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Detailed information for vg0206770457:

Variant ID: vg0206770457 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6770457
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGATTGCATTAAATACTTGACCAAGATTTCTGCCAATGAAGCCACAAGGCATGCATGCAACGCAGCATACAATGTTGTGTTCGTTTGCTTGTGTTGTAAC[A/T]
AATTCCCTTCACACGGAAGAGATACCTATTAGCATATGATTAATTAAGTATTAACTTTAAAAAACTTAAAAATGGATCAATAAAATTTTTAAAATAACTT

Reverse complement sequence

AAGTTATTTTAAAAATTTTATTGATCCATTTTTAAGTTTTTTAAAGTTAATACTTAATTAATCATATGCTAATAGGTATCTCTTCCGTGTGAAGGGAATT[T/A]
GTTACAACACAAGCAAACGAACACAACATTGTATGCTGCGTTGCATGCATGCCTTGTGGCTTCATTGGCAGAAATCTTGGTCAAGTATTTAATGCAATCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.10% 45.00% 0.76% 1.12% NA
All Indica  2759 88.30% 8.50% 1.30% 1.88% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 0.70% 99.30% 0.00% 0.00% NA
Indica I  595 94.50% 2.00% 1.68% 1.85% NA
Indica II  465 81.50% 17.20% 1.08% 0.22% NA
Indica III  913 90.00% 5.00% 1.10% 3.83% NA
Indica Intermediate  786 85.60% 12.30% 1.40% 0.64% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206770457 A -> T LOC_Os02g12840.1 upstream_gene_variant ; 856.0bp to feature; MODIFIER silent_mutation Average:46.335; most accessible tissue: Callus, score: 90.172 N N N N
vg0206770457 A -> T LOC_Os02g12830-LOC_Os02g12840 intergenic_region ; MODIFIER silent_mutation Average:46.335; most accessible tissue: Callus, score: 90.172 N N N N
vg0206770457 A -> DEL N N silent_mutation Average:46.335; most accessible tissue: Callus, score: 90.172 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206770457 NA 4.05E-09 mr1047 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
vg0206770457 NA 5.72E-15 mr1164 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
vg0206770457 1.44E-06 1.67E-08 mr1195 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
vg0206770457 NA 1.46E-29 mr1221 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
vg0206770457 NA 1.86E-14 mr1261 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
vg0206770457 NA 3.41E-09 mr1352 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
vg0206770457 NA 2.02E-42 mr1458 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
vg0206770457 NA 1.98E-06 mr1482 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
vg0206770457 NA 4.75E-23 mr1571 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
vg0206770457 NA 6.31E-20 mr1580 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
vg0206770457 8.55E-06 2.07E-07 mr1614 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
vg0206770457 NA 6.88E-06 mr1629 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
vg0206770457 NA 7.80E-09 mr1769 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
vg0206770457 NA 1.39E-06 mr1796 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
vg0206770457 NA 3.65E-17 mr1825 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
vg0206770457 NA 4.25E-24 mr1943 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
vg0206770457 NA 2.44E-55 mr1109_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
vg0206770457 NA 5.86E-18 mr1457_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
vg0206770457 NA 1.22E-46 mr1458_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
vg0206770457 NA 3.10E-07 mr1498_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
vg0206770457 NA 1.49E-30 mr1932_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
vg0206770457 NA 5.63E-07 mr1951_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