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Detailed information for vg0705438086:

Variant ID: vg0705438086 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 5438086
Reference Allele: GAlternative Allele: A,GT
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAAATGCTTGGAGAAAATAGTTGATGGTGAGGGATTGAGATCCTCTCTTCAAAGGCACCGTACCTTTGTTACTGACATATGGGCCCAGGGTCCATTGG[G/A,GT]
CCCACATGTCAGTGATAAAGGCACGTGCCTTTGAAGGTAGAGGAACCTGATCCGATTGTGAGGTCGACAAAGAGGTCACAATAGTTGGTCCAGGACCCGG

Reverse complement sequence

CCGGGTCCTGGACCAACTATTGTGACCTCTTTGTCGACCTCACAATCGGATCAGGTTCCTCTACCTTCAAAGGCACGTGCCTTTATCACTGACATGTGGG[C/T,AC]
CCAATGGACCCTGGGCCCATATGTCAGTAACAAAGGTACGGTGCCTTTGAAGAGAGGATCTCAATCCCTCACCATCAACTATTTTCTCCAAGCATTTTAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.30% 40.40% 0.04% 1.25% GT: 0.02%
All Indica  2759 95.80% 3.90% 0.00% 0.29% NA
All Japonica  1512 0.30% 96.40% 0.00% 3.31% NA
Aus  269 25.70% 74.00% 0.00% 0.00% GT: 0.37%
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 94.60% 5.00% 0.00% 0.33% NA
Indica Intermediate  786 93.90% 5.50% 0.00% 0.64% NA
Temperate Japonica  767 0.10% 94.40% 0.00% 5.48% NA
Tropical Japonica  504 0.60% 99.40% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 96.30% 0.00% 3.32% NA
VI/Aromatic  96 2.10% 95.80% 2.08% 0.00% NA
Intermediate  90 40.00% 58.90% 0.00% 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
vg0705438086 G -> DEL N N silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0705438086 G -> GT LOC_Os07g10130.1 upstream_gene_variant ; 2265.0bp to feature; MODIFIER silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0705438086 G -> GT LOC_Os07g10120.1 downstream_gene_variant ; 1908.0bp to feature; MODIFIER silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0705438086 G -> GT LOC_Os07g10120-LOC_Os07g10130 intergenic_region ; MODIFIER silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0705438086 G -> A LOC_Os07g10130.1 upstream_gene_variant ; 2266.0bp to feature; MODIFIER silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0705438086 G -> A LOC_Os07g10120.1 downstream_gene_variant ; 1907.0bp to feature; MODIFIER silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg0705438086 G -> A LOC_Os07g10120-LOC_Os07g10130 intergenic_region ; MODIFIER silent_mutation Average:82.345; most accessible tissue: Zhenshan97 panicle, score: 95.264 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)
vg0705438086 G A 0.02 -0.01 0.01 0.04 0.06 0.06
vg0705438086 G GT 0.08 0.07 0.08 0.06 0.09 0.13

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0705438086 NA 2.49E-25 mr1076 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
vg0705438086 NA 1.65E-38 mr1082 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
vg0705438086 NA 1.48E-29 mr1085 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
vg0705438086 NA 7.67E-56 mr1103 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
vg0705438086 NA 2.52E-61 mr1246 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
vg0705438086 NA 5.13E-11 mr1325 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
vg0705438086 NA 7.48E-13 mr1326 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
vg0705438086 NA 1.31E-18 mr1518 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
vg0705438086 1.94E-06 NA mr1757 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
vg0705438086 NA 2.79E-54 mr1861 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
vg0705438086 NA 9.84E-36 mr1107_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
vg0705438086 NA 5.81E-14 mr1326_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
vg0705438086 NA 9.83E-15 mr1333_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
vg0705438086 NA 4.67E-23 mr1386_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
vg0705438086 NA 9.50E-07 mr1548_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
vg0705438086 3.80E-13 NA mr1549_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
vg0705438086 2.32E-13 7.52E-13 mr1549_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
vg0705438086 2.20E-08 NA mr1550_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
vg0705438086 8.11E-11 5.34E-10 mr1550_2 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
vg0705438086 NA 5.54E-16 mr1686_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
vg0705438086 1.70E-10 NA mr1757_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
vg0705438086 4.24E-10 2.55E-09 mr1757_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