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Detailed information for vg0627387528:

Variant ID: vg0627387528 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27387528
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.32, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GGTAAAATCTCTCTCCCTTTTTTAAAGAGGGATAAAATTACTTTAAACATGTTAAGATTTCAAATTATACTATTAGACACTGAAAAACAGTATGCACAGG[G/A]
AAAAATCATGTCTTGTTTCCCGAAAGAGCTAATATTCTGACAAATGGTTAGGCAGTAGATTGTACAACGCCAAGAACAATGAATAATTTGTACAACACGA

Reverse complement sequence

TCGTGTTGTACAAATTATTCATTGTTCTTGGCGTTGTACAATCTACTGCCTAACCATTTGTCAGAATATTAGCTCTTTCGGGAAACAAGACATGATTTTT[C/T]
CCTGTGCATACTGTTTTTCAGTGTCTAATAGTATAATTTGAAATCTTAACATGTTTAAAGTAATTTTATCCCTCTTTAAAAAAGGGAGAGAGATTTTACC

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 62.10% 37.90% 0.06% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 1.20% 98.80% 0.00% 0.00% NA
Aus  269 56.10% 43.10% 0.74% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.30% 0.00% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 45.60% 53.30% 1.11% 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
vg0627387528 G -> A LOC_Os06g45300.1 downstream_gene_variant ; 669.0bp to feature; MODIFIER silent_mutation Average:75.764; most accessible tissue: Zhenshan97 flower, score: 85.885 N N N N
vg0627387528 G -> A LOC_Os06g45310.1 downstream_gene_variant ; 9.0bp to feature; MODIFIER silent_mutation Average:75.764; most accessible tissue: Zhenshan97 flower, score: 85.885 N N N N
vg0627387528 G -> A LOC_Os06g45300.2 downstream_gene_variant ; 669.0bp to feature; MODIFIER silent_mutation Average:75.764; most accessible tissue: Zhenshan97 flower, score: 85.885 N N N N
vg0627387528 G -> A LOC_Os06g45300-LOC_Os06g45310 intergenic_region ; MODIFIER silent_mutation Average:75.764; most accessible tissue: Zhenshan97 flower, score: 85.885 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627387528 NA 1.00E-19 Yield 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
vg0627387528 NA 7.33E-41 mr1509 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
vg0627387528 NA 2.30E-49 mr1558 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
vg0627387528 NA 5.44E-43 mr1591 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
vg0627387528 NA 1.44E-61 mr1671 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
vg0627387528 NA 3.36E-13 mr1744 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
vg0627387528 NA 2.54E-28 mr1793 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
vg0627387528 NA 3.86E-26 mr1051_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
vg0627387528 NA 8.48E-71 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
vg0627387528 NA 1.62E-73 mr1088_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
vg0627387528 NA 1.94E-50 mr1404_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
vg0627387528 NA 5.97E-16 mr1457_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
vg0627387528 NA 2.16E-47 mr1458_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
vg0627387528 NA 7.20E-44 mr1509_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
vg0627387528 NA 8.74E-57 mr1558_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
vg0627387528 NA 4.97E-22 mr1609_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
vg0627387528 NA 5.77E-92 mr1671_2 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
vg0627387528 NA 6.40E-45 mr1793_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
vg0627387528 NA 1.12E-30 mr1913_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