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Detailed information for vg1125547775:

Variant ID: vg1125547775 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25547775
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAAAATTGGAAGTTTGATTGAAATTGAAACGATGTGATGGAAAAATTAAAAATTTGTGTGCGTAGGAAAGTTTCGATGTGATGAAAAAGTTAAAAGTTT[G/A]
AAGAAAAAGTTGAGAACTAAACTCAGCCTATGCTTTGATCGCCAAAATTTGTTTAACATGAAGAAGAAGGAACAGAGAAAATGAGTTCAAACCCTCTGTG

Reverse complement sequence

CACAGAGGGTTTGAACTCATTTTCTCTGTTCCTTCTTCTTCATGTTAAACAAATTTTGGCGATCAAAGCATAGGCTGAGTTTAGTTCTCAACTTTTTCTT[C/T]
AAACTTTTAACTTTTTCATCACATCGAAACTTTCCTACGCACACAAATTTTTAATTTTTCCATCACATCGTTTCAATTTCAATCAAACTTCCAATTTTGG

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 96.30% 3.70% 0.04% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 87.70% 11.90% 0.37% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg1125547775 G -> A LOC_Os11g42450.1 upstream_gene_variant ; 4337.0bp to feature; MODIFIER silent_mutation Average:42.457; most accessible tissue: Callus, score: 73.239 N N N N
vg1125547775 G -> A LOC_Os11g42440.1 downstream_gene_variant ; 240.0bp to feature; MODIFIER silent_mutation Average:42.457; most accessible tissue: Callus, score: 73.239 N N N N
vg1125547775 G -> A LOC_Os11g42440-LOC_Os11g42450 intergenic_region ; MODIFIER silent_mutation Average:42.457; most accessible tissue: Callus, score: 73.239 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125547775 5.90E-16 1.28E-12 mr1191 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
vg1125547775 3.79E-13 1.77E-13 mr1644 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
vg1125547775 2.94E-20 2.27E-13 mr1191_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
vg1125547775 NA 2.65E-06 mr1662_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