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Detailed information for vg1011813560:

Variant ID: vg1011813560 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11813560
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


TTCACAATTTAAAGAGGTAAATTAATAAAACAAGAGCCAGAGGAACTATTTGACAAGTTTAAATGTCATCTATTATGGATTTTAAATCATAATTTACATT[G/A]
AAATGAGAAACGGAGGATGATAGACATAGAAGTTTCGAGGATAAACTAACAAAGGGATTTTATTATAAGAAAGAAAATGTGCAAACCTGGGAATTCATTA

Reverse complement sequence

TAATGAATTCCCAGGTTTGCACATTTTCTTTCTTATAATAAAATCCCTTTGTTAGTTTATCCTCGAAACTTCTATGTCTATCATCCTCCGTTTCTCATTT[C/T]
AATGTAAATTATGATTTAAAATCCATAATAGATGACATTTAAACTTGTCAAATAGTTCCTCTGGCTCTTGTTTTATTAATTTACCTCTTTAAATTGTGAA

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 93.50% 6.50% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 79.90% 20.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 61.30% 38.70% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 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
vg1011813560 G -> A LOC_Os10g22730.1 upstream_gene_variant ; 327.0bp to feature; MODIFIER silent_mutation Average:24.417; most accessible tissue: Callus, score: 72.344 N N N N
vg1011813560 G -> A LOC_Os10g22730.2 upstream_gene_variant ; 327.0bp to feature; MODIFIER silent_mutation Average:24.417; most accessible tissue: Callus, score: 72.344 N N N N
vg1011813560 G -> A LOC_Os10g22730.3 upstream_gene_variant ; 327.0bp to feature; MODIFIER silent_mutation Average:24.417; most accessible tissue: Callus, score: 72.344 N N N N
vg1011813560 G -> A LOC_Os10g22730.4 upstream_gene_variant ; 327.0bp to feature; MODIFIER silent_mutation Average:24.417; most accessible tissue: Callus, score: 72.344 N N N N
vg1011813560 G -> A LOC_Os10g22730-LOC_Os10g22740 intergenic_region ; MODIFIER silent_mutation Average:24.417; most accessible tissue: Callus, score: 72.344 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011813560 NA 1.06E-09 Heading_date 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
vg1011813560 3.90E-06 NA mr1335_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