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Detailed information for vg0220034325:

Variant ID: vg0220034325 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20034325
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAAATTACATATTTGCCCTGGGCCTTCTCCTCTCAACGCGTGAGTCGCCGCCGCGAGCCCGCGACGGAAGAAAGAGGCGGAAACGCCGCCACCCCCAAC[G/A]
CCGGAAACGCCGGCCGCTACGCCCAGCCGCCGGGGCTCACCTCCAAGATGCCGCCGCCACCCGTACTCGCTGGAACCGTCGCCGCCACCCCTCTTTGCCG

Reverse complement sequence

CGGCAAAGAGGGGTGGCGGCGACGGTTCCAGCGAGTACGGGTGGCGGCGGCATCTTGGAGGTGAGCCCCGGCGGCTGGGCGTAGCGGCCGGCGTTTCCGG[C/T]
GTTGGGGGTGGCGGCGTTTCCGCCTCTTTCTTCCGTCGCGGGCTCGCGGCGGCGACTCACGCGTTGAGAGGAGAAGGCCCAGGGCAAATATGTAATTTCA

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 93.30% 6.40% 0.28% 0.00% NA
All Indica  2759 91.70% 8.10% 0.18% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 74.30% 23.00% 2.60% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 73.30% 26.20% 0.43% 0.00% NA
Indica III  913 96.20% 3.70% 0.11% 0.00% NA
Indica Intermediate  786 91.30% 8.40% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg0220034325 G -> A LOC_Os02g33640.1 5_prime_UTR_variant ; 1516.0bp to feature; MODIFIER silent_mutation Average:71.849; most accessible tissue: Minghui63 flag leaf, score: 85.151 N N N N
vg0220034325 G -> A LOC_Os02g33630.1 upstream_gene_variant ; 4264.0bp to feature; MODIFIER silent_mutation Average:71.849; most accessible tissue: Minghui63 flag leaf, score: 85.151 N N N N
vg0220034325 G -> A LOC_Os02g33650.1 downstream_gene_variant ; 4919.0bp to feature; MODIFIER silent_mutation Average:71.849; most accessible tissue: Minghui63 flag leaf, score: 85.151 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)
vg0220034325 G A 0.06 0.0 0.02 0.02 0.05 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220034325 NA 4.37E-07 mr1114 Ind_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
vg0220034325 NA 2.03E-09 mr1319 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
vg0220034325 NA 2.89E-10 mr1332 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
vg0220034325 NA 6.47E-06 mr1884 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