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Detailed information for vg0715011230:

Variant ID: vg0715011230 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 15011230
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTCGCATCCGGATTGGAGCTGGAGGGTCTGATGTGAGGAATTGATCCGGGCCAGGAACAGGGGAAGGGAGGGAGGCCAAACCGGCCCCGTTTCCAATC[T/C]
GGGCCGGCCAAAACGAACGACGCTTCCGAGCCAGACCAGATTTGGAAATAGAGGCCGTTTCGGGCCTTACCGAACGAGGCCTAAGGCGTTGTCAGGGATG

Reverse complement sequence

CATCCCTGACAACGCCTTAGGCCTCGTTCGGTAAGGCCCGAAACGGCCTCTATTTCCAAATCTGGTCTGGCTCGGAAGCGTCGTTCGTTTTGGCCGGCCC[A/G]
GATTGGAAACGGGGCCGGTTTGGCCTCCCTCCCTTCCCCTGTTCCTGGCCCGGATCAATTCCTCACATCAGACCCTCCAGCTCCAATCCGGATGCGAGGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 5.80% 0.06% 0.00% NA
All Indica  2759 95.10% 4.80% 0.07% 0.00% NA
All Japonica  1512 94.40% 5.60% 0.00% 0.00% NA
Aus  269 92.90% 6.70% 0.37% 0.00% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 89.10% 10.70% 0.25% 0.00% NA
Temperate Japonica  767 89.30% 10.70% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0715011230 T -> C LOC_Os07g26120-LOC_Os07g26130 intergenic_region ; MODIFIER silent_mutation Average:97.471; most accessible tissue: Minghui63 root, score: 98.719 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)
vg0715011230 T C -0.2 -0.23 -0.22 -0.19 -0.15 -0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0715011230 8.78E-06 8.77E-06 mr1369_2 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
vg0715011230 4.41E-06 4.40E-06 mr1453_2 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
vg0715011230 NA 3.03E-06 mr1738_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
vg0715011230 2.97E-06 2.97E-06 mr1766_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
vg0715011230 NA 5.59E-06 mr1833_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