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Detailed information for vg1015148329:

Variant ID: vg1015148329 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15148329
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TCATAAACTCGTTTGCTGCAACAACTTTTTGACATTTTGGTGTTTGTTAAACTGATTTTCTTATAATCTTGTCAATATTATTATGGTATGAAAATACGAA[A/G]
CAATTGGAAGAGACGTGAAAGTTGGATAATATATATAATCATAATTCAATCTATAAACCAAACGACCAAAATTATATGTTCAAATTTTTAGAGCAATTTT

Reverse complement sequence

AAAATTGCTCTAAAAATTTGAACATATAATTTTGGTCGTTTGGTTTATAGATTGAATTATGATTATATATATTATCCAACTTTCACGTCTCTTCCAATTG[T/C]
TTCGTATTTTCATACCATAATAATATTGACAAGATTATAAGAAAATCAGTTTAACAAACACCAAAATGTCAAAAAGTTGTTGCAGCAAACGAGTTTATGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.10% 6.10% 0.89% 56.94% NA
All Indica  2759 3.30% 10.30% 0.94% 85.43% NA
All Japonica  1512 96.80% 0.00% 0.93% 2.31% NA
Aus  269 0.70% 0.00% 0.74% 98.51% NA
Indica I  595 2.40% 29.10% 1.18% 67.39% NA
Indica II  465 6.20% 0.40% 1.08% 92.26% NA
Indica III  913 1.10% 6.80% 0.66% 91.46% NA
Indica Intermediate  786 5.00% 6.00% 1.02% 88.04% NA
Temperate Japonica  767 97.50% 0.00% 1.83% 0.65% NA
Tropical Japonica  504 97.00% 0.00% 0.00% 2.98% NA
Japonica Intermediate  241 93.80% 0.00% 0.00% 6.22% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 57.80% 5.60% 0.00% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1015148329 A -> G LOC_Os10g29070.1 upstream_gene_variant ; 2289.0bp to feature; MODIFIER silent_mutation Average:6.903; most accessible tissue: Callus, score: 22.876 N N N N
vg1015148329 A -> G LOC_Os10g29090.1 upstream_gene_variant ; 2918.0bp to feature; MODIFIER silent_mutation Average:6.903; most accessible tissue: Callus, score: 22.876 N N N N
vg1015148329 A -> G LOC_Os10g29070-LOC_Os10g29090 intergenic_region ; MODIFIER silent_mutation Average:6.903; most accessible tissue: Callus, score: 22.876 N N N N
vg1015148329 A -> DEL N N silent_mutation Average:6.903; most accessible tissue: Callus, score: 22.876 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015148329 4.94E-06 NA mr1951 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
vg1015148329 8.34E-06 NA mr1951 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
vg1015148329 NA 4.11E-06 mr1031_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