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Detailed information for vg0802250534:

Variant ID: vg0802250534 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2250534
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.23, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GAGACAAAAGGGGTTTATATAGATTCGGGCAGCTGAGATGCGTAGTACCCTACTCCTGTGTTTGGGATTATGGATGAGTGTTACAAAGATTCCTTCCCTC[C/T]
AGAGAGCTCTTTCGCCCTACTTCTCCTAGAGTTCAGGTTTTCTTAGAGTCGTCCGTTTTTTTCTCGGTGGGCAAGGTTCTCCTTTTATAGTTCAAGGGGA

Reverse complement sequence

TCCCCTTGAACTATAAAAGGAGAACCTTGCCCACCGAGAAAAAAACGGACGACTCTAAGAAAACCTGAACTCTAGGAGAAGTAGGGCGAAAGAGCTCTCT[G/A]
GAGGGAAGGAATCTTTGTAACACTCATCCATAATCCCAAACACAGGAGTAGGGTACTACGCATCTCAGCTGCCCGAATCTATATAAACCCCTTTTGTCTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.90% 9.90% 0.13% 0.00% NA
All Indica  2759 87.20% 12.80% 0.00% 0.00% NA
All Japonica  1512 92.50% 7.20% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.30% 5.70% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 78.60% 21.40% 0.00% 0.00% NA
Indica Intermediate  786 87.70% 12.30% 0.00% 0.00% NA
Temperate Japonica  767 87.40% 12.50% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 93.40% 5.40% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg0802250534 C -> T LOC_Os08g04530-LOC_Os08g04540 intergenic_region ; MODIFIER silent_mutation Average:39.751; most accessible tissue: Minghui63 root, score: 55.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802250534 NA 2.30E-06 mr1425 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
vg0802250534 5.08E-06 5.08E-06 mr1524 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
vg0802250534 2.49E-06 2.14E-06 mr1751 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
vg0802250534 NA 5.53E-06 mr1780 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
vg0802250534 NA 8.43E-06 mr1790 Ind_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