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Detailed information for vg0102369472:

Variant ID: vg0102369472 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2369472
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAAATCATCCAGTGAGCCAGGTATATGCATCAGAATCCTCCAATGAGCCAAGCATATGCATCTGATCTGCCCACAATTGTCATTATACTATATGATTA[G/A]
CATTCCTCCATGCAAGCCAAGTTGCCAACGGAGAATCAAGGATCTAACAAGTTCCATCAGATCAGGGCCGGCCCTGCTTGTGCCCTTTTATCTTCCTCTT

Reverse complement sequence

AAGAGGAAGATAAAAGGGCACAAGCAGGGCCGGCCCTGATCTGATGGAACTTGTTAGATCCTTGATTCTCCGTTGGCAACTTGGCTTGCATGGAGGAATG[C/T]
TAATCATATAGTATAATGACAATTGTGGGCAGATCAGATGCATATGCTTGGCTCATTGGAGGATTCTGATGCATATACCTGGCTCACTGGATGATTTGAG

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 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 40.50% 59.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0102369472 G -> A LOC_Os01g05030.1 downstream_gene_variant ; 1554.0bp to feature; MODIFIER silent_mutation Average:36.933; most accessible tissue: Callus, score: 86.456 N N N N
vg0102369472 G -> A LOC_Os01g05040.1 downstream_gene_variant ; 57.0bp to feature; MODIFIER silent_mutation Average:36.933; most accessible tissue: Callus, score: 86.456 N N N N
vg0102369472 G -> A LOC_Os01g05050.1 downstream_gene_variant ; 2851.0bp to feature; MODIFIER silent_mutation Average:36.933; most accessible tissue: Callus, score: 86.456 N N N N
vg0102369472 G -> A LOC_Os01g05060.1 downstream_gene_variant ; 5000.0bp to feature; MODIFIER silent_mutation Average:36.933; most accessible tissue: Callus, score: 86.456 N N N N
vg0102369472 G -> A LOC_Os01g05030-LOC_Os01g05040 intergenic_region ; MODIFIER silent_mutation Average:36.933; most accessible tissue: Callus, score: 86.456 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102369472 6.68E-06 NA mr1228_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
vg0102369472 NA 1.29E-06 mr1597_2 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
vg0102369472 NA 5.80E-06 mr1912_2 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