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Detailed information for vg0601445283:

Variant ID: vg0601445283 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1445283
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GCATCGAGGAAGACGACGACTTGGCTGGGCCGTGGGCTGGGTCAGCGACCAGGCCCAAAGGCCCATAGGATCACAAATTTGTAGATACTGGAAGACTGGA[A/G]
GAGGGGACTTGATCATAAATTGGTAATCACTTGATCCAAATATATCATCTCTTGAGCCATATTTTTTCTTTGCTTTATAGTAGCAAATACGTCATCTCTA

Reverse complement sequence

TAGAGATGACGTATTTGCTACTATAAAGCAAAGAAAAAATATGGCTCAAGAGATGATATATTTGGATCAAGTGATTACCAATTTATGATCAAGTCCCCTC[T/C]
TCCAGTCTTCCAGTATCTACAAATTTGTGATCCTATGGGCCTTTGGGCCTGGTCGCTGACCCAGCCCACGGCCCAGCCAAGTCGTCGTCTTCCTCGATGC

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 66.20% 33.70% 0.08% 0.00% NA
All Indica  2759 50.40% 49.50% 0.11% 0.00% NA
All Japonica  1512 96.20% 3.80% 0.00% 0.00% NA
Aus  269 41.30% 58.40% 0.37% 0.00% NA
Indica I  595 11.90% 87.90% 0.17% 0.00% NA
Indica II  465 71.00% 29.00% 0.00% 0.00% NA
Indica III  913 62.00% 38.00% 0.00% 0.00% NA
Indica Intermediate  786 53.90% 45.80% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 89.10% 10.90% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0601445283 A -> G LOC_Os06g03676.1 upstream_gene_variant ; 120.0bp to feature; MODIFIER silent_mutation Average:96.892; most accessible tissue: Callus, score: 97.865 N N N N
vg0601445283 A -> G LOC_Os06g03682.1 downstream_gene_variant ; 224.0bp to feature; MODIFIER silent_mutation Average:96.892; most accessible tissue: Callus, score: 97.865 N N N N
vg0601445283 A -> G LOC_Os06g03682.2 downstream_gene_variant ; 224.0bp to feature; MODIFIER silent_mutation Average:96.892; most accessible tissue: Callus, score: 97.865 N N N N
vg0601445283 A -> G LOC_Os06g03676-LOC_Os06g03682 intergenic_region ; MODIFIER silent_mutation Average:96.892; most accessible tissue: Callus, score: 97.865 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0601445283 A G 0.04 0.04 0.01 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601445283 NA 2.05E-06 Spikelet_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
vg0601445283 NA 7.77E-12 mr1069 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
vg0601445283 NA 3.90E-06 mr1072 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
vg0601445283 NA 9.45E-14 mr1441 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
vg0601445283 NA 2.12E-07 mr1498 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
vg0601445283 NA 7.19E-06 mr1592 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
vg0601445283 NA 3.93E-09 mr1805 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
vg0601445283 NA 1.83E-06 mr1850 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
vg0601445283 NA 1.67E-08 mr1861 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
vg0601445283 NA 1.04E-06 mr1955 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
vg0601445283 NA 3.42E-08 mr1075_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
vg0601445283 NA 1.89E-09 mr1124_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
vg0601445283 NA 2.62E-09 mr1222_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
vg0601445283 NA 1.50E-16 mr1592_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
vg0601445283 NA 2.23E-06 mr1592_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
vg0601445283 NA 2.09E-13 mr1805_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
vg0601445283 NA 2.55E-07 mr1895_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