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Detailed information for vg1117087408:

Variant ID: vg1117087408 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17087408
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TAGCCACGTCATCAAAAATAGTTTCAACCGTTAGATTGATAATTCTTTCGAGTATTAGCCGTTAGATAAAAGTCCCCTCTACTTCCTCACCAATTAAACA[A/G]
CGCCATTAATCACCACCCCATCTAAATGCTATCTAATTAATCAGGTAGTCAATTGGACAATAATACAATCAAGATATCATATCATATTTACTATTCCAAC

Reverse complement sequence

GTTGGAATAGTAAATATGATATGATATCTTGATTGTATTATTGTCCAATTGACTACCTGATTAATTAGATAGCATTTAGATGGGGTGGTGATTAATGGCG[T/C]
TGTTTAATTGGTGAGGAAGTAGAGGGGACTTTTATCTAACGGCTAATACTCGAAAGAATTATCAATCTAACGGTTGAAACTATTTTTGATGACGTGGCTA

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 45.60% 14.20% 5.59% 34.68% NA
All Indica  2759 37.90% 21.30% 8.88% 31.97% NA
All Japonica  1512 54.00% 4.50% 0.60% 40.87% NA
Aus  269 87.70% 0.70% 0.37% 11.15% NA
Indica I  595 31.10% 8.90% 4.87% 55.13% NA
Indica II  465 52.90% 14.00% 16.34% 16.77% NA
Indica III  913 29.80% 34.40% 7.23% 28.59% NA
Indica Intermediate  786 43.50% 19.70% 9.41% 27.35% NA
Temperate Japonica  767 86.20% 0.00% 0.26% 13.56% NA
Tropical Japonica  504 19.60% 12.70% 0.79% 66.87% NA
Japonica Intermediate  241 23.70% 1.70% 1.24% 73.44% NA
VI/Aromatic  96 9.40% 2.10% 1.04% 87.50% NA
Intermediate  90 51.10% 12.20% 8.89% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117087408 A -> DEL N N silent_mutation Average:28.163; most accessible tissue: Zhenshan97 young leaf, score: 51.334 N N N N
vg1117087408 A -> G LOC_Os11g29430.1 downstream_gene_variant ; 513.0bp to feature; MODIFIER silent_mutation Average:28.163; most accessible tissue: Zhenshan97 young leaf, score: 51.334 N N N N
vg1117087408 A -> G LOC_Os11g29440.1 downstream_gene_variant ; 2570.0bp to feature; MODIFIER silent_mutation Average:28.163; most accessible tissue: Zhenshan97 young leaf, score: 51.334 N N N N
vg1117087408 A -> G LOC_Os11g29420-LOC_Os11g29430 intergenic_region ; MODIFIER silent_mutation Average:28.163; most accessible tissue: Zhenshan97 young leaf, score: 51.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117087408 NA 3.64E-06 mr1030 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
vg1117087408 NA 1.38E-06 mr1060 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
vg1117087408 NA 5.01E-06 mr1060 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
vg1117087408 NA 3.56E-06 mr1063 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
vg1117087408 8.56E-07 3.70E-09 mr1115 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
vg1117087408 NA 6.50E-07 mr1170 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
vg1117087408 NA 1.34E-06 mr1230 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
vg1117087408 2.52E-07 2.52E-07 mr1230 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
vg1117087408 NA 1.10E-06 mr1352 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
vg1117087408 7.19E-06 7.79E-08 mr1380 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
vg1117087408 NA 6.59E-08 mr1428 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
vg1117087408 2.02E-06 2.02E-06 mr1428 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
vg1117087408 NA 1.03E-06 mr1550 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
vg1117087408 NA 4.02E-06 mr1561 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
vg1117087408 NA 1.32E-06 mr1614 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
vg1117087408 NA 4.72E-06 mr1820 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
vg1117087408 1.88E-06 1.88E-06 mr1869 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
vg1117087408 NA 6.80E-06 mr1937 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
vg1117087408 NA 3.26E-06 mr1941 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
vg1117087408 5.65E-06 5.65E-06 mr1996 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