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Detailed information for vg0103361661:

Variant ID: vg0103361661 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3361661
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


TCTAGGAAAGAAACAACTATCAGCTTATTCTACTATAGATTATAACAATCTAGTTTATAGTAATCTGACTCAATAATCTAGATTATAATAATTTCAAGCT[G/A,T]
AAAGAAACAGGGCCTATAGTTAGAGAGAATCCTCCACCTGAATTTCGTGTACTACCTGCCTCTGAAATCTCGTACACGCAGCTTGTCCTTCAAGCTCGAG

Reverse complement sequence

CTCGAGCTTGAAGGACAAGCTGCGTGTACGAGATTTCAGAGGCAGGTAGTACACGAAATTCAGGTGGAGGATTCTCTCTAACTATAGGCCCTGTTTCTTT[C/T,A]
AGCTTGAAATTATTATAATCTAGATTATTGAGTCAGATTACTATAAACTAGATTGTTATAATCTATAGTAGAATAAGCTGATAGTTGTTTCTTTCCTAGA

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 57.50% 39.70% 2.16% 0.68% NA
All Indica  2759 39.40% 58.40% 1.23% 0.98% NA
All Japonica  1512 82.10% 15.00% 2.91% 0.00% NA
Aus  269 89.60% 3.70% 5.20% 1.49% NA
Indica I  595 59.30% 39.30% 1.34% 0.00% NA
Indica II  465 15.10% 83.90% 1.08% 0.00% NA
Indica III  913 43.40% 53.50% 0.66% 2.52% NA
Indica Intermediate  786 34.20% 63.40% 1.91% 0.51% NA
Temperate Japonica  767 82.70% 16.20% 1.17% 0.00% NA
Tropical Japonica  504 82.70% 15.10% 2.18% 0.00% NA
Japonica Intermediate  241 78.80% 11.20% 9.96% 0.00% NA
VI/Aromatic  96 95.80% 0.00% 4.17% 0.00% NA
Intermediate  90 60.00% 32.20% 6.67% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103361661 G -> T LOC_Os01g07130.1 upstream_gene_variant ; 985.0bp to feature; MODIFIER N Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> T LOC_Os01g07120.1 downstream_gene_variant ; 3218.0bp to feature; MODIFIER N Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> T LOC_Os01g07140.1 downstream_gene_variant ; 302.0bp to feature; MODIFIER N Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> T LOC_Os01g07120.2 downstream_gene_variant ; 457.0bp to feature; MODIFIER N Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> T LOC_Os01g07140.2 downstream_gene_variant ; 302.0bp to feature; MODIFIER N Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> T LOC_Os01g07120-LOC_Os01g07140 intergenic_region ; MODIFIER N Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> A LOC_Os01g07130.1 upstream_gene_variant ; 985.0bp to feature; MODIFIER silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> A LOC_Os01g07120.1 downstream_gene_variant ; 3218.0bp to feature; MODIFIER silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> A LOC_Os01g07140.1 downstream_gene_variant ; 302.0bp to feature; MODIFIER silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> A LOC_Os01g07120.2 downstream_gene_variant ; 457.0bp to feature; MODIFIER silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> A LOC_Os01g07140.2 downstream_gene_variant ; 302.0bp to feature; MODIFIER silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> A LOC_Os01g07120-LOC_Os01g07140 intergenic_region ; MODIFIER silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 N N N N
vg0103361661 G -> DEL N N silent_mutation Average:87.519; most accessible tissue: Minghui63 young leaf, score: 94.665 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)
vg0103361661 G A -0.01 -0.01 0.0 0.01 0.01 0.01
vg0103361661 G T -0.03 -0.04 -0.03 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103361661 NA 1.96E-11 mr1174 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
vg0103361661 NA 1.43E-06 mr1179 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
vg0103361661 NA 6.59E-06 mr1215 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
vg0103361661 NA 8.19E-06 mr1287 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
vg0103361661 4.58E-06 4.58E-06 mr1290 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
vg0103361661 3.33E-06 3.33E-06 mr1327 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
vg0103361661 NA 2.87E-06 mr1347 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
vg0103361661 NA 1.67E-06 mr1358 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
vg0103361661 NA 6.88E-07 mr1527 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
vg0103361661 1.37E-08 1.37E-08 mr1967 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