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Detailed information for vg0406260245:

Variant ID: vg0406260245 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6260245
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACATGGTTGCCACCTATTCGGCATGAGTTTCTCTCCCATCAGCTCTCCTCGTGCTGCCTTCACCGCCGAGACGAAATCCCTTGAATCACCGGATTTTGT[C/T]
CCCTTCCAGATCCCACCCCTCCCACCGATGCTCTCCCTCGGCCACTTTCTTCCACTACTCGCCAATGTTCTCCATCCCGCCGCCAAATCCCTCATGAAAA

Reverse complement sequence

TTTTCATGAGGGATTTGGCGGCGGGATGGAGAACATTGGCGAGTAGTGGAAGAAAGTGGCCGAGGGAGAGCATCGGTGGGAGGGGTGGGATCTGGAAGGG[G/A]
ACAAAATCCGGTGATTCAAGGGATTTCGTCTCGGCGGTGAAGGCAGCACGAGGAGAGCTGATGGGAGAGAAACTCATGCCGAATAGGTGGCAACCATGTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 2.00% 2.22% 1.25% NA
All Indica  2759 96.40% 0.00% 1.49% 2.10% NA
All Japonica  1512 89.80% 6.10% 4.03% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 81.90% 0.00% 7.74% 10.32% NA
Indica III  913 99.80% 0.00% 0.00% 0.22% NA
Indica Intermediate  786 98.30% 0.00% 0.64% 1.02% NA
Temperate Japonica  767 82.40% 10.40% 7.17% 0.00% NA
Tropical Japonica  504 97.40% 2.00% 0.60% 0.00% NA
Japonica Intermediate  241 97.50% 0.80% 1.24% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 1.10% 3.33% 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
vg0406260245 C -> DEL N N silent_mutation Average:71.486; most accessible tissue: Callus, score: 93.682 N N N N
vg0406260245 C -> T LOC_Os04g11440.1 upstream_gene_variant ; 1894.0bp to feature; MODIFIER silent_mutation Average:71.486; most accessible tissue: Callus, score: 93.682 N N N N
vg0406260245 C -> T LOC_Os04g11450.1 downstream_gene_variant ; 2338.0bp to feature; MODIFIER silent_mutation Average:71.486; most accessible tissue: Callus, score: 93.682 N N N N
vg0406260245 C -> T LOC_Os04g11440-LOC_Os04g11450 intergenic_region ; MODIFIER silent_mutation Average:71.486; most accessible tissue: Callus, score: 93.682 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406260245 NA 4.30E-06 mr1035 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
vg0406260245 NA 4.57E-10 mr1062 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
vg0406260245 1.66E-06 1.66E-06 mr1525 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
vg0406260245 NA 6.72E-06 mr1626 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
vg0406260245 6.43E-09 1.50E-11 mr1062_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
vg0406260245 2.81E-06 2.81E-06 mr1525_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
vg0406260245 NA 1.86E-08 mr1631_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