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Detailed information for vg1109870254:

Variant ID: vg1109870254 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9870254
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


TAACCGAGGCGTCTGTCATAAACGCCGCTGCGGCCGGTTTACTCGAGGGCGAACTCACAAGGAAAATCGCCAACAATGAGCCACAGACGCTTGAGCACCT[A/G]
CTTCGCATCATTGATGGGTACGCAAGGGGCGAAGAGGATTCCAAGCGACGGCAAGCAATACAAGCTGAGTATGATAAGGCTTTCATCACTGCTGCCCAAG

Reverse complement sequence

CTTGGGCAGCAGTGATGAAAGCCTTATCATACTCAGCTTGTATTGCTTGCCGTCGCTTGGAATCCTCTTCGCCCCTTGCGTACCCATCAATGATGCGAAG[T/C]
AGGTGCTCAAGCGTCTGTGGCTCATTGTTGGCGATTTTCCTTGTGAGTTCGCCCTCGAGTAAACCGGCCGCAGCGGCGTTTATGACAGACGCCTCGGTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 45.70% 22.90% 7.89% 23.55% NA
All Indica  2759 19.60% 37.10% 11.45% 31.86% NA
All Japonica  1512 96.70% 0.10% 0.93% 2.25% NA
Aus  269 16.70% 14.10% 11.15% 57.99% NA
Indica I  595 26.40% 39.20% 12.27% 22.18% NA
Indica II  465 11.00% 61.90% 9.89% 17.20% NA
Indica III  913 15.40% 23.00% 11.83% 49.73% NA
Indica Intermediate  786 24.30% 37.30% 11.32% 27.10% NA
Temperate Japonica  767 96.60% 0.10% 0.91% 2.35% NA
Tropical Japonica  504 96.80% 0.00% 0.60% 2.58% NA
Japonica Intermediate  241 96.70% 0.40% 1.66% 1.24% NA
VI/Aromatic  96 62.50% 3.10% 9.38% 25.00% NA
Intermediate  90 56.70% 16.70% 4.44% 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
vg1109870254 A -> DEL LOC_Os11g17690.1 N frameshift_variant Average:12.679; most accessible tissue: Callus, score: 43.672 N N N N
vg1109870254 A -> G LOC_Os11g17690.1 synonymous_variant ; p.Leu118Leu; LOW synonymous_codon Average:12.679; most accessible tissue: Callus, score: 43.672 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109870254 NA 1.11E-06 mr1189 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
vg1109870254 NA 2.96E-06 mr1291 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
vg1109870254 2.08E-07 3.89E-14 mr1457 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
vg1109870254 7.09E-07 2.30E-09 mr1457 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
vg1109870254 NA 4.12E-08 mr1559 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
vg1109870254 NA 2.86E-06 mr1625 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
vg1109870254 NA 9.51E-06 mr1698 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
vg1109870254 NA 4.30E-06 mr1725 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
vg1109870254 NA 8.89E-06 mr1742 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
vg1109870254 NA 1.82E-07 mr1892 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
vg1109870254 NA 2.04E-06 mr1892 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