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Detailed information for vg0128444157:

Variant ID: vg0128444157 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28444157
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTTTGCTACAGGACACTGCTTATATATGGTTTTAGCTTTAGGACACTGCCTAAACTAACTTTTGGGAAAAACACTTCATAAACATGGTAATTTGCCA[G/A]
TAGACATCACGCCGATTAAAATAATGATTTCCGGTTGAAGAGAAGAGAGAAATAACGTGAAATGTAAAAAATACCCTTAGACCCACATGTCAGCTTTCTA

Reverse complement sequence

TAGAAAGCTGACATGTGGGTCTAAGGGTATTTTTTACATTTCACGTTATTTCTCTCTTCTCTTCAACCGGAAATCATTATTTTAATCGGCGTGATGTCTA[C/T]
TGGCAAATTACCATGTTTATGAAGTGTTTTTCCCAAAAGTTAGTTTAGGCAGTGTCCTAAAGCTAAAACCATATATAAGCAGTGTCCTGTAGCAAAATTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 5.60% 0.13% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 88.70% 10.90% 0.40% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.30% 0.52% 0.00% NA
Tropical Japonica  504 77.20% 22.80% 0.00% 0.00% NA
Japonica Intermediate  241 82.60% 16.60% 0.83% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0128444157 G -> A LOC_Os01g49450.1 upstream_gene_variant ; 1953.0bp to feature; MODIFIER silent_mutation Average:62.479; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 N N N N
vg0128444157 G -> A LOC_Os01g49460.1 upstream_gene_variant ; 336.0bp to feature; MODIFIER silent_mutation Average:62.479; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 N N N N
vg0128444157 G -> A LOC_Os01g49470.1 downstream_gene_variant ; 3730.0bp to feature; MODIFIER silent_mutation Average:62.479; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 N N N N
vg0128444157 G -> A LOC_Os01g49470.2 downstream_gene_variant ; 3750.0bp to feature; MODIFIER silent_mutation Average:62.479; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 N N N N
vg0128444157 G -> A LOC_Os01g49450-LOC_Os01g49460 intergenic_region ; MODIFIER silent_mutation Average:62.479; most accessible tissue: Zhenshan97 flag leaf, score: 84.146 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128444157 1.57E-06 1.57E-06 mr1877_2 Jap_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