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Detailed information for vg0224078729:

Variant ID: vg0224078729 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24078729
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCTTGGATAAGGATTTCGCACCAGTCGACGTCGCATCGCCCTCGCCCGGGAGCGACTTTTCTTTCTACGCAGAAGTGTTTAGGTTCAAAGTTTTTCTT[C/T]
AAACTATTAACTTTTTCATCACATCAAAACTTTCTTACACACATAAATTTTCATTTTTTCCATCACATTGTTTCAATTTTAATCCAACTTTCAATTTTGA

Reverse complement sequence

TCAAAATTGAAAGTTGGATTAAAATTGAAACAATGTGATGGAAAAAATGAAAATTTATGTGTGTAAGAAAGTTTTGATGTGATGAAAAAGTTAATAGTTT[G/A]
AAGAAAAACTTTGAACCTAAACACTTCTGCGTAGAAAGAAAAGTCGCTCCCGGGCGAGGGCGATGCGACGTCGACTGGTGCGAAATCCTTATCCAAGCTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.20% 4.80% 0.00% 0.00% NA
All Indica  2759 93.40% 6.60% 0.00% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 89.50% 10.50% 0.00% 0.00% NA
Indica III  913 90.50% 9.50% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 3.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0224078729 C -> T LOC_Os02g39840.1 upstream_gene_variant ; 3952.0bp to feature; MODIFIER silent_mutation Average:97.801; most accessible tissue: Minghui63 root, score: 99.179 N N N N
vg0224078729 C -> T LOC_Os02g39850.1 upstream_gene_variant ; 1975.0bp to feature; MODIFIER silent_mutation Average:97.801; most accessible tissue: Minghui63 root, score: 99.179 N N N N
vg0224078729 C -> T LOC_Os02g39840.3 upstream_gene_variant ; 3952.0bp to feature; MODIFIER silent_mutation Average:97.801; most accessible tissue: Minghui63 root, score: 99.179 N N N N
vg0224078729 C -> T LOC_Os02g39840.2 upstream_gene_variant ; 3952.0bp to feature; MODIFIER silent_mutation Average:97.801; most accessible tissue: Minghui63 root, score: 99.179 N N N N
vg0224078729 C -> T LOC_Os02g39840-LOC_Os02g39850 intergenic_region ; MODIFIER silent_mutation Average:97.801; most accessible tissue: Minghui63 root, score: 99.179 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)
vg0224078729 C T 0.02 -0.02 -0.04 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224078729 NA 7.86E-07 mr1170 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
vg0224078729 5.50E-07 5.50E-07 mr1341_2 Ind_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