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Detailed information for vg0806225198:

Variant ID: vg0806225198 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6225198
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGATTTATTGCACTATGAAATATCCCATCCAATCTTAGGTTGTGTTCTTATCTCAGGTTTTCCAACTCATCTCTCTTGTTTTCCACGCGCACGCTTTTT[A/G]
AAATGCTAAACGGTGTTTTTTTTTTGCAAAAAGTTTCTATACTAAAATTGCTTAACAAAATCACATTTATCCATTTTTGAAAAAAAAGCCAATACTTAAT

Reverse complement sequence

ATTAAGTATTGGCTTTTTTTTCAAAAATGGATAAATGTGATTTTGTTAAGCAATTTTAGTATAGAAACTTTTTGCAAAAAAAAAACACCGTTTAGCATTT[T/C]
AAAAAGCGTGCGCGTGGAAAACAAGAGAGATGAGTTGGAAAACCTGAGATAAGAACACAACCTAAGATTGGATGGGATATTTCATAGTGCAATAAATCTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.70% 0.17% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 88.60% 11.00% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 1.00% 0.26% 0.00% NA
Tropical Japonica  504 73.40% 26.00% 0.60% 0.00% NA
Japonica Intermediate  241 88.00% 11.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 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
vg0806225198 A -> G LOC_Os08g10580.1 upstream_gene_variant ; 1074.0bp to feature; MODIFIER silent_mutation Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0806225198 A -> G LOC_Os08g10570.1 downstream_gene_variant ; 1145.0bp to feature; MODIFIER silent_mutation Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0806225198 A -> G LOC_Os08g10570.2 downstream_gene_variant ; 1145.0bp to feature; MODIFIER silent_mutation Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N
vg0806225198 A -> G LOC_Os08g10570-LOC_Os08g10580 intergenic_region ; MODIFIER silent_mutation Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806225198 1.29E-06 7.97E-09 mr1039_2 Jap_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
vg0806225198 NA 9.13E-08 mr1632_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