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Detailed information for vg0908831499:

Variant ID: vg0908831499 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 8831499
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTAGCTGTGGGAGGAACCCCCCCTATTATCCAGCGGTCTCGGTGGGGTGCGACAGGATGGCGACGCGACGGTGACAAGAGCGACGGCGACGGACAGAG[A/G]
TAACGACTTGGATAGGGGGCGCCGGGCTATGCCCTAGGGTGACGCGGGGTTGTCGTGGCGGCCGTTATCACTCCATCCCGAGGGCGACGTGTGAGGGGAC

Reverse complement sequence

GTCCCCTCACACGTCGCCCTCGGGATGGAGTGATAACGGCCGCCACGACAACCCCGCGTCACCCTAGGGCATAGCCCGGCGCCCCCTATCCAAGTCGTTA[T/C]
CTCTGTCCGTCGCCGTCGCTCTTGTCACCGTCGCGTCGCCATCCTGTCGCACCCCACCGAGACCGCTGGATAATAGGGGGGGTTCCTCCCACAGCTAATG

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 68.30% 2.00% 15.26% 14.52% NA
All Indica  2759 54.80% 3.10% 22.00% 20.12% NA
All Japonica  1512 96.10% 0.30% 1.52% 2.12% NA
Aus  269 43.10% 1.10% 25.65% 30.11% NA
Indica I  595 65.40% 3.50% 24.71% 6.39% NA
Indica II  465 78.70% 4.50% 5.59% 11.18% NA
Indica III  913 30.90% 2.50% 30.34% 36.25% NA
Indica Intermediate  786 60.40% 2.50% 19.97% 17.05% NA
Temperate Japonica  767 97.90% 0.00% 0.26% 1.83% NA
Tropical Japonica  504 93.80% 0.40% 2.98% 2.78% NA
Japonica Intermediate  241 95.00% 0.80% 2.49% 1.66% NA
VI/Aromatic  96 69.80% 0.00% 16.67% 13.54% NA
Intermediate  90 86.70% 1.10% 6.67% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0908831499 A -> G LOC_Os09g14820.1 upstream_gene_variant ; 4566.0bp to feature; MODIFIER silent_mutation Average:79.291; most accessible tissue: Minghui63 panicle, score: 99.163 N N N N
vg0908831499 A -> G LOC_Os09g14820-LOC_Os09g14830 intergenic_region ; MODIFIER silent_mutation Average:79.291; most accessible tissue: Minghui63 panicle, score: 99.163 N N N N
vg0908831499 A -> DEL N N silent_mutation Average:79.291; most accessible tissue: Minghui63 panicle, score: 99.163 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)
vg0908831499 A G -0.28 -0.32 -0.25 -0.08 -0.22 -0.24

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0908831499 NA 8.77E-06 mr1808 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