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Detailed information for vg0124571825:

Variant ID: vg0124571825 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24571825
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTCACATATATACTCTGTTCATTTCATATTATATGTTGTTTGACTTTTTTTTAATCAAAATTATTTAGACTTGATAAAAAATAACAATATCTAGGACAC[C/T]
AAATTAGTTCCATTAAATTTAACTTTGAATAAATTTTGATTCAACGTTTGTTTTATATTGAAAATGTTATTATATTTTATTATGAGACGGGGTGAGTAGT

Reverse complement sequence

ACTACTCACCCCGTCTCATAATAAAATATAATAACATTTTCAATATAAAACAAACGTTGAATCAAAATTTATTCAAAGTTAAATTTAATGGAACTAATTT[G/A]
GTGTCCTAGATATTGTTATTTTTTATCAAGTCTAAATAATTTTGATTAAAAAAAAGTCAAACAACATATAATATGAAATGAACAGAGTATATATGTGACG

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 97.90% 1.70% 0.42% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 93.60% 5.20% 1.26% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 87.70% 10.20% 2.09% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0124571825 C -> T LOC_Os01g43060.1 upstream_gene_variant ; 290.0bp to feature; MODIFIER silent_mutation Average:83.166; most accessible tissue: Callus, score: 97.439 N N N N
vg0124571825 C -> T LOC_Os01g43070.1 upstream_gene_variant ; 1157.0bp to feature; MODIFIER silent_mutation Average:83.166; most accessible tissue: Callus, score: 97.439 N N N N
vg0124571825 C -> T LOC_Os01g43070.2 upstream_gene_variant ; 1157.0bp to feature; MODIFIER silent_mutation Average:83.166; most accessible tissue: Callus, score: 97.439 N N N N
vg0124571825 C -> T LOC_Os01g43050.1 downstream_gene_variant ; 3162.0bp to feature; MODIFIER silent_mutation Average:83.166; most accessible tissue: Callus, score: 97.439 N N N N
vg0124571825 C -> T LOC_Os01g43080.1 downstream_gene_variant ; 3478.0bp to feature; MODIFIER silent_mutation Average:83.166; most accessible tissue: Callus, score: 97.439 N N N N
vg0124571825 C -> T LOC_Os01g43060-LOC_Os01g43070 intergenic_region ; MODIFIER silent_mutation Average:83.166; most accessible tissue: Callus, score: 97.439 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124571825 NA 1.05E-08 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
vg0124571825 3.94E-06 NA mr1095 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
vg0124571825 NA 4.52E-06 mr1358 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
vg0124571825 2.67E-06 2.67E-06 mr1589 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