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Detailed information for vg0407370896:

Variant ID: vg0407370896 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7370896
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTTTGCAACCTCAAAAAAAGGCCAACAAAAATAGTATGACACTTTTCTGTTGGGCACCTTTTTATCTGCATCGTAGTAATTCCAAAGAATTATCTAACC[G/A]
CACAAAAAGCATTTTAATGGTATTGGGCTATTTTATTGTGAGCAATTTTGCCAAAGCAAAAAATATGCCTAAGTCCCTAAGGGTCACAACCAGCCACACC

Reverse complement sequence

GGTGTGGCTGGTTGTGACCCTTAGGGACTTAGGCATATTTTTTGCTTTGGCAAAATTGCTCACAATAAAATAGCCCAATACCATTAAAATGCTTTTTGTG[C/T]
GGTTAGATAATTCTTTGGAATTACTACGATGCAGATAAAAAGGTGCCCAACAGAAAAGTGTCATACTATTTTTGTTGGCCTTTTTTTGAGGTTGCAAAGC

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 96.50% 1.50% 1.33% 0.66% NA
All Indica  2759 95.60% 2.50% 1.85% 0.04% NA
All Japonica  1512 97.60% 0.00% 0.40% 1.98% NA
Aus  269 98.90% 0.40% 0.74% 0.00% NA
Indica I  595 89.70% 7.90% 2.35% 0.00% NA
Indica II  465 97.40% 0.90% 1.51% 0.22% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 94.10% 2.30% 3.56% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 93.30% 0.00% 0.99% 5.75% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 0.00% 4.44% 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
vg0407370896 G -> DEL N N silent_mutation Average:48.225; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0407370896 G -> A LOC_Os04g13290.1 upstream_gene_variant ; 407.0bp to feature; MODIFIER silent_mutation Average:48.225; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0407370896 G -> A LOC_Os04g13280-LOC_Os04g13290 intergenic_region ; MODIFIER silent_mutation Average:48.225; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407370896 NA 1.60E-07 mr1038 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
vg0407370896 NA 1.29E-08 mr1389 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
vg0407370896 NA 7.81E-06 mr1937 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
vg0407370896 NA 1.32E-07 mr1008_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
vg0407370896 NA 6.98E-08 mr1015_2 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
vg0407370896 NA 7.87E-08 mr1038_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
vg0407370896 NA 8.40E-07 mr1389_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