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Detailed information for vg0715912863:

Variant ID: vg0715912863 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15912863
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTTTAATATTTTAAAAAATAGACTTAAAAATAGTAAATGTCAAAAATGCCCTTGCCTCCAACCATCTCCGAACTCCGATCAGCATAGCCGTGCCGGAG[G/A]
AGAGGCACGCACGTGCAGCTTTTCCCCCCTCCTCCAGCGTCGTCTCGCCTCCGCGCGCTCCCCGCCGGCGACGGCCCCGCCCCCTTGCCTCCTCTCTCGC

Reverse complement sequence

GCGAGAGAGGAGGCAAGGGGGCGGGGCCGTCGCCGGCGGGGAGCGCGCGGAGGCGAGACGACGCTGGAGGAGGGGGGAAAAGCTGCACGTGCGTGCCTCT[C/T]
CTCCGGCACGGCTATGCTGATCGGAGTTCGGAGATGGTTGGAGGCAAGGGCATTTTTGACATTTACTATTTTTAAGTCTATTTTTTAAAATATTAAAATG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.10% 12.70% 0.13% 0.06% NA
All Indica  2759 98.30% 1.60% 0.07% 0.11% NA
All Japonica  1512 64.90% 34.90% 0.20% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 98.10% 1.30% 0.00% 0.65% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.70% 0.25% 0.00% NA
Temperate Japonica  767 86.60% 13.30% 0.13% 0.00% NA
Tropical Japonica  504 28.20% 71.60% 0.20% 0.00% NA
Japonica Intermediate  241 72.60% 27.00% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0715912863 G -> DEL N N silent_mutation Average:93.128; most accessible tissue: Minghui63 panicle, score: 96.623 N N N N
vg0715912863 G -> A LOC_Os07g27350.1 upstream_gene_variant ; 9.0bp to feature; MODIFIER silent_mutation Average:93.128; most accessible tissue: Minghui63 panicle, score: 96.623 N N N N
vg0715912863 G -> A LOC_Os07g27340.1 downstream_gene_variant ; 4064.0bp to feature; MODIFIER silent_mutation Average:93.128; most accessible tissue: Minghui63 panicle, score: 96.623 N N N N
vg0715912863 G -> A LOC_Os07g27340-LOC_Os07g27350 intergenic_region ; MODIFIER silent_mutation Average:93.128; most accessible tissue: Minghui63 panicle, score: 96.623 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)
vg0715912863 G A -0.02 -0.02 0.0 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715912863 NA 4.74E-06 mr1790 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
vg0715912863 2.67E-06 2.66E-06 mr1755_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