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Detailed information for vg0228555700:

Variant ID: vg0228555700 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28555700
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTTTTCTCTCTTCTGTCTCTTCTCTCTTCTATTCTGCGGCGGGTGGTGTGGCAATGGCGGCGTGCTTCCGCTGCGCGCGGCACGGCATCTGGCCCCAC[G/C]
GGGCCCAGCCTGGCGACCTCCGTCTACGATACTCACCTCGGCCTTGCCACGCTGTCCTGGACGCGCACCTCCCTCAGCCTCTCGCTCCGCGCCATGCTCC

Reverse complement sequence

GGAGCATGGCGCGGAGCGAGAGGCTGAGGGAGGTGCGCGTCCAGGACAGCGTGGCAAGGCCGAGGTGAGTATCGTAGACGGAGGTCGCCAGGCTGGGCCC[C/G]
GTGGGGCCAGATGCCGTGCCGCGCGCAGCGGAAGCACGCCGCCATTGCCACACCACCCGCCGCAGAATAGAAGAGAGAAGAGACAGAAGAGAGAAAAGAG

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 92.40% 7.00% 0.21% 0.30% NA
All Indica  2759 95.00% 4.40% 0.14% 0.51% NA
All Japonica  1512 99.60% 0.20% 0.20% 0.00% NA
Aus  269 22.70% 76.20% 1.12% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 95.70% 3.70% 0.00% 0.65% NA
Indica III  913 95.40% 3.80% 0.00% 0.77% NA
Indica Intermediate  786 90.60% 8.50% 0.38% 0.51% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.40% 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 95.60% 4.40% 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
vg0228555700 G -> DEL N N silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46750.1 upstream_gene_variant ; 3816.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46770.1 upstream_gene_variant ; 94.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46750.2 upstream_gene_variant ; 3821.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46750.3 upstream_gene_variant ; 3821.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46750.5 upstream_gene_variant ; 3821.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46750.4 upstream_gene_variant ; 3816.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46760.1 downstream_gene_variant ; 1939.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46780.1 downstream_gene_variant ; 2386.0bp to feature; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0228555700 G -> C LOC_Os02g46760-LOC_Os02g46770 intergenic_region ; MODIFIER silent_mutation Average:77.808; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228555700 3.68E-06 NA mr1200_2 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