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Detailed information for vg0801574405:

Variant ID: vg0801574405 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1574405
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCACCCCCCCGGGCGCCGGCGCCGCCCGCGAAACCCTAGAGCTCTCCCCCTCCTCGAGCGGGGGGAGGCGTAGGGCGGCGAGAGAGGAGGAGGAGGAGG[C/A]
GGCTAGGCTTACGGCTTCTCCTCTCTCTCTCTCTCTCTTTCTCTCTCCTCTGTCTCCGCGCTCGGCTATCTCTCTCTTTCTTTCTCTCTCTTCTCGCTTC

Reverse complement sequence

GAAGCGAGAAGAGAGAGAAAGAAAGAGAGAGATAGCCGAGCGCGGAGACAGAGGAGAGAGAAAGAGAGAGAGAGAGAGAGGAGAAGCCGTAAGCCTAGCC[G/T]
CCTCCTCCTCCTCCTCTCTCGCCGCCCTACGCCTCCCCCCGCTCGAGGAGGGGGAGAGCTCTAGGGTTTCGCGGGCGGCGCCGGCGCCCGGGGGGGTGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.60% 6.20% 0.13% 0.00% NA
All Indica  2759 97.50% 2.40% 0.18% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 18.20% 81.40% 0.37% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 96.90% 3.00% 0.11% 0.00% NA
Indica Intermediate  786 95.00% 4.60% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0801574405 C -> A LOC_Os08g03360.1 upstream_gene_variant ; 1342.0bp to feature; MODIFIER silent_mutation Average:98.713; most accessible tissue: Minghui63 panicle, score: 99.795 N N N N
vg0801574405 C -> A LOC_Os08g03370.1 upstream_gene_variant ; 3742.0bp to feature; MODIFIER silent_mutation Average:98.713; most accessible tissue: Minghui63 panicle, score: 99.795 N N N N
vg0801574405 C -> A LOC_Os08g03360-LOC_Os08g03370 intergenic_region ; MODIFIER silent_mutation Average:98.713; most accessible tissue: Minghui63 panicle, score: 99.795 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)
vg0801574405 C A 0.0 0.01 0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801574405 9.79E-06 NA mr1014 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
vg0801574405 NA 7.50E-08 mr1530 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
vg0801574405 NA 1.42E-06 mr1803 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