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Detailed information for vg0412422045:

Variant ID: vg0412422045 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12422045
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGAGTGCCTTCCCAGGTTTCTTTTCGATTCGAGTTCTAGGACCAGCACCGTAGAGAGTAGTCACAATGTTAAATACTATCAGTAGTTTCTATATTTTCC[G/A]
GGGAACCATTGTTTATATATAAGACAGAGCTATAAAACTATTCACATAAAATTTGTCCTGGCAGACAAATTTGCGTCGTTATGCACACACTCGCTCAGCA

Reverse complement sequence

TGCTGAGCGAGTGTGTGCATAACGACGCAAATTTGTCTGCCAGGACAAATTTTATGTGAATAGTTTTATAGCTCTGTCTTATATATAAACAATGGTTCCC[C/T]
GGAAAATATAGAAACTACTGATAGTATTTAACATTGTGACTACTCTCTACGGTGCTGGTCCTAGAACTCGAATCGAAAAGAAACCTGGGAAGGCACTCCA

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 73.90% 25.90% 0.15% 0.00% NA
All Indica  2759 55.60% 44.10% 0.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 28.60% 71.30% 0.17% 0.00% NA
Indica II  465 74.00% 25.60% 0.43% 0.00% NA
Indica III  913 58.80% 41.00% 0.22% 0.00% NA
Indica Intermediate  786 61.60% 38.20% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0412422045 G -> A LOC_Os04g21940.1 upstream_gene_variant ; 1704.0bp to feature; MODIFIER silent_mutation Average:52.387; most accessible tissue: Callus, score: 88.494 N N N N
vg0412422045 G -> A LOC_Os04g21950.1 upstream_gene_variant ; 3519.0bp to feature; MODIFIER silent_mutation Average:52.387; most accessible tissue: Callus, score: 88.494 N N N N
vg0412422045 G -> A LOC_Os04g21930.1 downstream_gene_variant ; 2152.0bp to feature; MODIFIER silent_mutation Average:52.387; most accessible tissue: Callus, score: 88.494 N N N N
vg0412422045 G -> A LOC_Os04g21930-LOC_Os04g21940 intergenic_region ; MODIFIER silent_mutation Average:52.387; most accessible tissue: Callus, score: 88.494 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412422045 3.39E-06 NA mr1386 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
vg0412422045 1.42E-06 7.07E-10 mr1386 Ind_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
vg0412422045 NA 4.14E-10 mr1403 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
vg0412422045 NA 1.69E-07 mr1403 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
vg0412422045 NA 9.18E-06 mr1414 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
vg0412422045 NA 5.00E-08 mr1830 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
vg0412422045 NA 1.14E-10 mr1846 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
vg0412422045 NA 7.38E-11 mr1830_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
vg0412422045 4.42E-08 7.12E-14 mr1846_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
vg0412422045 8.75E-07 7.08E-23 mr1846_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