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Detailed information for vg0919843915:

Variant ID: vg0919843915 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19843915
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.05, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


ATGCATTCCCCCTGGTCTCCATTTAGGACTACCTTGGAAGTGGCGGTGGAAAAGAGCAAACAGATCCAATTTCTCCACCGGGGGCCAAAACCCATGTTTT[G/C]
CATCAGTTCAAGTAAATATTCCCAGGAGACCGAATCAAAAGCTCTAGCAATGTCTAGCTTGAAAAAAAGTGTTGGCTTTTTGCTGGCATTTAGGTTCCTG

Reverse complement sequence

CAGGAACCTAAATGCCAGCAAAAAGCCAACACTTTTTTTCAAGCTAGACATTGCTAGAGCTTTTGATTCGGTCTCCTGGGAATATTTACTTGAACTGATG[C/G]
AAAACATGGGTTTTGGCCCCCGGTGGAGAAATTGGATCTGTTTGCTCTTTTCCACCGCCACTTCCAAGGTAGTCCTAAATGGAGACCAGGGGGAATGCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.80% 38.80% 8.38% 0.06% NA
All Indica  2759 86.10% 6.80% 7.10% 0.00% NA
All Japonica  1512 0.50% 99.30% 0.26% 0.00% NA
Aus  269 32.30% 1.50% 65.06% 1.12% NA
Indica I  595 95.80% 3.40% 0.84% 0.00% NA
Indica II  465 87.30% 6.20% 6.45% 0.00% NA
Indica III  913 85.70% 7.40% 6.90% 0.00% NA
Indica Intermediate  786 78.50% 9.00% 12.47% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 99.80% 0.20% 0.00% NA
Japonica Intermediate  241 1.20% 97.50% 1.24% 0.00% NA
VI/Aromatic  96 3.10% 88.50% 8.33% 0.00% NA
Intermediate  90 23.30% 62.20% 14.44% 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
vg0919843915 G -> DEL LOC_Os09g33610.1 N frameshift_variant Average:34.917; most accessible tissue: Minghui63 root, score: 51.763 N N N N
vg0919843915 G -> C LOC_Os09g33610.1 missense_variant ; p.Gln1426Glu; MODERATE nonsynonymous_codon ; Q1426E Average:34.917; most accessible tissue: Minghui63 root, score: 51.763 unknown unknown TOLERATED 0.16

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919843915 4.13E-11 5.73E-13 mr1216 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
vg0919843915 1.03E-08 2.78E-15 mr1216 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
vg0919843915 NA 1.33E-12 mr1326 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
vg0919843915 NA 8.98E-06 mr1532 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
vg0919843915 NA 5.55E-13 mr1744 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
vg0919843915 NA 6.87E-07 mr1796 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
vg0919843915 NA 3.31E-06 mr1881 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
vg0919843915 NA 9.91E-08 mr1990 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
vg0919843915 NA 2.67E-06 mr1246_2 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
vg0919843915 2.60E-06 NA mr1676_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
vg0919843915 1.99E-07 3.35E-12 mr1676_2 Ind_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