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Detailed information for vg0134372447:

Variant ID: vg0134372447 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34372447
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TAAATGAAAATTACCGAAAGGAGTTAAATGGTGCCTTGCTACCGGGAGGGGCCGGGATACCAAACTTAGGTGGTGATTAGTGGTATAGGTCATCAAGCAC[A/C]
TGGGAATAGGCCCTGCCCAAGCGCCCTCCCGAGATCGGACTCGAGGGAGGGTAAGACCGGAACGAGGTCTAGCCCGAGCGATCTTGTCTCACGGACTATC

Reverse complement sequence

GATAGTCCGTGAGACAAGATCGCTCGGGCTAGACCTCGTTCCGGTCTTACCCTCCCTCGAGTCCGATCTCGGGAGGGCGCTTGGGCAGGGCCTATTCCCA[T/G]
GTGCTTGATGACCTATACCACTAATCACCACCTAAGTTTGGTATCCCGGCCCCTCCCGGTAGCAAGGCACCATTTAACTCCTTTCGGTAATTTTCATTTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.00% 21.00% 0.00% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 39.60% 60.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 14.60% 85.40% 0.00% 0.00% NA
Tropical Japonica  504 66.30% 33.70% 0.00% 0.00% NA
Japonica Intermediate  241 63.10% 36.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0134372447 A -> C LOC_Os01g59420.1 downstream_gene_variant ; 4875.0bp to feature; MODIFIER silent_mutation Average:95.772; most accessible tissue: Minghui63 flag leaf, score: 100.0 N N N N
vg0134372447 A -> C LOC_Os01g59430.1 downstream_gene_variant ; 3411.0bp to feature; MODIFIER silent_mutation Average:95.772; most accessible tissue: Minghui63 flag leaf, score: 100.0 N N N N
vg0134372447 A -> C LOC_Os01g59420-LOC_Os01g59430 intergenic_region ; MODIFIER silent_mutation Average:95.772; most accessible tissue: Minghui63 flag leaf, score: 100.0 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)
vg0134372447 A C -0.05 -0.05 -0.05 -0.05 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134372447 NA 2.70E-09 mr1658 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
vg0134372447 6.11E-06 NA mr1679 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
vg0134372447 9.54E-09 NA mr1720 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
vg0134372447 3.99E-07 NA mr1720 Jap_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
vg0134372447 NA 7.94E-13 mr1182_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
vg0134372447 NA 3.09E-10 mr1282_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
vg0134372447 NA 8.63E-08 mr1399_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