTGTTTTAAGAAAGCGTCAATTTTTAT[T/C,TG]
GTGATGTGTGCTCTATCACAAATCTCGAGCAAAGAAGAATAAGATTGTATCGTGATTTATGATAGAACCTAGGGTGTGGCTAATTGGTGCGTAACTGCGT

Reverse complement sequence

ACGCAGTTACGCACCAATTAGCCACACCCTAGGTTCTATCATAAATCACGATACAATCTTATTCTTCTTTGCTCGAGATTTGTGATAGAGCACACATCAC[A/G,CA]
ATAAAAATTGACGCTTTCTTAAAACAAAAAAACCTCAGGTTTGACTCCCGCTCAGGCGCCCGATGGGAGGAGGTTAAAATCGGGCGCTGACGGCAGCGTT

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 88.30% 10.30% 0.04% 0.00% TG: 1.29%
All Indica  2759 89.90% 8.70% 0.07% 0.00% TG: 1.34%
All Japonica  1512 85.40% 14.60% 0.00% 0.00% TG: 0.07%
Aus  269 96.30% 0.40% 0.00% 0.00% TG: 3.35%
Indica I  595 88.10% 11.80% 0.00% 0.00% TG: 0.17%
Indica II  465 96.30% 1.70% 0.00% 0.00% TG: 1.94%
Indica III  913 91.30% 6.20% 0.11% 0.00% TG: 2.30%
Indica Intermediate  786 85.60% 13.50% 0.13% 0.00% TG: 0.76%
Temperate Japonica  767 78.90% 21.10% 0.00% 0.00% NA
Tropical Japonica  504 93.10% 6.90% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 9.50% 0.00% 0.00% TG: 0.41%
VI/Aromatic  96 71.90% 13.50% 0.00% 0.00% TG: 14.58%
Intermediate  90 84.40% 15.60% 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
vg0224699387 T -> TG LOC_Os02g40750.1 upstream_gene_variant ; 940.0bp to feature; MODIFIER silent_mutation Average:39.971; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0224699387 T -> TG LOC_Os02g40760.1 downstream_gene_variant ; 1586.0bp to feature; MODIFIER silent_mutation Average:39.971; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0224699387 T -> TG LOC_Os02g40750-LOC_Os02g40760 intergenic_region ; MODIFIER silent_mutation Average:39.971; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0224699387 T -> C LOC_Os02g40750.1 upstream_gene_variant ; 939.0bp to feature; MODIFIER silent_mutation Average:39.971; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0224699387 T -> C LOC_Os02g40760.1 downstream_gene_variant ; 1587.0bp to feature; MODIFIER silent_mutation Average:39.971; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0224699387 T -> C LOC_Os02g40750-LOC_Os02g40760 intergenic_region ; MODIFIER silent_mutation Average:39.971; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224699387 9.43E-07 1.36E-06 mr1265_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
vg0224699387 NA 7.92E-06 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
vg0224699387 5.53E-06 1.49E-06 mr1528_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