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Detailed information for vg1016458801:

Variant ID: vg1016458801 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16458801
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTGGCGACGATCTCGTGCGGAGAGGGACCCGGTGGCTAGCGGCCACCTCATGTGGAGAGGGACCTCGGCGGCGACCTCGTGCGGAGAGGGACCTCGGC[G/A]
GTGACCTCACATGGAGAGGGACCCCGGCGGTGACCTTGGTGGATTGACGAGTGAGTTTGTGCATCTTGCTTGTGTTCTTCATCTGTGATGGGAACTATTG

Reverse complement sequence

CAATAGTTCCCATCACAGATGAAGAACACAAGCAAGATGCACAAACTCACTCGTCAATCCACCAAGGTCACCGCCGGGGTCCCTCTCCATGTGAGGTCAC[C/T]
GCCGAGGTCCCTCTCCGCACGAGGTCGCCGCCGAGGTCCCTCTCCACATGAGGTGGCCGCTAGCCACCGGGTCCCTCTCCGCACGAGATCGTCGCCAGCC

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 88.20% 11.80% 0.02% 0.00% NA
All Indica  2759 80.10% 19.90% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.90% 8.10% 0.00% 0.00% NA
Indica II  465 76.60% 23.40% 0.00% 0.00% NA
Indica III  913 72.90% 26.90% 0.11% 0.00% NA
Indica Intermediate  786 81.40% 18.60% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 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
vg1016458801 G -> A LOC_Os10g31370.1 upstream_gene_variant ; 3724.0bp to feature; MODIFIER silent_mutation Average:77.775; most accessible tissue: Zhenshan97 young leaf, score: 90.175 N N N N
vg1016458801 G -> A LOC_Os10g31380.1 upstream_gene_variant ; 1603.0bp to feature; MODIFIER silent_mutation Average:77.775; most accessible tissue: Zhenshan97 young leaf, score: 90.175 N N N N
vg1016458801 G -> A LOC_Os10g31380-LOC_Os10g31390 intergenic_region ; MODIFIER silent_mutation Average:77.775; most accessible tissue: Zhenshan97 young leaf, score: 90.175 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016458801 NA 1.04E-06 mr1425 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
vg1016458801 1.83E-06 1.83E-06 mr1866 Ind_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