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Detailed information for vg0916354642:

Variant ID: vg0916354642 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16354642
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, A: 0.27, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


AAGTTCCAGATCTTCCAGTCCCCCGGTCGGTCTAATCGTTGGGCGGCTATGTCCCAATCTCAATGTCGATTTGAGTGCACTACTACCAAGGCTTTCCAAA[C/A]
CAATTCCCGAATAATACACTGAGCATTGACTTTCTTGCTTTAACTAACCTGACGCCAGGCCCTTTTGCTCTAGCCTCTACTCCTTGTCATTGATTTCTAG

Reverse complement sequence

CTAGAAATCAATGACAAGGAGTAGAGGCTAGAGCAAAAGGGCCTGGCGTCAGGTTAGTTAAAGCAAGAAAGTCAATGCTCAGTGTATTATTCGGGAATTG[G/T]
TTTGGAAAGCCTTGGTAGTAGTGCACTCAAATCGACATTGAGATTGGGACATAGCCGCCCAACGATTAGACCGACCGGGGGACTGGAAGATCTGGAACTT

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 64.00% 35.60% 0.04% 0.28% NA
All Indica  2759 98.50% 1.00% 0.07% 0.40% NA
All Japonica  1512 0.30% 99.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.00% 0.50% NA
Indica II  465 97.80% 1.90% 0.00% 0.22% NA
Indica III  913 99.20% 0.40% 0.00% 0.33% NA
Indica Intermediate  786 97.30% 1.90% 0.25% 0.51% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 32.20% 65.60% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0916354642 C -> DEL N N silent_mutation Average:57.81; most accessible tissue: Minghui63 flag leaf, score: 94.537 N N N N
vg0916354642 C -> A LOC_Os09g26910.1 upstream_gene_variant ; 4377.0bp to feature; MODIFIER silent_mutation Average:57.81; most accessible tissue: Minghui63 flag leaf, score: 94.537 N N N N
vg0916354642 C -> A LOC_Os09g26920.1 upstream_gene_variant ; 2065.0bp to feature; MODIFIER silent_mutation Average:57.81; most accessible tissue: Minghui63 flag leaf, score: 94.537 N N N N
vg0916354642 C -> A LOC_Os09g26910-LOC_Os09g26920 intergenic_region ; MODIFIER silent_mutation Average:57.81; most accessible tissue: Minghui63 flag leaf, score: 94.537 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916354642 NA 1.19E-14 mr1146 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
vg0916354642 NA 1.79E-06 mr1315 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
vg0916354642 NA 1.35E-22 mr1383 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
vg0916354642 NA 1.67E-06 mr1392 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
vg0916354642 NA 6.97E-14 mr1653 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
vg0916354642 NA 6.02E-06 mr1681 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
vg0916354642 NA 1.47E-35 mr1682 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
vg0916354642 NA 3.22E-19 mr1754 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
vg0916354642 NA 3.91E-07 mr1810 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
vg0916354642 NA 1.19E-72 mr1865 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
vg0916354642 NA 6.71E-07 mr1979 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
vg0916354642 NA 8.62E-07 mr1321_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
vg0916354642 NA 8.74E-10 mr1349_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
vg0916354642 NA 3.34E-07 mr1749_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
vg0916354642 NA 1.03E-90 mr1865_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