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Detailed information for vg0141963794:

Variant ID: vg0141963794 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41963794
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAATACAAGACCCATTTCACGTTTGCATAGCGCTACAGTATTTTTGGTCTTCTCCAACAATAAGACTTAAAAAATAACCCTTAATGTAAATAGGTCTT[C/T]
AGGAGAGAGAATACTCGGATTTAGATTATGCCTCTTATAGCACGCAAAATGGGTCTTCTGTATAGGTACTCTATTGGAGGCTGAAATAGTACTATCGGAG

Reverse complement sequence

CTCCGATAGTACTATTTCAGCCTCCAATAGAGTACCTATACAGAAGACCCATTTTGCGTGCTATAAGAGGCATAATCTAAATCCGAGTATTCTCTCTCCT[G/A]
AAGACCTATTTACATTAAGGGTTATTTTTTAAGTCTTATTGTTGGAGAAGACCAAAAATACTGTAGCGCTATGCAAACGTGAAATGGGTCTTGTATTTTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.40% 5.30% 6.88% 17.48% NA
All Indica  2759 80.40% 0.10% 1.30% 18.16% NA
All Japonica  1512 49.90% 15.70% 13.76% 20.63% NA
Aus  269 72.50% 0.00% 27.51% 0.00% NA
Indica I  595 81.20% 0.00% 1.01% 17.82% NA
Indica II  465 74.40% 0.00% 2.37% 23.23% NA
Indica III  913 85.90% 0.10% 0.22% 13.80% NA
Indica Intermediate  786 77.10% 0.30% 2.16% 20.48% NA
Temperate Japonica  767 80.40% 5.20% 8.21% 6.13% NA
Tropical Japonica  504 13.50% 27.60% 19.25% 39.68% NA
Japonica Intermediate  241 29.00% 24.10% 19.92% 26.97% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 67.80% 10.00% 7.78% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0141963794 C -> T LOC_Os01g72350.1 upstream_gene_variant ; 332.0bp to feature; MODIFIER silent_mutation Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979 N N N N
vg0141963794 C -> T LOC_Os01g72350.2 upstream_gene_variant ; 332.0bp to feature; MODIFIER silent_mutation Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979 N N N N
vg0141963794 C -> T LOC_Os01g72340.1 downstream_gene_variant ; 1007.0bp to feature; MODIFIER silent_mutation Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979 N N N N
vg0141963794 C -> T LOC_Os01g72340-LOC_Os01g72350 intergenic_region ; MODIFIER silent_mutation Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979 N N N N
vg0141963794 C -> DEL N N silent_mutation Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979 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)
vg0141963794 C T -0.04 -0.03 -0.01 -0.01 -0.04 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141963794 NA 1.20E-12 mr1449 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
vg0141963794 NA 2.60E-07 mr1668 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
vg0141963794 6.36E-06 1.06E-16 mr1871 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
vg0141963794 1.19E-07 1.92E-26 mr1042_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
vg0141963794 NA 3.57E-08 mr1042_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
vg0141963794 NA 3.80E-09 mr1502_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
vg0141963794 NA 1.31E-08 mr1543_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
vg0141963794 NA 3.62E-12 mr1680_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
vg0141963794 2.85E-06 1.09E-15 mr1742_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
vg0141963794 NA 6.71E-09 mr1742_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
vg0141963794 1.80E-11 2.81E-32 mr1871_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
vg0141963794 NA 4.03E-11 mr1871_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