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Detailed information for vg0917910484:

Variant ID: vg0917910484 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 17910484
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACAAAGGCCCTGTTTGGAGGAGTAGCCGAGAGTTATTTTAAGAGCTATTTTTTTAGCTCAAGAAATAGCCCTTCAATGAAATAGCCCTTGAGCTGTTT[G/T]
GATGCAAGAGCTACTTGACCTTTAGTACACTTTCCCAATCATAACTACCCATTTTCTCTCTTTCTCCACTAGATCTTTTGTGCATGTGTCTTGGTGTGGC

Reverse complement sequence

GCCACACCAAGACACATGCACAAAAGATCTAGTGGAGAAAGAGAGAAAATGGGTAGTTATGATTGGGAAAGTGTACTAAAGGTCAAGTAGCTCTTGCATC[C/A]
AAACAGCTCAAGGGCTATTTCATTGAAGGGCTATTTCTTGAGCTAAAAAAATAGCTCTTAAAATAACTCTCGGCTACTCCTCCAAACAGGGCCTTTGTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.90% 0.30% 0.55% 54.21% NA
All Indica  2759 6.70% 0.40% 0.83% 92.06% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 98.90% 0.70% 0.00% 0.37% NA
Indica I  595 4.90% 1.20% 0.34% 93.61% NA
Indica II  465 6.90% 0.00% 0.65% 92.47% NA
Indica III  913 4.50% 0.20% 1.20% 94.09% NA
Indica Intermediate  786 10.40% 0.40% 0.89% 88.30% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% 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 74.40% 0.00% 3.33% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0917910484 G -> DEL N N silent_mutation Average:76.648; most accessible tissue: Callus, score: 93.395 N N N N
vg0917910484 G -> T LOC_Os09g29460-LOC_Os09g29470 intergenic_region ; MODIFIER silent_mutation Average:76.648; most accessible tissue: Callus, score: 93.395 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0917910484 NA 9.98E-09 mr1047 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
vg0917910484 NA 1.41E-14 mr1164 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
vg0917910484 NA 2.08E-61 mr1246 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
vg0917910484 NA 1.01E-25 mr1571 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
vg0917910484 NA 1.75E-07 mr1707 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
vg0917910484 NA 3.49E-36 mr1224_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
vg0917910484 NA 5.01E-32 mr1571_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
vg0917910484 NA 2.51E-33 mr1598_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