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Detailed information for vg1106566073:

Variant ID: vg1106566073 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 6566073
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGATAGGCACGATATTGCTCTCATTAACTTCAGATAGACCAGGCTTCTAGATCTTAAATTTAGAAGAGCCATCTTTACCAGCTGAAGACGGCGATGCT[G/A]
GTGGTTTCTCAGCCATGGGAAAATGCTGTTGTGATTCTGACTTCTAATAGTCCCATCGGGTGTGCCAAAAGCGTGTTGATGTGAAAACACGAGGCCTGGG

Reverse complement sequence

CCCAGGCCTCGTGTTTTCACATCAACACGCTTTTGGCACACCCGATGGGACTATTAGAAGTCAGAATCACAACAGCATTTTCCCATGGCTGAGAAACCAC[C/T]
AGCATCGCCGTCTTCAGCTGGTAAAGATGGCTCTTCTAAATTTAAGATCTAGAAGCCTGGTCTATCTGAAGTTAATGAGAGCAATATCGTGCCTATCACT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.10% 34.70% 3.75% 11.49% NA
All Indica  2759 33.30% 54.50% 4.35% 7.87% NA
All Japonica  1512 76.90% 3.00% 2.31% 17.79% NA
Aus  269 59.50% 24.50% 5.20% 10.78% NA
Indica I  595 28.70% 62.70% 5.04% 3.53% NA
Indica II  465 24.50% 66.90% 4.52% 4.09% NA
Indica III  913 41.00% 42.80% 3.29% 12.92% NA
Indica Intermediate  786 33.10% 54.50% 4.96% 7.51% NA
Temperate Japonica  767 72.60% 2.60% 2.61% 22.16% NA
Tropical Japonica  504 82.90% 3.80% 1.98% 11.31% NA
Japonica Intermediate  241 77.60% 2.90% 2.07% 17.43% NA
VI/Aromatic  96 66.70% 9.40% 3.12% 20.83% NA
Intermediate  90 68.90% 16.70% 5.56% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1106566073 G -> A LOC_Os11g11820.1 missense_variant ; p.Pro6Leu; MODERATE nonsynonymous_codon ; P6L Average:31.096; most accessible tissue: Zhenshan97 panicle, score: 46.362 unknown unknown DELETERIOUS 0.00
vg1106566073 G -> DEL LOC_Os11g11820.1 N frameshift_variant Average:31.096; most accessible tissue: Zhenshan97 panicle, score: 46.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1106566073 NA 5.40E-08 mr1084_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
vg1106566073 NA 3.77E-07 mr1205_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
vg1106566073 NA 3.57E-07 mr1302_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
vg1106566073 NA 5.30E-08 mr1376_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
vg1106566073 NA 4.58E-06 mr1407_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
vg1106566073 NA 2.53E-08 mr1431_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
vg1106566073 NA 3.69E-08 mr1604_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
vg1106566073 NA 2.20E-08 mr1659_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
vg1106566073 5.04E-06 5.04E-06 mr1670_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
vg1106566073 NA 4.13E-08 mr1824_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
vg1106566073 NA 2.39E-07 mr1869_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
vg1106566073 NA 2.30E-06 mr1878_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