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Detailed information for vg0511433628:

Variant ID: vg0511433628 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 11433628
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, A: 0.13, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CTACGTACTTTTGCTTCCACACAACAAGGAGATATAGTGCAAAAAGATTCTTGCAGGAGGATCAGACATCCACAAATTCAGCAGATAAAAACAAAAAAAA[T/A]
TTGCAGGCAACCGTATAGAAATTCTCAATAAATATTTTTTTATTTGCAAAATATTTTTCTTAAATAATTAATCCATAATAATTGTTTTTAGAAAATAATT

Reverse complement sequence

AATTATTTTCTAAAAACAATTATTATGGATTAATTATTTAAGAAAAATATTTTGCAAATAAAAAAATATTTATTGAGAATTTCTATACGGTTGCCTGCAA[A/T]
TTTTTTTTGTTTTTATCTGCTGAATTTGTGGATGTCTGATCCTCCTGCAAGAATCTTTTTGCACTATATCTCCTTGTTGTGTGGAAGCAAAAGTACGTAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.30% 13.10% 0.68% 0.00% NA
All Indica  2759 84.90% 14.00% 1.12% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 20.40% 79.60% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 74.60% 21.10% 4.30% 0.00% NA
Indica III  913 78.90% 20.90% 0.22% 0.00% NA
Indica Intermediate  786 86.90% 12.00% 1.15% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 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 87.80% 11.10% 1.11% 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
vg0511433628 T -> A LOC_Os05g19630.1 downstream_gene_variant ; 2669.0bp to feature; MODIFIER silent_mutation Average:50.872; most accessible tissue: Zhenshan97 flag leaf, score: 83.205 N N N N
vg0511433628 T -> A LOC_Os05g19630.2 downstream_gene_variant ; 2669.0bp to feature; MODIFIER silent_mutation Average:50.872; most accessible tissue: Zhenshan97 flag leaf, score: 83.205 N N N N
vg0511433628 T -> A LOC_Os05g19620.1 intron_variant ; MODIFIER silent_mutation Average:50.872; most accessible tissue: Zhenshan97 flag leaf, score: 83.205 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0511433628 NA 6.82E-09 mr1039 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
vg0511433628 1.51E-06 NA mr1039_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
vg0511433628 NA 1.07E-09 mr1039_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
vg0511433628 5.30E-09 NA mr1632_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
vg0511433628 5.51E-06 1.10E-09 mr1632_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