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Detailed information for vg0224512632:

Variant ID: vg0224512632 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24512632
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAGCTCACAATGATTTTCAGCAAAATGAGGTCTTTTGTCCTCGTTGTAGTCCATTTACTAGCTCACCACCGTCTTTCTAAGAGGATCTCCTAGTTGCA[A/T]
CTACACATCAAACCAACAGAATGGATGAACCATGCAACTGTGCAAGAGTGGTGAGGGAAAACCATCTCGGCACAAAACATGCCCTAGAAAGTACTCTCAA

Reverse complement sequence

TTGAGAGTACTTTCTAGGGCATGTTTTGTGCCGAGATGGTTTTCCCTCACCACTCTTGCACAGTTGCATGGTTCATCCATTCTGTTGGTTTGATGTGTAG[T/A]
TGCAACTAGGAGATCCTCTTAGAAAGACGGTGGTGAGCTAGTAAATGGACTACAACGAGGACAAAAGACCTCATTTTGCTGAAAATCATTGTGAGCTTCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.00% 5.90% 0.08% 0.00% NA
All Indica  2759 93.00% 7.00% 0.07% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 78.10% 21.20% 0.74% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 89.70% 9.90% 0.43% 0.00% NA
Indica III  913 90.00% 10.00% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 6.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 87.50% 12.50% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0224512632 A -> T LOC_Os02g40440.1 upstream_gene_variant ; 3742.0bp to feature; MODIFIER silent_mutation Average:48.417; most accessible tissue: Callus, score: 70.608 N N N N
vg0224512632 A -> T LOC_Os02g40430-LOC_Os02g40440 intergenic_region ; MODIFIER silent_mutation Average:48.417; most accessible tissue: Callus, score: 70.608 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224512632 NA 1.90E-06 mr1170 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
vg0224512632 NA 9.97E-06 mr1808 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
vg0224512632 4.09E-06 1.94E-06 mr1964 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