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Detailed information for vg0807824555:

Variant ID: vg0807824555 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7824555
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCACGATCGTAGCACCTTAAGCCTTGCGGTGATTCTAGAGTCGCCAACCACCTCGATCTAGCAAAGAGCTAAATCTAGATGGGTTTTGATAACTAAACC[G/A]
GCTAGCGGAGCCGATTTCTAGATAACTACCTGTCTCATGGGCAAAACAGAAGGTTTTCAGGACAAACATACAAAGAGATGTCGCACTCTCGCAGCGGCGG

Reverse complement sequence

CCGCCGCTGCGAGAGTGCGACATCTCTTTGTATGTTTGTCCTGAAAACCTTCTGTTTTGCCCATGAGACAGGTAGTTATCTAGAAATCGGCTCCGCTAGC[C/T]
GGTTTAGTTATCAAAACCCATCTAGATTTAGCTCTTTGCTAGATCGAGGTGGTTGGCGACTCTAGAATCACCGCAAGGCTTAAGGTGCTACGATCGTGCT

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 95.70% 2.50% 0.21% 1.63% NA
All Indica  2759 96.90% 0.00% 0.33% 2.75% NA
All Japonica  1512 92.60% 7.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 98.30% 0.00% 0.22% 1.51% NA
Indica III  913 92.30% 0.10% 0.88% 6.68% NA
Indica Intermediate  786 99.10% 0.00% 0.00% 0.89% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 68.00% 32.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0807824555 G -> A LOC_Os08g13160.1 downstream_gene_variant ; 3907.0bp to feature; MODIFIER silent_mutation Average:38.995; most accessible tissue: Callus, score: 55.732 N N N N
vg0807824555 G -> A LOC_Os08g13170.1 downstream_gene_variant ; 586.0bp to feature; MODIFIER silent_mutation Average:38.995; most accessible tissue: Callus, score: 55.732 N N N N
vg0807824555 G -> A LOC_Os08g13160-LOC_Os08g13170 intergenic_region ; MODIFIER silent_mutation Average:38.995; most accessible tissue: Callus, score: 55.732 N N N N
vg0807824555 G -> DEL N N silent_mutation Average:38.995; most accessible tissue: Callus, score: 55.732 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807824555 NA 2.08E-06 mr1123 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
vg0807824555 NA 5.15E-06 mr1242 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
vg0807824555 1.12E-06 NA mr1757 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
vg0807824555 NA 2.36E-06 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