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Detailed information for vg0142970300:

Variant ID: vg0142970300 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42970300
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, G: 0.13, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAGCCGAACCACTTCAAAAAAATTTGGCGTGTAAAGCTTATTTATTTATTTATTATCCACTGCGATTGGGCCGTGGGCCTTTGGTATTTTGGAGGCCC[A/G]
TTTAATCTGGATAGTTCGGCCCCGGAGCAAAGCATCATCAGTACTTGGTGTCGTCTCCAAGAGAGGGAGGAGACGAGAGGCGAGATCCACGACGTCGCCG

Reverse complement sequence

CGGCGACGTCGTGGATCTCGCCTCTCGTCTCCTCCCTCTCTTGGAGACGACACCAAGTACTGATGATGCTTTGCTCCGGGGCCGAACTATCCAGATTAAA[T/C]
GGGCCTCCAAAATACCAAAGGCCCACGGCCCAATCGCAGTGGATAATAAATAAATAAATAAGCTTTACACGCCAAATTTTTTTGAAGTGGTTCGGCTCCA

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 53.60% 46.30% 0.08% 0.00% NA
All Indica  2759 88.90% 11.10% 0.00% 0.00% NA
All Japonica  1512 1.70% 98.20% 0.13% 0.00% NA
Aus  269 9.30% 90.70% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 83.80% 16.20% 0.00% 0.00% NA
Indica Intermediate  786 84.60% 15.40% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.20% 0.13% 0.00% NA
Tropical Japonica  504 3.20% 96.60% 0.20% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 32.20% 65.60% 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
vg0142970300 A -> G LOC_Os01g74170.1 upstream_gene_variant ; 156.0bp to feature; MODIFIER silent_mutation Average:97.293; most accessible tissue: Callus, score: 99.738 N N N N
vg0142970300 A -> G LOC_Os01g74180.1 upstream_gene_variant ; 40.0bp to feature; MODIFIER silent_mutation Average:97.293; most accessible tissue: Callus, score: 99.738 N N N N
vg0142970300 A -> G LOC_Os01g74180.2 upstream_gene_variant ; 315.0bp to feature; MODIFIER silent_mutation Average:97.293; most accessible tissue: Callus, score: 99.738 N N N N
vg0142970300 A -> G LOC_Os01g74170-LOC_Os01g74180 intergenic_region ; MODIFIER silent_mutation Average:97.293; most accessible tissue: Callus, score: 99.738 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)
vg0142970300 A G -0.05 -0.1 -0.1 -0.09 -0.08 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142970300 NA 6.70E-10 mr1151 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
vg0142970300 NA 9.37E-15 mr1164 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
vg0142970300 NA 6.96E-08 mr1249 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
vg0142970300 NA 1.69E-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
vg0142970300 NA 8.97E-10 mr1524 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
vg0142970300 NA 2.18E-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
vg0142970300 NA 9.80E-08 mr1676 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
vg0142970300 NA 2.48E-11 mr1713 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
vg0142970300 NA 1.98E-08 mr1827 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
vg0142970300 NA 9.39E-13 mr1151_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
vg0142970300 NA 2.24E-45 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
vg0142970300 NA 9.70E-13 mr1521_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
vg0142970300 NA 2.04E-61 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
vg0142970300 6.65E-07 2.52E-08 mr1676_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
vg0142970300 NA 7.62E-29 mr1825_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
vg0142970300 NA 1.55E-20 mr1922_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
vg0142970300 NA 3.75E-08 mr1940_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