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Detailed information for vg1126328086:

Variant ID: vg1126328086 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26328086
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAAAAATATACATCTATATGTATATATATAAGTATATTTAACAATGAATCAATTGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGAC[G/A]
AACGGTCAAGCATATTTAAAAAAGTCAACGGCATCAAATATTTAGAAACGGGGGAGTATTAATAAGCAACGTGCTAATTGACACTCGGGATTTTTTTTAT

Reverse complement sequence

ATAAAAAAAATCCCGAGTGTCAATTAGCACGTTGCTTATTAATACTCCCCCGTTTCTAAATATTTGATGCCGTTGACTTTTTTAAATATGCTTGACCGTT[C/T]
GTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCAATTGATTCATTGTTAAATATACTTATATATATACATATAGATGTATATTTTTAAA

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 98.60% 1.40% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 96.50% 3.50% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 93.90% 6.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1126328086 G -> A LOC_Os11g43650.1 upstream_gene_variant ; 1602.0bp to feature; MODIFIER silent_mutation Average:29.509; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg1126328086 G -> A LOC_Os11g43640-LOC_Os11g43650 intergenic_region ; MODIFIER silent_mutation Average:29.509; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126328086 NA 2.12E-06 mr1069 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
vg1126328086 NA 4.71E-07 mr1149 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
vg1126328086 1.10E-06 5.75E-07 mr1441 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