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Detailed information for vg0905069340:

Variant ID: vg0905069340 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5069340
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGCAGCATCACCAACAGTCATCATATTTCATTCCCAAAACGGATTTTGAGGGGTTTTTTTTTACAAATCAGATCCAACATATTCCCAAAAGCCTTACA[T/C]
TAGTTTTGGAGTTCCCATCTCCATATATTTCATTATGTAGATTTGAGGGTGAGAGAGCGACTCCCAATCTCTCGTTCGCGTGTTTCTCTCTCCTTCCCTG

Reverse complement sequence

CAGGGAAGGAGAGAGAAACACGCGAACGAGAGATTGGGAGTCGCTCTCTCACCCTCAAATCTACATAATGAAATATATGGAGATGGGAACTCCAAAACTA[A/G]
TGTAAGGCTTTTGGGAATATGTTGGATCTGATTTGTAAAAAAAAACCCCTCAAAATCCGTTTTGGGAATGAAATATGATGACTGTTGGTGATGCTGCGAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.30% 16.70% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 50.90% 49.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 72.20% 27.80% 0.00% 0.00% NA
Tropical Japonica  504 18.80% 81.20% 0.00% 0.00% NA
Japonica Intermediate  241 49.80% 50.20% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0905069340 T -> C LOC_Os09g09420.1 downstream_gene_variant ; 3847.0bp to feature; MODIFIER silent_mutation Average:41.108; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N
vg0905069340 T -> C LOC_Os09g09420-LOC_Os09g09430 intergenic_region ; MODIFIER silent_mutation Average:41.108; most accessible tissue: Zhenshan97 flag leaf, score: 63.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905069340 7.56E-07 NA mr1334 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
vg0905069340 NA 8.47E-07 mr1554 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
vg0905069340 NA 1.52E-11 mr1097_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
vg0905069340 NA 3.22E-09 mr1354_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
vg0905069340 NA 3.71E-07 mr1786_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