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Detailed information for vg0918111646:

Variant ID: vg0918111646 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18111646
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTCTCGGTTATACGCGGTCACACTGAGCTCGTGTTAGCCTCGCGCAGGAAGGGGGAGACGCCGCGGCCGCGGGGGCTGCTGCTGCCGTGCAGCAGCAG[G/C]
AGGAGGAGGAGGTGGAGGCGAAGCCCCAGTTGCTGCGTGAAGACGACTCGTAATTCGCGATCTCCCTCTGTTACTATGCTCCTTGTTTTACTGCAATGCG

Reverse complement sequence

CGCATTGCAGTAAAACAAGGAGCATAGTAACAGAGGGAGATCGCGAATTACGAGTCGTCTTCACGCAGCAACTGGGGCTTCGCCTCCACCTCCTCCTCCT[C/G]
CTGCTGCTGCACGGCAGCAGCAGCCCCCGCGGCCGCGGCGTCTCCCCCTTCCTGCGCGAGGCTAACACGAGCTCAGTGTGACCGCGTATAACCGAGAGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 3.00% 0.32% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.80% 9.20% 0.99% 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 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 72.20% 25.20% 2.58% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0918111646 G -> C LOC_Os09g29790.1 upstream_gene_variant ; 2333.0bp to feature; MODIFIER silent_mutation Average:87.418; most accessible tissue: Zhenshan97 flower, score: 92.326 N N N N
vg0918111646 G -> C LOC_Os09g29810.1 upstream_gene_variant ; 3479.0bp to feature; MODIFIER silent_mutation Average:87.418; most accessible tissue: Zhenshan97 flower, score: 92.326 N N N N
vg0918111646 G -> C LOC_Os09g29800.1 intron_variant ; MODIFIER silent_mutation Average:87.418; most accessible tissue: Zhenshan97 flower, score: 92.326 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918111646 NA 6.67E-12 mr1490 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
vg0918111646 NA 1.96E-07 mr1746 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
vg0918111646 NA 1.74E-09 mr1951 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
vg0918111646 NA 1.74E-09 mr1019_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