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Detailed information for vg0127787157:

Variant ID: vg0127787157 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27787157
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTAGAGTATCATAAAGATGGAAGCACTAATCCCGATAACACAAGCCATCATAACAAGTTTTACCTCTTGTTGAAGATCGAAACTGATGCAGCTCAACC[C/T,A]
GAAAGCAAGAACTCGTCGAAATAAAACTAAAGCAAAAAGGTGGCGATGCGCTGAAATTGTATTGAACGTGTGTGTGTTTAATTACATAGGGCTCGGGGTC

Reverse complement sequence

GACCCCGAGCCCTATGTAATTAAACACACACACGTTCAATACAATTTCAGCGCATCGCCACCTTTTTGCTTTAGTTTTATTTCGACGAGTTCTTGCTTTC[G/A,T]
GGTTGAGCTGCATCAGTTTCGATCTTCAACAAGAGGTAAAACTTGTTATGATGGCTTGTGTTATCGGGATTAGTGCTTCCATCTTTATGATACTCTAATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.90% 0.40% 1.63% 7.02% NA
All Indica  2759 85.00% 0.60% 2.68% 11.71% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.13% NA
Aus  269 98.10% 1.10% 0.37% 0.37% NA
Indica I  595 87.40% 0.20% 4.20% 8.24% NA
Indica II  465 77.20% 0.90% 4.30% 17.63% NA
Indica III  913 87.00% 1.00% 0.55% 11.50% NA
Indica Intermediate  786 85.60% 0.30% 3.05% 11.07% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 1.04% 1.04% NA
Intermediate  90 93.30% 0.00% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0127787157 C -> T LOC_Os01g48446.1 upstream_gene_variant ; 4891.0bp to feature; MODIFIER silent_mutation Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> T LOC_Os01g48480.1 upstream_gene_variant ; 768.0bp to feature; MODIFIER silent_mutation Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> T LOC_Os01g48470.1 downstream_gene_variant ; 946.0bp to feature; MODIFIER silent_mutation Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> T LOC_Os01g48490.1 downstream_gene_variant ; 4364.0bp to feature; MODIFIER silent_mutation Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> T LOC_Os01g48470-LOC_Os01g48480 intergenic_region ; MODIFIER silent_mutation Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> A LOC_Os01g48446.1 upstream_gene_variant ; 4891.0bp to feature; MODIFIER N Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> A LOC_Os01g48480.1 upstream_gene_variant ; 768.0bp to feature; MODIFIER N Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> A LOC_Os01g48470.1 downstream_gene_variant ; 946.0bp to feature; MODIFIER N Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> A LOC_Os01g48490.1 downstream_gene_variant ; 4364.0bp to feature; MODIFIER N Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> A LOC_Os01g48470-LOC_Os01g48480 intergenic_region ; MODIFIER N Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0127787157 C -> DEL N N silent_mutation Average:10.448; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127787157 1.28E-06 NA mr1866 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