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Detailed information for vg1216284181:

Variant ID: vg1216284181 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16284181
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTACTATTTTCGAGTTCCTGGGAGTTCATACCATGTTCTCAGGAATAATACACAAATGTCCCAATAGGAATCTCGTTTGTTGTATAGTGATGACGTAT[A/G]
TGTTAGACATGGAAGGCATCATGAATTCTAGGTGGCCACATTTCCAGAGATCTAGTTGATAATTTCCAAAGTAGGATTAATGATCGACAAGGTAGTCAAA

Reverse complement sequence

TTTGACTACCTTGTCGATCATTAATCCTACTTTGGAAATTATCAACTAGATCTCTGGAAATGTGGCCACCTAGAATTCATGATGCCTTCCATGTCTAACA[T/C]
ATACGTCATCACTATACAACAAACGAGATTCCTATTGGGACATTTGTGTATTATTCCTGAGAACATGGTATGAACTCCCAGGAACTCGAAAATAGTAACA

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 90.60% 3.40% 0.17% 5.78% NA
All Indica  2759 91.40% 5.80% 0.04% 2.75% NA
All Japonica  1512 99.70% 0.10% 0.07% 0.13% NA
Aus  269 44.60% 0.00% 0.37% 55.02% NA
Indica I  595 96.80% 0.20% 0.00% 3.03% NA
Indica II  465 80.60% 17.80% 0.00% 1.51% NA
Indica III  913 92.20% 4.90% 0.11% 2.74% NA
Indica Intermediate  786 92.60% 4.10% 0.00% 3.31% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.40% 0.41% 0.83% NA
VI/Aromatic  96 51.00% 1.00% 3.12% 44.79% NA
Intermediate  90 93.30% 0.00% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216284181 A -> DEL N N silent_mutation Average:53.865; most accessible tissue: Callus, score: 66.322 N N N N
vg1216284181 A -> G LOC_Os12g27650.1 downstream_gene_variant ; 4300.0bp to feature; MODIFIER silent_mutation Average:53.865; most accessible tissue: Callus, score: 66.322 N N N N
vg1216284181 A -> G LOC_Os12g27650-LOC_Os12g27670 intergenic_region ; MODIFIER silent_mutation Average:53.865; most accessible tissue: Callus, score: 66.322 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216284181 NA 1.04E-06 mr1188 Ind_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
vg1216284181 4.82E-06 5.64E-07 mr1679_2 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
vg1216284181 NA 1.67E-06 mr1711_2 Ind_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
vg1216284181 5.41E-06 NA mr1902_2 Ind_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