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Detailed information for vg1109134145:

Variant ID: vg1109134145 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9134145
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAGGGTTTATATATCCGATCGAAATATAAGTTAATTGTTCTCGTAAAAATTCTCATGTATAAAGCTTATATGTTACTCCCTCTGGTTCTATATTAATT[G/A]
ACGTTTTGGACAAAGTTAAGGTTAAACTTTTATAGCTTTCACCATCAATAACTTTAAAAATATTTAGTTTAAAGAAACTAGAAAAACATATATAGATTTG

Reverse complement sequence

CAAATCTATATATGTTTTTCTAGTTTCTTTAAACTAAATATTTTTAAAGTTATTGATGGTGAAAGCTATAAAAGTTTAACCTTAACTTTGTCCAAAACGT[C/T]
AATTAATATAGAACCAGAGGGAGTAACATATAAGCTTTATACATGAGAATTTTTACGAGAACAATTAACTTATATTTCGATCGGATATATAAACCCTTAA

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 89.70% 8.20% 2.09% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 74.20% 19.40% 6.35% 0.00% NA
Aus  269 98.90% 0.40% 0.74% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 76.10% 14.10% 9.78% 0.00% NA
Tropical Japonica  504 69.40% 28.40% 2.18% 0.00% NA
Japonica Intermediate  241 78.00% 17.80% 4.15% 0.00% NA
VI/Aromatic  96 49.00% 50.00% 1.04% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1109134145 G -> A LOC_Os11g16500.1 downstream_gene_variant ; 547.0bp to feature; MODIFIER silent_mutation Average:35.859; most accessible tissue: Zhenshan97 young leaf, score: 47.311 N N N N
vg1109134145 G -> A LOC_Os11g16510.1 downstream_gene_variant ; 2750.0bp to feature; MODIFIER silent_mutation Average:35.859; most accessible tissue: Zhenshan97 young leaf, score: 47.311 N N N N
vg1109134145 G -> A LOC_Os11g16480-LOC_Os11g16500 intergenic_region ; MODIFIER silent_mutation Average:35.859; most accessible tissue: Zhenshan97 young leaf, score: 47.311 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109134145 NA 7.60E-07 mr1583 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
vg1109134145 5.37E-07 1.41E-08 mr1072_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
vg1109134145 1.25E-06 4.87E-08 mr1075_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
vg1109134145 NA 8.88E-07 mr1077_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
vg1109134145 NA 1.90E-07 mr1124_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
vg1109134145 NA 6.84E-07 mr1149_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
vg1109134145 NA 9.76E-07 mr1441_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