Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0611061199:

Variant ID: vg0611061199 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11061199
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.24, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


AAATCATTTGCCCTAGAATTATCATGTCTAGCAATATGTCTAATAGAAAAATACAGTCCCTCAAACTCACACTCACGCACACAGCTCACACATCAGAGGC[G/A]
GAAGAAGATGAGAGAACAGAGAGCACAAACACTTGGTGCTGCTGAACTAATTTGAGCTGCAGCTGCTCTACTACTTTATAGAAGCAAATGTCAACTATCT

Reverse complement sequence

AGATAGTTGACATTTGCTTCTATAAAGTAGTAGAGCAGCTGCAGCTCAAATTAGTTCAGCAGCACCAAGTGTTTGTGCTCTCTGTTCTCTCATCTTCTTC[C/T]
GCCTCTGATGTGTGAGCTGTGTGCGTGAGTGTGAGTTTGAGGGACTGTATTTTTCTATTAGACATATTGCTAGACATGATAATTCTAGGGCAAATGATTT

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 71.20% 28.80% 0.00% 0.00% NA
All Indica  2759 57.00% 43.00% 0.00% 0.00% NA
All Japonica  1512 94.00% 6.00% 0.00% 0.00% NA
Aus  269 78.10% 21.90% 0.00% 0.00% NA
Indica I  595 20.70% 79.30% 0.00% 0.00% NA
Indica II  465 91.80% 8.20% 0.00% 0.00% NA
Indica III  913 62.00% 38.00% 0.00% 0.00% NA
Indica Intermediate  786 58.10% 41.90% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 87.90% 12.10% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 0.00% 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
vg0611061199 G -> A LOC_Os06g19420.1 downstream_gene_variant ; 2850.0bp to feature; MODIFIER silent_mutation Average:60.654; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N
vg0611061199 G -> A LOC_Os06g19410.1 intron_variant ; MODIFIER silent_mutation Average:60.654; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611061199 1.04E-06 1.04E-06 mr1165 Jap_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
vg0611061199 3.98E-08 3.98E-08 mr1478 Jap_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
vg0611061199 NA 5.03E-06 mr1531 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
vg0611061199 NA 2.17E-07 mr1557 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
vg0611061199 NA 5.96E-09 mr1860 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
vg0611061199 7.03E-15 4.30E-17 mr1165_2 Jap_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
vg0611061199 6.90E-08 6.90E-08 mr1477_2 Jap_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
vg0611061199 2.10E-06 2.10E-06 mr1478_2 Jap_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
vg0611061199 NA 6.88E-06 mr1629_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
vg0611061199 NA 6.55E-10 mr1860_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
vg0611061199 NA 2.60E-06 mr1931_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
vg0611061199 1.11E-11 1.11E-11 mr1971_2 Jap_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