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Detailed information for vg0812788939:

Variant ID: vg0812788939 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12788939
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGGCAATATCGCTATCTAACCTACAATCGGCTAACATCGATCTGTCAGTAGAAGACAGCCGACTAGGTTAAATACCGATGTTGACTTAGATTATATAGGA[T/A]
ATCCACCACTCTATGACACATCCAACGGCTTAATTGTCTAGATATTGTCTTTTTTTTCATACTTATAGCTGCATCAGTTGGATTTGATCTTATGAGTCGT

Reverse complement sequence

ACGACTCATAAGATCAAATCCAACTGATGCAGCTATAAGTATGAAAAAAAAGACAATATCTAGACAATTAAGCCGTTGGATGTGTCATAGAGTGGTGGAT[A/T]
TCCTATATAATCTAAGTCAACATCGGTATTTAACCTAGTCGGCTGTCTTCTACTGACAGATCGATGTTAGCCGATTGTAGGTTAGATAGCGATATTGCCG

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 99.90% 0.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0812788939 T -> A LOC_Os08g21460.1 upstream_gene_variant ; 1015.0bp to feature; MODIFIER N Average:17.286; most accessible tissue: Minghui63 flag leaf, score: 28.142 N N N N
vg0812788939 T -> A LOC_Os08g21450.1 downstream_gene_variant ; 3079.0bp to feature; MODIFIER N Average:17.286; most accessible tissue: Minghui63 flag leaf, score: 28.142 N N N N
vg0812788939 T -> A LOC_Os08g21450-LOC_Os08g21460 intergenic_region ; MODIFIER N Average:17.286; most accessible tissue: Minghui63 flag leaf, score: 28.142 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812788939 4.45E-07 1.92E-06 mr1519 Ind_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
vg0812788939 7.03E-06 8.07E-06 mr1768 Ind_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