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Detailed information for vg1200352550:

Variant ID: vg1200352550 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 352550
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, A: 0.15, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TAAACAATCTTTATTACAGATCTAGCAAGTTCTTAATACTCTTGCTTCAACATAAGTTCTCTATACAACCTACACAGGATTCACCGATGCGTATACCAGC[T/A]
GAGCAATTCCTTACTTTAAGGGCATATGGTGCACCGCCAGTCATAGTAGCGCTTGCAGCACAAGGTGCTTTTCGTGGATTCATGGATACAAAGACACCGT

Reverse complement sequence

ACGGTGTCTTTGTATCCATGAATCCACGAAAAGCACCTTGTGCTGCAAGCGCTACTATGACTGGCGGTGCACCATATGCCCTTAAAGTAAGGAATTGCTC[A/T]
GCTGGTATACGCATCGGTGAATCCTGTGTAGGTTGTATAGAGAACTTATGTTGAAGCAAGAGTATTAAGAACTTGCTAGATCTGTAATAAAGATTGTTTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 6.20% 0.00% 0.00% NA
All Indica  2759 89.90% 10.10% 0.00% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 85.70% 14.30% 0.00% 0.00% NA
Indica Intermediate  786 89.70% 10.30% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 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
vg1200352550 T -> A LOC_Os12g01580.1 synonymous_variant ; p.Ala240Ala; LOW synonymous_codon Average:59.373; most accessible tissue: Callus, score: 83.049 N N N N
vg1200352550 T -> A LOC_Os12g01580.2 synonymous_variant ; p.Ala29Ala; LOW synonymous_codon Average:59.373; most accessible tissue: Callus, score: 83.049 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200352550 NA 3.45E-08 Awn_length Ind_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