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Detailed information for vg0225218022:

Variant ID: vg0225218022 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25218022
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAATAAGCCTATTTTTGAAAGCGGACCTCTTAAGGGACCGCACGAGAAAATATATTTTTGCAGGCGGGCCTCCTAAGGATCCACCTAAATTCTAAGTT[A/T]
CCTCCTTATTTTTCTCTAACATTTCAAAATTTTTCATCCTTATCCACTCATCTCTCTCTCTCACCTTCTATCCTCATTATTTTCTCTCCACTCTCTCACC

Reverse complement sequence

GGTGAGAGAGTGGAGAGAAAATAATGAGGATAGAAGGTGAGAGAGAGAGATGAGTGGATAAGGATGAAAAATTTTGAAATGTTAGAGAAAAATAAGGAGG[T/A]
AACTTAGAATTTAGGTGGATCCTTAGGAGGCCCGCCTGCAAAAATATATTTTCTCGTGCGGTCCCTTAAGAGGTCCGCTTTCAAAAATAGGCTTATTTTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.70% 12.90% 0.34% 0.00% NA
All Indica  2759 82.20% 17.20% 0.58% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 74.70% 25.30% 0.00% 0.00% NA
Indica I  595 61.30% 36.60% 2.02% 0.00% NA
Indica II  465 93.50% 6.20% 0.22% 0.00% NA
Indica III  913 84.90% 15.10% 0.00% 0.00% NA
Indica Intermediate  786 88.30% 11.30% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 43.80% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0225218022 A -> T LOC_Os02g41970.1 upstream_gene_variant ; 2940.0bp to feature; MODIFIER silent_mutation Average:45.671; most accessible tissue: Callus, score: 71.666 N N N N
vg0225218022 A -> T LOC_Os02g41961.1 downstream_gene_variant ; 1599.0bp to feature; MODIFIER silent_mutation Average:45.671; most accessible tissue: Callus, score: 71.666 N N N N
vg0225218022 A -> T LOC_Os02g41961-LOC_Os02g41970 intergenic_region ; MODIFIER silent_mutation Average:45.671; most accessible tissue: Callus, score: 71.666 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225218022 NA 1.56E-09 mr1067 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
vg0225218022 NA 6.61E-07 mr1962 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
vg0225218022 NA 3.35E-06 mr1074_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
vg0225218022 NA 1.10E-07 mr1123_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
vg0225218022 NA 2.10E-06 mr1242_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
vg0225218022 NA 6.15E-06 mr1291_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
vg0225218022 NA 2.60E-08 mr1496_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
vg0225218022 NA 1.84E-06 mr1558_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
vg0225218022 NA 1.57E-09 mr1835_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
vg0225218022 NA 1.03E-13 mr1904_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
vg0225218022 NA 9.35E-08 mr1904_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
vg0225218022 NA 1.30E-07 mr1936_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
vg0225218022 NA 3.55E-10 mr1962_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