Search for Variation information by Variation ID:

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

Detailed information for vg0909297791:

Variant ID: vg0909297791 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9297791
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, C: 0.17, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTATTCAAAAACTTTTGTGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATGAATCAAATGATATGAAAAGAATTAATAATTACTT[C/A]
AATTTTTTTTAATAAGACGAACGGTCAAATATTTTGAAACGGAGGGAGCATAAAAATGTTCGACTGAGCCGACAAGGATGCACGCTTTCTCATTGCGATT

Reverse complement sequence

AATCGCAATGAGAAAGCGTGCATCCTTGTCGGCTCAGTCGAACATTTTTATGCTCCCTCCGTTTCAAAATATTTGACCGTTCGTCTTATTAAAAAAAATT[G/T]
AAGTAATTATTAATTCTTTTCATATCATTTGATTCATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCACAAAAGTTTTTGAATAAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.80% 34.30% 2.45% 0.47% NA
All Indica  2759 86.00% 12.70% 1.34% 0.00% NA
All Japonica  1512 22.00% 71.70% 4.89% 1.46% NA
Aus  269 48.30% 50.90% 0.74% 0.00% NA
Indica I  595 87.70% 9.60% 2.69% 0.00% NA
Indica II  465 96.80% 1.70% 1.51% 0.00% NA
Indica III  913 79.60% 19.80% 0.55% 0.00% NA
Indica Intermediate  786 85.60% 13.20% 1.15% 0.00% NA
Temperate Japonica  767 12.30% 76.50% 8.34% 2.87% NA
Tropical Japonica  504 27.80% 71.00% 1.19% 0.00% NA
Japonica Intermediate  241 40.70% 57.70% 1.66% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 56.70% 40.00% 3.33% 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
vg0909297791 C -> DEL N N silent_mutation Average:46.459; most accessible tissue: Callus, score: 84.408 N N N N
vg0909297791 C -> A LOC_Os09g15260-LOC_Os09g15270 intergenic_region ; MODIFIER silent_mutation Average:46.459; most accessible tissue: Callus, score: 84.408 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909297791 NA 3.35E-23 mr1548 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
vg0909297791 NA 3.57E-06 mr1298_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
vg0909297791 NA 8.98E-28 mr1617_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
vg0909297791 NA 2.49E-19 mr1637_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
vg0909297791 1.13E-06 NA mr1702_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
vg0909297791 NA 1.41E-06 mr1702_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
vg0909297791 NA 7.16E-14 mr1713_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
vg0909297791 NA 4.53E-07 mr1727_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
vg0909297791 NA 3.60E-06 mr1729_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
vg0909297791 NA 7.23E-06 mr1731_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
vg0909297791 NA 1.18E-08 mr1741_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
vg0909297791 NA 6.71E-08 mr1783_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
vg0909297791 NA 2.95E-06 mr1785_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