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Detailed information for vg1224489196:

Variant ID: vg1224489196 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24489196
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AATCAACTAGCAGATATTTCATGATTTATAATTTTTTATTCAAGTCATGCATTTAGTCAATTTATCCAGCACCATACACCCATACAAAACCTAAATATTG[G/A]
TAATCTGAAATATCCTTATTTATGTCATCCAGTAACTAATGCTTGCTTATTCAGGTGGCGAAAGAGAGTGCCGATGTCATAATTCTGGACGACAACTTCT

Reverse complement sequence

AGAAGTTGTCGTCCAGAATTATGACATCGGCACTCTCTTTCGCCACCTGAATAAGCAAGCATTAGTTACTGGATGACATAAATAAGGATATTTCAGATTA[C/T]
CAATATTTAGGTTTTGTATGGGTGTATGGTGCTGGATAAATTGACTAAATGCATGACTTGAATAAAAAATTATAAATCATGAAATATCTGCTAGTTGATT

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 94.10% 5.70% 0.17% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 83.50% 16.00% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.70% 2.70% 0.52% 0.00% NA
Tropical Japonica  504 75.60% 24.00% 0.40% 0.00% NA
Japonica Intermediate  241 57.70% 41.50% 0.83% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1224489196 G -> A LOC_Os12g39670.1 upstream_gene_variant ; 3333.0bp to feature; MODIFIER silent_mutation Average:49.126; most accessible tissue: Callus, score: 77.756 N N N N
vg1224489196 G -> A LOC_Os12g39660.1 intron_variant ; MODIFIER silent_mutation Average:49.126; most accessible tissue: Callus, score: 77.756 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224489196 NA 1.18E-08 Grain_weight Jap_All YES 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