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Detailed information for vg0514963938:

Variant ID: vg0514963938 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 14963938
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


AGTCTTTCAGTCAATGGACTGGCGTTGGCCTTCTTGGTAGTCTCCGTATCTTGTGATAAATATCTCAGGGTAGAGTGTAATATATTTTGAATTTTTGTGG[A/G]
CTGTAAGAAATACTTGAAAATAGAGAAGGAATCTATCTAGCTAAGCTTTCTTACTCCGGATGGAGTGTGTACGAGTGTTTTCTCACTTCGCGACTTCGAT

Reverse complement sequence

ATCGAAGTCGCGAAGTGAGAAAACACTCGTACACACTCCATCCGGAGTAAGAAAGCTTAGCTAGATAGATTCCTTCTCTATTTTCAAGTATTTCTTACAG[T/C]
CCACAAAAATTCAAAATATATTACACTCTACCCTGAGATATTTATCACAAGATACGGAGACTACCAAGAAGGCCAACGCCAGTCCATTGACTGAAAGACT

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 54.70% 33.70% 6.52% 5.04% NA
All Indica  2759 38.50% 47.90% 8.95% 4.68% NA
All Japonica  1512 75.50% 14.70% 2.78% 7.01% NA
Aus  269 87.40% 10.00% 2.60% 0.00% NA
Indica I  595 29.70% 53.60% 13.95% 2.69% NA
Indica II  465 49.50% 35.30% 7.53% 7.74% NA
Indica III  913 38.10% 49.60% 7.56% 4.71% NA
Indica Intermediate  786 39.10% 49.00% 7.63% 4.33% NA
Temperate Japonica  767 94.00% 2.10% 1.30% 2.61% NA
Tropical Japonica  504 49.00% 37.10% 3.97% 9.92% NA
Japonica Intermediate  241 72.20% 7.90% 4.98% 14.94% NA
VI/Aromatic  96 86.50% 3.10% 7.29% 3.12% NA
Intermediate  90 72.20% 22.20% 5.56% 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
vg0514963938 A -> DEL N N silent_mutation Average:15.21; most accessible tissue: Callus, score: 37.498 N N N N
vg0514963938 A -> G LOC_Os05g25720.1 downstream_gene_variant ; 61.0bp to feature; MODIFIER silent_mutation Average:15.21; most accessible tissue: Callus, score: 37.498 N N N N
vg0514963938 A -> G LOC_Os05g25720-LOC_Os05g25740 intergenic_region ; MODIFIER silent_mutation Average:15.21; most accessible tissue: Callus, score: 37.498 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0514963938 1.35E-07 1.35E-07 mr1076_2 Jap_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
vg0514963938 NA 1.67E-07 mr1082_2 Jap_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
vg0514963938 1.80E-07 NA mr1083_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
vg0514963938 5.64E-06 1.33E-09 mr1083_2 Jap_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
vg0514963938 1.50E-06 NA mr1155_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
vg0514963938 1.75E-06 NA mr1226_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
vg0514963938 NA 7.24E-07 mr1226_2 Jap_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
vg0514963938 1.32E-06 7.81E-09 mr1408_2 Jap_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