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Detailed information for vg0222271516:

Variant ID: vg0222271516 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22271516
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTATAATATACCGACGACTTTATCAATTGTTCTACAATACGCTATTGGGTTGGGCCTTTTTTTTCAAAAATACCTAAAATATCCTTAGAGACATACAA[G/A]
ATTAACAATTGATTTATCTCATTAGAAGTTTCAAAAAAATATGAAAAGTTTTATGTGGCCTTGTTACACAACATGGAAGTTTGTATAATGTTTCAAGTTT

Reverse complement sequence

AAACTTGAAACATTATACAAACTTCCATGTTGTGTAACAAGGCCACATAAAACTTTTCATATTTTTTTGAAACTTCTAATGAGATAAATCAATTGTTAAT[C/T]
TTGTATGTCTCTAAGGATATTTTAGGTATTTTTGAAAAAAAAGGCCCAACCCAATAGCGTATTGTAGAACAATTGATAAAGTCGTCGGTATATTATAGAA

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 86.90% 2.80% 3.47% 6.88% NA
All Indica  2759 80.90% 2.10% 5.51% 11.49% NA
All Japonica  1512 99.30% 0.10% 0.26% 0.33% NA
Aus  269 78.80% 20.10% 1.12% 0.00% NA
Indica I  595 78.80% 0.70% 9.41% 11.09% NA
Indica II  465 63.70% 1.30% 7.53% 27.53% NA
Indica III  913 95.00% 0.70% 1.86% 2.52% NA
Indica Intermediate  786 76.50% 5.20% 5.60% 12.72% NA
Temperate Japonica  767 99.50% 0.00% 0.26% 0.26% NA
Tropical Japonica  504 99.40% 0.00% 0.20% 0.40% NA
Japonica Intermediate  241 98.80% 0.40% 0.41% 0.41% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 91.10% 0.00% 5.56% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0222271516 G -> A LOC_Os02g36890.1 downstream_gene_variant ; 1274.0bp to feature; MODIFIER silent_mutation Average:27.286; most accessible tissue: Callus, score: 66.752 N N N N
vg0222271516 G -> A LOC_Os02g36890-LOC_Os02g36910 intergenic_region ; MODIFIER silent_mutation Average:27.286; most accessible tissue: Callus, score: 66.752 N N N N
vg0222271516 G -> DEL N N silent_mutation Average:27.286; most accessible tissue: Callus, score: 66.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222271516 1.82E-07 NA mr1098_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
vg0222271516 1.03E-06 NA mr1098_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
vg0222271516 3.67E-07 NA mr1099_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
vg0222271516 2.23E-07 NA mr1099_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
vg0222271516 1.21E-07 NA mr1113_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
vg0222271516 2.81E-07 1.25E-16 mr1114_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
vg0222271516 8.80E-08 NA mr1117_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
vg0222271516 1.68E-08 1.88E-17 mr1119_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
vg0222271516 4.11E-07 NA mr1120_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
vg0222271516 1.99E-06 NA mr1120_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
vg0222271516 3.90E-09 NA mr1123_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
vg0222271516 7.05E-08 1.00E-06 mr1123_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
vg0222271516 2.91E-08 NA mr1150_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
vg0222271516 8.79E-07 NA mr1150_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
vg0222271516 5.60E-09 NA mr1240_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
vg0222271516 6.98E-08 NA mr1242_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
vg0222271516 7.59E-06 1.22E-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
vg0222271516 3.50E-09 NA mr1247_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
vg0222271516 6.78E-08 8.08E-06 mr1247_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
vg0222271516 NA 2.10E-06 mr1378_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
vg0222271516 3.71E-08 NA mr1496_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
vg0222271516 1.34E-06 NA mr1936_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
vg0222271516 NA 2.53E-06 mr1968_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