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Detailed information for vg0906972834:

Variant ID: vg0906972834 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6972834
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATATTTTTTTAATATTTTTACTAGCTTAGCTACTCTAAAGTGTTTCTTAGAATCTCACAAGTTATTTCTAGCGATAGAAATTTATGAATCTGGATCC[G/A]
TGGTAATATTTGGTTGAATCAGTTATTTCTATTTTAAGTAAATATAATTATTAAAACCATTTTAATGTATATGTACAAGCACTAACTACACGATCGATTT

Reverse complement sequence

AAATCGATCGTGTAGTTAGTGCTTGTACATATACATTAAAATGGTTTTAATAATTATATTTACTTAAAATAGAAATAACTGATTCAACCAAATATTACCA[C/T]
GGATCCAGATTCATAAATTTCTATCGCTAGAAATAACTTGTGAGATTCTAAGAAACACTTTAGAGTAGCTAAGCTAGTAAAAATATTAAAAAAATATTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.80% 1.10% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.40% 3.40% 0.26% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.10% 6.40% 0.52% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0906972834 G -> A LOC_Os09g12250.1 upstream_gene_variant ; 2660.0bp to feature; MODIFIER silent_mutation Average:50.511; most accessible tissue: Callus, score: 82.315 N N N N
vg0906972834 G -> A LOC_Os09g12240-LOC_Os09g12250 intergenic_region ; MODIFIER silent_mutation Average:50.511; most accessible tissue: Callus, score: 82.315 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906972834 NA 3.22E-08 mr1210 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
vg0906972834 NA 4.71E-08 mr1305 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
vg0906972834 NA 8.22E-06 mr1379 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
vg0906972834 NA 1.58E-09 mr1585 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
vg0906972834 NA 7.32E-09 mr1586 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
vg0906972834 4.10E-06 4.10E-06 mr1649 Jap_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
vg0906972834 NA 4.34E-07 mr1585_2 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