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Detailed information for vg0912106235:

Variant ID: vg0912106235 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 12106235
Reference Allele: ACTAlternative Allele: GCT,A,TCT
Primary Allele: ACTSecondary Allele: GCT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTTCATATCATTTGATTCATTATTAAATATACTTTCATATACACATAAAGTTTTACATATTTCATAATTTTTTTAATAAGACGAACGGTTAAACATGT[ACT/GCT,A,TCT]
AAAAAGTTAACGGTGTCAAACATTTTGAAACGGAGGGAGTATAGTAGTAGAACCTCGTTTGACAAACCGTTTCGACCGGTGCATCGTGCAAGTGAGAGTT

Reverse complement sequence

AACTCTCACTTGCACGATGCACCGGTCGAAACGGTTTGTCAAACGAGGTTCTACTACTATACTCCCTCCGTTTCAAAATGTTTGACACCGTTAACTTTTT[AGT/AGC,T,AGA]
ACATGTTTAACCGTTCGTCTTATTAAAAAAATTATGAAATATGTAAAACTTTATGTGTATATGAAAGTATATTTAATAATGAATCAAATGATATGAAAAG

Allele Frequencies:

Populations Population SizeFrequency of ACT(primary allele) Frequency of GCT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.70% 30.90% 1.65% 5.37% A: 0.34%; TCT: 0.02%
All Indica  2759 45.10% 51.50% 0.94% 2.43% A: 0.07%
All Japonica  1512 98.90% 0.60% 0.33% 0.13% NA
Aus  269 11.90% 4.80% 13.75% 64.31% A: 5.20%
Indica I  595 60.20% 38.70% 1.01% 0.17% NA
Indica II  465 73.50% 18.90% 1.94% 5.59% NA
Indica III  913 24.90% 72.80% 0.44% 1.86% NA
Indica Intermediate  786 40.20% 55.70% 0.89% 2.93% A: 0.25%
Temperate Japonica  767 99.30% 0.40% 0.26% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 96.70% 1.70% 0.83% 0.83% NA
VI/Aromatic  96 78.10% 5.20% 4.17% 11.46% TCT: 1.04%
Intermediate  90 80.00% 12.20% 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
vg0912106235 ACT -> TCT LOC_Os09g20190.1 downstream_gene_variant ; 2629.0bp to feature; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> TCT LOC_Os09g20200.1 downstream_gene_variant ; 3858.0bp to feature; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> TCT LOC_Os09g20190-LOC_Os09g20200 intergenic_region ; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> DEL N N silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> A LOC_Os09g20190.1 downstream_gene_variant ; 2630.0bp to feature; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> A LOC_Os09g20200.1 downstream_gene_variant ; 3857.0bp to feature; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> A LOC_Os09g20190-LOC_Os09g20200 intergenic_region ; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> GCT LOC_Os09g20190.1 downstream_gene_variant ; 2629.0bp to feature; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> GCT LOC_Os09g20200.1 downstream_gene_variant ; 3858.0bp to feature; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 N N N N
vg0912106235 ACT -> GCT LOC_Os09g20190-LOC_Os09g20200 intergenic_region ; MODIFIER silent_mutation Average:55.905; most accessible tissue: Minghui63 root, score: 95.353 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)
vg0912106235 ACT A -0.18 0.0 -0.08 -0.15 -0.11 -0.1
vg0912106235 ACT GCT 0.0 0.01 0.0 0.01 0.0 0.0
vg0912106235 ACT TCT -0.04 -0.04 -0.03 -0.04 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0912106235 NA 4.00E-15 Plant_height Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0912106235 NA 8.76E-06 mr1098 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
vg0912106235 NA 2.27E-08 mr1133 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
vg0912106235 NA 5.35E-09 mr1141 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
vg0912106235 NA 6.06E-08 mr1180 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
vg0912106235 NA 1.19E-07 mr1183 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
vg0912106235 NA 9.43E-08 mr1503 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
vg0912106235 NA 1.29E-07 mr1063_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
vg0912106235 NA 1.90E-06 mr1133_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
vg0912106235 NA 7.92E-10 mr1180_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
vg0912106235 NA 7.76E-08 mr1183_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
vg0912106235 NA 3.72E-07 mr1348_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
vg0912106235 NA 1.45E-11 mr1349_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
vg0912106235 NA 7.89E-06 mr1349_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
vg0912106235 NA 4.99E-07 mr1452_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
vg0912106235 NA 9.16E-06 mr1452_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
vg0912106235 NA 6.48E-06 mr1462_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
vg0912106235 NA 2.29E-07 mr1540_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
vg0912106235 NA 1.01E-09 mr1568_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
vg0912106235 NA 3.59E-06 mr1568_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
vg0912106235 NA 5.12E-11 mr1627_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
vg0912106235 NA 6.14E-06 mr1667_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
vg0912106235 NA 1.13E-06 mr1732_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
vg0912106235 NA 3.62E-09 mr1895_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
vg0912106235 NA 2.33E-07 mr1895_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
vg0912106235 NA 3.20E-06 mr1899_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
vg0912106235 NA 2.71E-07 mr1933_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
vg0912106235 NA 4.82E-09 mr1946_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
vg0912106235 NA 4.82E-09 mr1948_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