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Detailed information for vg0611634340:

Variant ID: vg0611634340 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11634340
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.27, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:


GAAATTTTGAATAGTTTTTGAGAATTCAAATTTGAAGTGGTAAAATTCAACCGAAATTAATCAAAATTATCTAATTTTGGCCAAATAAAGTCATATCGCC[G/A]
TGTTCGGAATCCAATATTAAATCAAAGAGGTGAACCCTGATACAAACTTGGTATGTTGGAACTTCGAACCTAGCTACGTGTTCAGAACCCTTCCCTCCCA

Reverse complement sequence

TGGGAGGGAAGGGTTCTGAACACGTAGCTAGGTTCGAAGTTCCAACATACCAAGTTTGTATCAGGGTTCACCTCTTTGATTTAATATTGGATTCCGAACA[C/T]
GGCGATATGACTTTATTTGGCCAAAATTAGATAATTTTGATTAATTTCGGTTGAATTTTACCACTTCAAATTTGAATTCTCAAAAACTATTCAAAATTTC

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 78.00% 20.70% 0.76% 0.53% NA
All Indica  2759 92.40% 7.50% 0.14% 0.00% NA
All Japonica  1512 50.00% 46.40% 1.92% 1.65% NA
Aus  269 88.50% 11.20% 0.37% 0.00% NA
Indica I  595 96.10% 3.70% 0.17% 0.00% NA
Indica II  465 91.40% 8.40% 0.22% 0.00% NA
Indica III  913 91.50% 8.50% 0.00% 0.00% NA
Indica Intermediate  786 91.20% 8.50% 0.25% 0.00% NA
Temperate Japonica  767 30.00% 68.10% 1.96% 0.00% NA
Tropical Japonica  504 77.80% 18.80% 0.20% 3.17% NA
Japonica Intermediate  241 55.60% 35.30% 5.39% 3.73% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 82.20% 15.60% 2.22% 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
vg0611634340 G -> A LOC_Os06g20270.1 upstream_gene_variant ; 3053.0bp to feature; MODIFIER silent_mutation Average:43.346; most accessible tissue: Minghui63 root, score: 52.955 N N N N
vg0611634340 G -> A LOC_Os06g20280.1 downstream_gene_variant ; 2950.0bp to feature; MODIFIER silent_mutation Average:43.346; most accessible tissue: Minghui63 root, score: 52.955 N N N N
vg0611634340 G -> A LOC_Os06g20270-LOC_Os06g20280 intergenic_region ; MODIFIER silent_mutation Average:43.346; most accessible tissue: Minghui63 root, score: 52.955 N N N N
vg0611634340 G -> DEL N N silent_mutation Average:43.346; most accessible tissue: Minghui63 root, score: 52.955 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611634340 3.54E-06 NA Awn_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0611634340 9.43E-06 NA mr1068 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
vg0611634340 4.04E-06 NA mr1144 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
vg0611634340 9.08E-08 NA mr1065_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
vg0611634340 2.55E-09 NA mr1068_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
vg0611634340 4.23E-08 NA mr1078_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
vg0611634340 8.87E-08 NA mr1087_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
vg0611634340 5.14E-12 6.58E-09 mr1087_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
vg0611634340 2.15E-08 NA mr1090_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
vg0611634340 1.46E-07 NA mr1091_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
vg0611634340 8.25E-07 NA mr1096_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
vg0611634340 NA 2.77E-06 mr1096_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
vg0611634340 3.20E-08 NA mr1108_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
vg0611634340 7.17E-06 NA mr1111_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
vg0611634340 1.59E-09 NA mr1111_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
vg0611634340 2.29E-08 NA mr1112_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
vg0611634340 3.10E-07 NA mr1121_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
vg0611634340 1.25E-06 NA mr1144_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
vg0611634340 1.29E-06 NA mr1211_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
vg0611634340 7.72E-08 NA mr1234_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
vg0611634340 9.45E-09 NA mr1526_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
vg0611634340 6.17E-08 4.46E-09 mr1695_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