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Detailed information for vg0329444805:

Variant ID: vg0329444805 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 29444805
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTACATGTAATTAACTACTTCCTCCGTCCCAAAAAAATAAACCTTAGCCACAAATACGTGACGTATCCTAGTATAATGAATCTTAACAGATTTATGTTC[G/A]
GATTTATTGTACTAAAAAATATCATGTCTATATCTAGGTTAGTTTTTTCTTAAGGACGGAGTGACTCTTATCAAGGAGTTCTAGAAAAACTACTCCTTGT

Reverse complement sequence

ACAAGGAGTAGTTTTTCTAGAACTCCTTGATAAGAGTCACTCCGTCCTTAAGAAAAAACTAACCTAGATATAGACATGATATTTTTTAGTACAATAAATC[C/T]
GAACATAAATCTGTTAAGATTCATTATACTAGGATACGTCACGTATTTGTGGCTAAGGTTTATTTTTTTGGGACGGAGGAAGTAGTTAATTACATGTAGC

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 71.00% 0.20% 0.11% 28.71% NA
All Indica  2759 51.10% 0.30% 0.18% 48.39% NA
All Japonica  1512 99.60% 0.00% 0.00% 0.40% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 47.60% 0.00% 0.00% 52.44% NA
Indica II  465 48.60% 0.00% 0.22% 51.18% NA
Indica III  913 48.30% 0.80% 0.22% 50.71% NA
Indica Intermediate  786 58.70% 0.10% 0.25% 40.97% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.39% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 83.30% 0.00% 0.00% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0329444805 G -> A LOC_Os03g51459.1 downstream_gene_variant ; 3338.0bp to feature; MODIFIER silent_mutation Average:56.149; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0329444805 G -> A LOC_Os03g51450-LOC_Os03g51459 intergenic_region ; MODIFIER silent_mutation Average:56.149; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N
vg0329444805 G -> DEL N N silent_mutation Average:56.149; most accessible tissue: Minghui63 panicle, score: 85.556 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)
vg0329444805 G A 0.0 -0.01 -0.01 -0.03 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0329444805 NA 1.05E-06 mr1717 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
vg0329444805 NA 3.58E-11 mr1827 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