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Detailed information for vg0222926098:

Variant ID: vg0222926098 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22926098
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTAATTCATTTTTCAAGTTTGTAATAATTAAAACTCAATTAGTCGCACATTATTACCACATCGTTTTGCGTGAAACACTTAATCTTTATCTTCAGGA[G/T]
ATTAAAACACCACCTTAGTAATGACAAAACCCAAGAAAATTATACCTTCGCCTTTCTTGTTCATTCTTCTAATATTCCTCTTGCGAAGGGGTACCAGTCG

Reverse complement sequence

CGACTGGTACCCCTTCGCAAGAGGAATATTAGAAGAATGAACAAGAAAGGCGAAGGTATAATTTTCTTGGGTTTTGTCATTACTAAGGTGGTGTTTTAAT[C/A]
TCCTGAAGATAAAGATTAAGTGTTTCACGCAAAACGATGTGGTAATAATGTGCGACTAATTGAGTTTTAATTATTACAAACTTGAAAAATGAATTAATAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.20% 41.80% 1.02% 0.00% NA
All Indica  2759 90.60% 8.00% 1.41% 0.00% NA
All Japonica  1512 2.60% 97.00% 0.33% 0.00% NA
Aus  269 45.00% 54.60% 0.37% 0.00% NA
Indica I  595 91.60% 5.00% 3.36% 0.00% NA
Indica II  465 95.70% 3.00% 1.29% 0.00% NA
Indica III  913 87.70% 12.30% 0.00% 0.00% NA
Indica Intermediate  786 90.10% 8.30% 1.65% 0.00% NA
Temperate Japonica  767 0.70% 98.80% 0.52% 0.00% NA
Tropical Japonica  504 6.20% 93.80% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 97.90% 0.41% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 34.40% 62.20% 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
vg0222926098 G -> T LOC_Os02g37920.1 upstream_gene_variant ; 1609.0bp to feature; MODIFIER silent_mutation Average:64.002; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0222926098 G -> T LOC_Os02g37930.1 upstream_gene_variant ; 1498.0bp to feature; MODIFIER silent_mutation Average:64.002; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0222926098 G -> T LOC_Os02g37940.1 downstream_gene_variant ; 4875.0bp to feature; MODIFIER silent_mutation Average:64.002; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0222926098 G -> T LOC_Os02g37940.2 downstream_gene_variant ; 4875.0bp to feature; MODIFIER silent_mutation Average:64.002; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0222926098 G -> T LOC_Os02g37920-LOC_Os02g37930 intergenic_region ; MODIFIER silent_mutation Average:64.002; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222926098 NA 1.94E-35 mr1110 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
vg0222926098 7.87E-07 NA mr1113 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
vg0222926098 1.40E-09 NA mr1114 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
vg0222926098 2.21E-08 NA mr1116 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
vg0222926098 2.27E-07 NA mr1117 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
vg0222926098 1.08E-06 NA mr1118 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
vg0222926098 2.21E-06 NA mr1119 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
vg0222926098 1.67E-07 NA mr1123 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
vg0222926098 1.29E-09 NA mr1242 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
vg0222926098 8.59E-09 NA mr1496 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
vg0222926098 NA 1.16E-14 mr1592 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
vg0222926098 7.52E-06 NA mr1917 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
vg0222926098 NA 2.17E-38 mr1110_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
vg0222926098 7.77E-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
vg0222926098 4.98E-08 NA 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
vg0222926098 1.19E-06 NA mr1117_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
vg0222926098 7.74E-08 NA mr1118_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
vg0222926098 8.01E-06 NA mr1119_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
vg0222926098 3.02E-06 NA mr1123_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
vg0222926098 8.11E-10 NA mr1242_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
vg0222926098 2.58E-09 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