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Detailed information for vg0220811012:

Variant ID: vg0220811012 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20811012
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAACCCCATCAACCATCTCGCTCCTCCATGCAGGAAGTCAGCAACACCAGTTGATGACACCAACACACAAGACATTTGATAATTTAATATTTTTTCCA[G/T]
TGTCCAATTTATTTTAATTAAAACTTATAGGATTGATACTCTATCCGTAAAAAAAAGAAAAACCTAAAACACGCTGTGACCAGGATGTAACCTCTCTTAA

Reverse complement sequence

TTAAGAGAGGTTACATCCTGGTCACAGCGTGTTTTAGGTTTTTCTTTTTTTTACGGATAGAGTATCAATCCTATAAGTTTTAATTAAAATAAATTGGACA[C/A]
TGGAAAAAATATTAAATTATCAAATGTCTTGTGTGTTGGTGTCATCAACTGGTGTTGCTGACTTCCTGCATGGAGGAGCGAGATGGTTGATGGGGTTGAG

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 75.50% 24.40% 0.02% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 34.40% 65.60% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 31.60% 68.40% 0.00% 0.00% NA
Tropical Japonica  504 32.70% 67.30% 0.00% 0.00% NA
Japonica Intermediate  241 46.90% 53.10% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 52.20% 46.70% 1.11% 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
vg0220811012 G -> T LOC_Os02g34690.1 upstream_gene_variant ; 328.0bp to feature; MODIFIER silent_mutation Average:74.761; most accessible tissue: Callus, score: 93.886 N N N N
vg0220811012 G -> T LOC_Os02g34680-LOC_Os02g34690 intergenic_region ; MODIFIER silent_mutation Average:74.761; most accessible tissue: Callus, score: 93.886 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220811012 NA 4.34E-13 mr1128_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
vg0220811012 NA 3.34E-07 mr1205_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
vg0220811012 NA 2.24E-06 mr1272_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
vg0220811012 NA 9.99E-08 mr1275_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
vg0220811012 NA 2.41E-14 mr1575_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
vg0220811012 NA 4.74E-07 mr1604_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
vg0220811012 NA 7.88E-10 mr1646_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
vg0220811012 8.06E-06 NA mr1770_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
vg0220811012 NA 9.35E-07 mr1770_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
vg0220811012 NA 8.53E-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
vg0220811012 NA 7.94E-08 mr1921_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