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Detailed information for vg0513922749:

Variant ID: vg0513922749 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 13922749
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, A: 0.43, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TGCATCTTCTCTGTAATCGAAAGAAAAAAAAACACGAGAATGAGAGATCGGACGACCAGCGGGGTTGCAAAAATCGGCGCTCCCCCCGCTCTCTGCCCCC[G/A]
CGCGCATGTATGCCACCTGGGCCGACCACGGTCCTTACCTCCACATGTAACAAATCACCTACATATTTTGGAAACTCTATATTAAGATAATATAGTTTAT

Reverse complement sequence

ATAAACTATATTATCTTAATATAGAGTTTCCAAAATATGTAGGTGATTTGTTACATGTGGAGGTAAGGACCGTGGTCGGCCCAGGTGGCATACATGCGCG[C/T]
GGGGGCAGAGAGCGGGGGGAGCGCCGATTTTTGCAACCCCGCTGGTCGTCCGATCTCTCATTCTCGTGTTTTTTTTTCTTTCGATTACAGAGAAGATGCA

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 67.40% 32.10% 0.17% 0.30% NA
All Indica  2759 45.50% 54.00% 0.18% 0.36% NA
All Japonica  1512 99.80% 0.10% 0.00% 0.13% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 60.20% 39.30% 0.34% 0.17% NA
Indica II  465 34.40% 64.70% 0.43% 0.43% NA
Indica III  913 41.50% 58.20% 0.00% 0.33% NA
Indica Intermediate  786 45.40% 53.90% 0.13% 0.51% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 78.90% 15.60% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0513922749 G -> DEL N N silent_mutation Average:91.732; most accessible tissue: Minghui63 root, score: 96.28 N N N N
vg0513922749 G -> A LOC_Os05g24140.1 upstream_gene_variant ; 4923.0bp to feature; MODIFIER silent_mutation Average:91.732; most accessible tissue: Minghui63 root, score: 96.28 N N N N
vg0513922749 G -> A LOC_Os05g24120-LOC_Os05g24140 intergenic_region ; MODIFIER silent_mutation Average:91.732; most accessible tissue: Minghui63 root, score: 96.28 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)
vg0513922749 G A 0.05 0.03 0.01 0.0 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0513922749 NA 2.59E-06 mr1074_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
vg0513922749 4.37E-06 2.57E-06 mr1500_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
vg0513922749 NA 3.74E-06 mr1551_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
vg0513922749 NA 1.57E-07 mr1819_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