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Detailed information for vg0313900900:

Variant ID: vg0313900900 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13900900
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTGCAGCTGGCTACAGATCTGTAGCTCGCTGCTTTTCTCTCTCATCTTTTATCTTATTAAAATATATTTATAGCTAGCTAATAATCTAATAATCTGCTA[A/T]
TGTATATGCTCTTGCTTCTTCAAATGCCAACGAGTAGTACTAGCACTAGCACACTTGACACTCCCCAATAAAAAAGTTGCACAGTAGATTTAATGTGCAT

Reverse complement sequence

ATGCACATTAAATCTACTGTGCAACTTTTTTATTGGGGAGTGTCAAGTGTGCTAGTGCTAGTACTACTCGTTGGCATTTGAAGAAGCAAGAGCATATACA[T/A]
TAGCAGATTATTAGATTATTAGCTAGCTATAAATATATTTTAATAAGATAAAAGATGAGAGAGAAAAGCAGCGAGCTACAGATCTGTAGCCAGCTGCAGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.80% 37.10% 0.11% 0.00% NA
All Indica  2759 98.30% 1.60% 0.07% 0.00% NA
All Japonica  1512 2.50% 97.40% 0.13% 0.00% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.20% 0.13% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 2.20% 97.60% 0.20% 0.00% NA
Japonica Intermediate  241 5.00% 94.60% 0.41% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 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
vg0313900900 A -> T LOC_Os03g24410.1 upstream_gene_variant ; 3809.0bp to feature; MODIFIER silent_mutation Average:70.396; most accessible tissue: Callus, score: 95.137 N N N N
vg0313900900 A -> T LOC_Os03g24400-LOC_Os03g24410 intergenic_region ; MODIFIER silent_mutation Average:70.396; most accessible tissue: Callus, score: 95.137 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)
vg0313900900 A T 0.02 -0.02 -0.01 0.05 0.03 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313900900 NA 2.57E-26 mr1072 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
vg0313900900 7.50E-06 NA mr1550 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
vg0313900900 NA 1.37E-08 mr1595 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
vg0313900900 NA 7.40E-11 mr1751 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
vg0313900900 1.75E-06 NA mr1757 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
vg0313900900 NA 1.98E-25 mr1051_2 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
vg0313900900 NA 5.08E-55 mr1124_2 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
vg0313900900 1.21E-07 NA mr1550_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