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Detailed information for vg0728762565:

Variant ID: vg0728762565 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 28762565
Reference Allele: AAlternative Allele: T,AT
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAAGGCTGCGTTCGTTTGTATGATATAGGATGAGAAAACACCTCGTTTTCCGCGCGCACACTTCCCAAACTACTAAACGGTGTGTTTTTTGCAAAAAA[A/T,AT]
TTCTATAGGAAAGTTGCTTTAAAAAGTCATATTAATCTATTTTTGAAATTTAAAATAGTTAATACTCAATTAATCATGCGCAAATGGCTCACCTCGTTTT

Reverse complement sequence

AAAACGAGGTGAGCCATTTGCGCATGATTAATTGAGTATTAACTATTTTAAATTTCAAAAATAGATTAATATGACTTTTTAAAGCAACTTTCCTATAGAA[T/A,AT]
TTTTTTGCAAAAAACACACCGTTTAGTAGTTTGGGAAGTGTGCGCGCGGAAAACGAGGTGTTTTCTCATCCTATATCATACAAACGAACGCAGCCTTATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.80% 27.40% 2.01% 0.00% AT: 19.72%
All Indica  2759 20.10% 43.40% 3.33% 0.00% AT: 33.16%
All Japonica  1512 99.40% 0.50% 0.00% 0.00% AT: 0.13%
Aus  269 81.40% 18.20% 0.00% 0.00% AT: 0.37%
Indica I  595 40.70% 41.20% 7.56% 0.00% AT: 10.59%
Indica II  465 10.80% 29.50% 1.72% 0.00% AT: 58.06%
Indica III  913 8.40% 61.00% 0.88% 0.00% AT: 29.68%
Indica Intermediate  786 23.50% 33.00% 3.94% 0.00% AT: 39.57%
Temperate Japonica  767 99.90% 0.00% 0.00% 0.00% AT: 0.13%
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.00% 0.00% AT: 0.41%
VI/Aromatic  96 72.90% 24.00% 0.00% 0.00% AT: 3.12%
Intermediate  90 63.30% 21.10% 3.33% 0.00% AT: 12.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728762565 A -> AT LOC_Os07g48160.1 upstream_gene_variant ; 1857.0bp to feature; MODIFIER silent_mutation Average:73.056; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0728762565 A -> AT LOC_Os07g48150.1 downstream_gene_variant ; 1842.0bp to feature; MODIFIER silent_mutation Average:73.056; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0728762565 A -> AT LOC_Os07g48150-LOC_Os07g48160 intergenic_region ; MODIFIER silent_mutation Average:73.056; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0728762565 A -> T LOC_Os07g48160.1 upstream_gene_variant ; 1858.0bp to feature; MODIFIER silent_mutation Average:73.056; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0728762565 A -> T LOC_Os07g48150.1 downstream_gene_variant ; 1841.0bp to feature; MODIFIER silent_mutation Average:73.056; most accessible tissue: Zhenshan97 flower, score: 90.95 N N N N
vg0728762565 A -> T LOC_Os07g48150-LOC_Os07g48160 intergenic_region ; MODIFIER silent_mutation Average:73.056; most accessible tissue: Zhenshan97 flower, score: 90.95 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)
vg0728762565 A AT -0.03 -0.06 -0.07 -0.03 -0.1 -0.19
vg0728762565 A T 0.0 0.0 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728762565 6.45E-07 NA mr1038 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
vg0728762565 2.40E-06 5.91E-06 mr1038 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
vg0728762565 2.78E-08 NA mr1389 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
vg0728762565 2.61E-07 1.52E-06 mr1389 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
vg0728762565 6.18E-07 NA mr1038_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
vg0728762565 2.25E-06 NA mr1038_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
vg0728762565 9.83E-09 1.06E-06 mr1389_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
vg0728762565 4.52E-08 2.40E-08 mr1389_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
vg0728762565 4.08E-06 NA mr1457_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