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Detailed information for vg0125462906:

Variant ID: vg0125462906 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25462906
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGACTTAAATTCTAGAGTATTACCCAATCACCCATTTATTTAATTTCTACCTATTTTACCGCTGAACCCCCTCACCTAAGTTCCACCCTAACTGCATT[G/T]
TAGCCTTTTATCTTCTTTCTTAAAATATGCCAAGAATATTTAAAACCCTTATGTTTATGGGTAGATGAGTACTTCATCCAGTTCTATAATTCTTGACGTT

Reverse complement sequence

AACGTCAAGAATTATAGAACTGGATGAAGTACTCATCTACCCATAAACATAAGGGTTTTAAATATTCTTGGCATATTTTAAGAAAGAAGATAAAAGGCTA[C/A]
AATGCAGTTAGGGTGGAACTTAGGTGAGGGGGTTCAGCGGTAAAATAGGTAGAAATTAAATAAATGGGTGATTGGGTAATACTCTAGAATTTAAGTCATG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.00% 13.00% 0.00% 0.00% NA
All Indica  2759 94.20% 5.80% 0.00% 0.00% NA
All Japonica  1512 71.30% 28.70% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 84.80% 15.20% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 75.60% 24.40% 0.00% 0.00% NA
Tropical Japonica  504 72.80% 27.20% 0.00% 0.00% NA
Japonica Intermediate  241 54.40% 45.60% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0125462906 G -> T LOC_Os01g44390.2 3_prime_UTR_variant ; 520.0bp to feature; MODIFIER silent_mutation Average:45.268; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0125462906 G -> T LOC_Os01g44380.1 upstream_gene_variant ; 3362.0bp to feature; MODIFIER silent_mutation Average:45.268; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0125462906 G -> T LOC_Os01g44394.1 upstream_gene_variant ; 3457.0bp to feature; MODIFIER silent_mutation Average:45.268; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N
vg0125462906 G -> T LOC_Os01g44390.1 intron_variant ; MODIFIER silent_mutation Average:45.268; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125462906 1.71E-07 1.68E-06 mr1219 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
vg0125462906 4.21E-07 NA mr1219_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
vg0125462906 NA 6.25E-06 mr1219_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