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Detailed information for vg0920993132:

Variant ID: vg0920993132 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 20993132
Reference Allele: AAlternative Allele: ATAGGGCATTTTTTAAAATTTG,G
Primary Allele: ASecondary Allele: ATAGGGCATTTTTTAAAATT TG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAAGGTTTACCTTCTTTGCTTCCGCAGGAACGCTCTGTAGCGGTATTCTACAGACAACTTATCAGAAAAGGAGTTATCTATCCAACAAGGCAAAATTT[A/ATAGGGCATTTTTTAAAATTTG,G]
CTATAGGGCACCAAAAAATTACGGTTTTTGCTATGAGACATCCGAAGATCGTGAATCTTTTCGTGGACACTGTAAAAAAGTGGACACTCCTCCTATTATT

Reverse complement sequence

AATAATAGGAGGAGTGTCCACTTTTTTACAGTGTCCACGAAAAGATTCACGATCTTCGGATGTCTCATAGCAAAAACCGTAATTTTTTGGTGCCCTATAG[T/CAAATTTTAAAAAATGCCCTAT,C]
AAATTTTGCCTTGTTGGATAGATAACTCCTTTTCTGATAAGTTGTCTGTAGAATACCGCTACAGAGCGTTCCTGCGGAAGCAAAGAAGGTAAACCTTTAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of ATAGGGCATTTTTTAAAATT TG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.40% 32.20% 0.80% 0.02% G: 20.55%
All Indica  2759 16.30% 54.70% 1.23% 0.04% G: 27.73%
All Japonica  1512 99.60% 0.00% 0.13% 0.00% G: 0.26%
Aus  269 32.00% 0.00% 0.00% 0.00% G: 68.03%
Indica I  595 11.80% 53.60% 3.53% 0.17% G: 30.92%
Indica II  465 5.40% 63.00% 0.65% 0.00% G: 30.97%
Indica III  913 20.50% 59.70% 0.00% 0.00% G: 19.82%
Indica Intermediate  786 21.20% 44.90% 1.27% 0.00% G: 32.57%
Temperate Japonica  767 99.60% 0.00% 0.13% 0.00% G: 0.26%
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.00% G: 0.83%
VI/Aromatic  96 92.70% 0.00% 0.00% 0.00% G: 7.29%
Intermediate  90 71.10% 13.30% 2.22% 0.00% G: 13.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0920993132 A -> G LOC_Os09g36380.1 downstream_gene_variant ; 2101.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.301 N N N N
vg0920993132 A -> G LOC_Os09g36370.1 intron_variant ; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.301 N N N N
vg0920993132 A -> DEL N N silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.301 N N N N
vg0920993132 A -> ATAGGGCATTTTTTAAAATTTG LOC_Os09g36380.1 downstream_gene_variant ; 2100.0bp to feature; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.301 N N N N
vg0920993132 A -> ATAGGGCATTTTTTAAAATTTG LOC_Os09g36370.1 intron_variant ; MODIFIER silent_mutation Average:82.859; most accessible tissue: Zhenshan97 root, score: 91.301 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)
vg0920993132 A ATAGG* -0.41 -0.28 -0.38 -0.37 -0.45 -0.42
vg0920993132 A G -0.01 -0.01 -0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920993132 NA 3.47E-06 mr1006 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
vg0920993132 NA 5.08E-06 mr1011 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
vg0920993132 NA 9.71E-06 mr1013 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
vg0920993132 NA 1.64E-06 mr1052 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
vg0920993132 NA 7.79E-06 mr1296_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
vg0920993132 NA 4.49E-07 mr1378_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
vg0920993132 NA 1.09E-06 mr1550_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
vg0920993132 NA 7.85E-21 mr1627_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
vg0920993132 NA 7.42E-11 mr1739_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
vg0920993132 5.04E-06 2.77E-09 mr1793_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