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Detailed information for vg1218320197:

Variant ID: vg1218320197 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18320197
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGGGCATTAATTTTCTTTGGCTGCAGCACTATTCAAGGTCCAAAATTTTCATGGAAAGCTTCTTTATTTTAAATTAGGTCTTTGTTCCTTAAAAAAAA[G/A]
TAGGTGCGCTACCAAATAAAAAGTGCTATTTGCGAAAGGAACTCATAATTTATTATATGGAACTGACCTCAAGCATGGAGTTCTGGATTTTGTGATGCCA

Reverse complement sequence

TGGCATCACAAAATCCAGAACTCCATGCTTGAGGTCAGTTCCATATAATAAATTATGAGTTCCTTTCGCAAATAGCACTTTTTATTTGGTAGCGCACCTA[C/T]
TTTTTTTTAAGGAACAAAGACCTAATTTAAAATAAAGAAGCTTTCCATGAAAATTTTGGACCTTGAATAGTGCTGCAGCCAAAGAAAATTAATGCCCAGA

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 99.00% 0.40% 0.53% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 97.20% 1.30% 1.52% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 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% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 94.90% 2.60% 2.48% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1218320197 G -> A LOC_Os12g30520.1 upstream_gene_variant ; 1130.0bp to feature; MODIFIER silent_mutation Average:45.521; most accessible tissue: Callus, score: 85.67 N N N N
vg1218320197 G -> A LOC_Os12g30520-LOC_Os12g30540 intergenic_region ; MODIFIER silent_mutation Average:45.521; most accessible tissue: Callus, score: 85.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218320197 NA 5.52E-12 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1218320197 4.66E-06 1.38E-07 mr1201 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
vg1218320197 NA 3.06E-06 mr1219 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
vg1218320197 2.72E-08 5.11E-09 mr1274 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
vg1218320197 NA 3.11E-06 mr1274_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