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Detailed information for vg0605437555:

Variant ID: vg0605437555 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5437555
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.06, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


CGAACCTGCGATTCACCTGTAAATCCAATCATCTCCAAAACCACTTCGTGAACAAAACCAATAATCTCTAATACCCAATTATTCATCACAGAATAATAAT[A/C]
AAAAACACCTTTGATTTTATAATCTCCCCCTTGATGAACACATTGGCAAACCAATAAAAAATGTTTTGGTGTTTGGAAAAATAAAAACAAAAGTGATAAA

Reverse complement sequence

TTTATCACTTTTGTTTTTATTTTTCCAAACACCAAAACATTTTTTATTGGTTTGCCAATGTGTTCATCAAGGGGGAGATTATAAAATCAAAGGTGTTTTT[T/G]
ATTATTATTCTGTGATGAATAATTGGGTATTAGAGATTATTGGTTTTGTTCACGAAGTGGTTTTGGAGATGATTGGATTTACAGGTGAATCGCAGGTTCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.80% 8.20% 0.02% 0.00% NA
All Indica  2759 87.60% 12.40% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 77.60% 22.40% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 85.80% 14.20% 0.00% 0.00% NA
Indica Intermediate  786 89.80% 10.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0605437555 A -> C LOC_Os06g10540.1 upstream_gene_variant ; 3773.0bp to feature; MODIFIER silent_mutation Average:37.649; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0605437555 A -> C LOC_Os06g10550.1 downstream_gene_variant ; 1137.0bp to feature; MODIFIER silent_mutation Average:37.649; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N
vg0605437555 A -> C LOC_Os06g10540-LOC_Os06g10550 intergenic_region ; MODIFIER silent_mutation Average:37.649; most accessible tissue: Minghui63 panicle, score: 50.413 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0605437555 4.69E-12 2.79E-26 mr1201 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
vg0605437555 1.26E-13 1.13E-27 mr1201 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
vg0605437555 2.87E-09 6.05E-18 mr1219 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
vg0605437555 8.95E-11 6.83E-22 mr1219 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
vg0605437555 2.54E-11 1.61E-22 mr1274 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
vg0605437555 2.04E-14 2.30E-23 mr1274 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
vg0605437555 1.61E-10 3.25E-21 mr1201_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
vg0605437555 3.41E-13 4.06E-22 mr1201_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
vg0605437555 1.18E-06 1.87E-13 mr1219_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
vg0605437555 3.28E-09 3.34E-16 mr1219_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
vg0605437555 7.49E-09 1.90E-20 mr1274_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
vg0605437555 1.15E-10 4.53E-21 mr1274_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