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Detailed information for vg1107488855:

Variant ID: vg1107488855 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7488855
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCATGATCAATTGCACAATTCATTCTTATCTTCAAGGCACTAACCAACTCAACCCCAAGTCATTACTTATATGTTGTTGTCTTGAGTTACTTATATTTA[A/G]
TCATTTATTACATACTTTTATTCTAAGAAGTGCCTTACAAAGTCTTAAGAAAATGCCTTTATATATCAGGCACAGTTTAAAGTGCCGAAAGAATACCTCT

Reverse complement sequence

AGAGGTATTCTTTCGGCACTTTAAACTGTGCCTGATATATAAAGGCATTTTCTTAAGACTTTGTAAGGCACTTCTTAGAATAAAAGTATGTAATAAATGA[T/C]
TAAATATAAGTAACTCAAGACAACAACATATAAGTAATGACTTGGGGTTGAGTTGGTTAGTGCCTTGAAGATAAGAATGAATTGTGCAATTGATCATGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.60% 12.40% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 67.70% 32.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 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 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 66.40% 33.60% 0.00% 0.00% NA
Tropical Japonica  504 74.40% 25.60% 0.00% 0.00% NA
Japonica Intermediate  241 57.70% 42.30% 0.00% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg1107488855 A -> G LOC_Os11g13660.1 downstream_gene_variant ; 1598.0bp to feature; MODIFIER silent_mutation Average:23.167; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N
vg1107488855 A -> G LOC_Os11g13660-LOC_Os11g13670 intergenic_region ; MODIFIER silent_mutation Average:23.167; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107488855 2.50E-06 2.50E-06 mr1244 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
vg1107488855 NA 6.68E-06 mr1740 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
vg1107488855 7.72E-06 NA mr1961 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
vg1107488855 NA 8.45E-08 mr1961 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