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Detailed information for vg0816158006:

Variant ID: vg0816158006 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16158006
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTATATCCTTGCTCCACACAAATTTCAAATTCTTATACCCATGAAACTCCTCAACAAAATCCTTAGCCTACTCCTTTAAGTCCCTTTTGCTTTACCTTC[G/A]
AACAAGCTCCAAATCAAAATTCCAAATTCATTCCTTTGAAATTTGTTTCCATCAAACCCAATGCTATTCATCCCGGCAAAAATTCCTATAAAACATCATT

Reverse complement sequence

AATGATGTTTTATAGGAATTTTTGCCGGGATGAATAGCATTGGGTTTGATGGAAACAAATTTCAAAGGAATGAATTTGGAATTTTGATTTGGAGCTTGTT[C/T]
GAAGGTAAAGCAAAAGGGACTTAAAGGAGTAGGCTAAGGATTTTGTTGAGGAGTTTCATGGGTATAAGAATTTGAAATTTGTGTGGAGCAAGGATATAAA

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 73.20% 26.70% 0.08% 0.00% NA
All Indica  2759 96.90% 3.00% 0.11% 0.00% NA
All Japonica  1512 31.00% 68.90% 0.07% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 95.30% 4.50% 0.17% 0.00% NA
Indica II  465 95.70% 3.90% 0.43% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.30% 0.00% 0.00% NA
Temperate Japonica  767 2.20% 97.80% 0.00% 0.00% NA
Tropical Japonica  504 75.80% 24.00% 0.20% 0.00% NA
Japonica Intermediate  241 29.00% 71.00% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0816158006 G -> A LOC_Os08g26530.1 downstream_gene_variant ; 4122.0bp to feature; MODIFIER silent_mutation Average:22.719; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 N N N N
vg0816158006 G -> A LOC_Os08g26544.1 downstream_gene_variant ; 112.0bp to feature; MODIFIER silent_mutation Average:22.719; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 N N N N
vg0816158006 G -> A LOC_Os08g26530-LOC_Os08g26544 intergenic_region ; MODIFIER silent_mutation Average:22.719; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816158006 NA 3.61E-06 mr1077 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
vg0816158006 NA 4.12E-07 mr1227 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
vg0816158006 NA 5.95E-07 mr1584 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
vg0816158006 NA 1.91E-07 mr1045_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
vg0816158006 NA 1.57E-25 mr1077_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
vg0816158006 NA 4.99E-06 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
vg0816158006 NA 1.20E-26 mr1441_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
vg0816158006 NA 3.07E-07 mr1482_2 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
vg0816158006 NA 5.93E-07 mr1498_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