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Detailed information for vg0401209853:

Variant ID: vg0401209853 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1209853
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAAAAAATTTGAATAGGACAAATGATCAAACGTTGATAAAAAATAAACATCGTTATACATTAATAAAATGGAGTTAGTATATGTGTATGGAGAGGTGTA[T/A]
GCATGGCTGATTGACAAACTATACAATATTTGAAGATTTACATTGTCTACCTTGGGGAGAGACGACACGATGATGCTGATGTCGTCACTGGTTCCCACCA

Reverse complement sequence

TGGTGGGAACCAGTGACGACATCAGCATCATCGTGTCGTCTCTCCCCAAGGTAGACAATGTAAATCTTCAAATATTGTATAGTTTGTCAATCAGCCATGC[A/T]
TACACCTCTCCATACACATATACTAACTCCATTTTATTAATGTATAACGATGTTTATTTTTTATCAACGTTTGATCATTTGTCCTATTCAAATTTTTTGT

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 99.40% 0.60% 0.00% 0.00% NA
All Japonica  1512 81.90% 18.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 72.60% 27.40% 0.00% 0.00% NA
Tropical Japonica  504 96.00% 4.00% 0.00% 0.00% NA
Japonica Intermediate  241 81.70% 18.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0401209853 T -> A LOC_Os04g02980.1 upstream_gene_variant ; 31.0bp to feature; MODIFIER silent_mutation Average:46.003; most accessible tissue: Minghui63 root, score: 79.068 N N N N
vg0401209853 T -> A LOC_Os04g02970-LOC_Os04g02980 intergenic_region ; MODIFIER silent_mutation Average:46.003; most accessible tissue: Minghui63 root, score: 79.068 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401209853 6.47E-07 NA mr1648_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
vg0401209853 2.01E-06 NA mr1672_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