Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0914433559:

Variant ID: vg0914433559 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 14433559
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TTTATGGCTGCACCATTTAATTTTCCACGTCATATGTTTGATCTGTACCACCATATTCTATCACATAATTAAAGAGGACAAGAACAAAAGTACGTGTCAT[A/T]
TGCATTTATCCATTCATGACTCAATTCTTTATCCTTCCACATCATCAACTCCACCTCCAACTCATTCTATCCCTAAGAATAAATGAAGAGATAAGAAAGC

Reverse complement sequence

GCTTTCTTATCTCTTCATTTATTCTTAGGGATAGAATGAGTTGGAGGTGGAGTTGATGATGTGGAAGGATAAAGAATTGAGTCATGAATGGATAAATGCA[T/A]
ATGACACGTACTTTTGTTCTTGTCCTCTTTAATTATGTGATAGAATATGGTGGTACAGATCAAACATATGACGTGGAAAATTAAATGGTGCAGCCATAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.30% 3.90% 7.83% 0.00% NA
All Indica  2759 99.70% 0.10% 0.22% 0.00% NA
All Japonica  1512 65.60% 11.20% 23.15% 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 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 99.40% 0.30% 0.38% 0.00% NA
Temperate Japonica  767 90.90% 2.00% 7.17% 0.00% NA
Tropical Japonica  504 33.50% 25.00% 41.47% 0.00% NA
Japonica Intermediate  241 52.30% 12.00% 35.68% 0.00% NA
VI/Aromatic  96 89.60% 5.20% 5.21% 0.00% NA
Intermediate  90 84.40% 5.60% 10.00% 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
vg0914433559 A -> T LOC_Os09g24290.1 upstream_gene_variant ; 812.0bp to feature; MODIFIER silent_mutation Average:34.123; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0914433559 A -> T LOC_Os09g24280-LOC_Os09g24290 intergenic_region ; MODIFIER silent_mutation Average:34.123; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0914433559 NA 8.59E-06 mr1502 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
vg0914433559 4.34E-06 8.58E-08 mr1543 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
vg0914433559 NA 5.88E-08 mr1543 Jap_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
vg0914433559 NA 8.12E-09 mr1449_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