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Detailed information for vg0430619183:

Variant ID: vg0430619183 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30619183
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGATATGGTTAGGTGTGTTAAGTTCACGTCAAAATTGAAAGTTTGGTTAAAATTAGAACAATGTGATGGAAAAATTAAAAATTTGTGTGAGTAGAAAA[A/G]
TTTTGATGCTTGAAAAGTTGAAAGTTTGAAGAAAAAGTTGGAAACTGAACCATGCCTTACTTACACTCTTCTATTGACCTAAATATCTTGTCCATACTGT

Reverse complement sequence

ACAGTATGGACAAGATATTTAGGTCAATAGAAGAGTGTAAGTAAGGCATGGTTCAGTTTCCAACTTTTTCTTCAAACTTTCAACTTTTCAAGCATCAAAA[T/C]
TTTTCTACTCACACAAATTTTTAATTTTTCCATCACATTGTTCTAATTTTAACCAAACTTTCAATTTTGACGTGAACTTAACACACCTAACCATATCCCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.90% 23.50% 0.38% 0.25% NA
All Indica  2759 86.70% 12.70% 0.18% 0.36% NA
All Japonica  1512 60.10% 39.00% 0.73% 0.13% NA
Aus  269 83.60% 16.00% 0.37% 0.00% NA
Indica I  595 97.30% 2.40% 0.00% 0.34% NA
Indica II  465 84.10% 15.70% 0.00% 0.22% NA
Indica III  913 80.80% 18.70% 0.22% 0.22% NA
Indica Intermediate  786 87.20% 11.80% 0.38% 0.64% NA
Temperate Japonica  767 69.40% 29.50% 1.17% 0.00% NA
Tropical Japonica  504 40.30% 59.50% 0.00% 0.20% NA
Japonica Intermediate  241 72.20% 26.60% 0.83% 0.41% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 61.10% 37.80% 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
vg0430619183 A -> DEL N N silent_mutation Average:89.057; most accessible tissue: Minghui63 young leaf, score: 97.03 N N N N
vg0430619183 A -> G LOC_Os04g51680.1 upstream_gene_variant ; 3008.0bp to feature; MODIFIER silent_mutation Average:89.057; most accessible tissue: Minghui63 young leaf, score: 97.03 N N N N
vg0430619183 A -> G LOC_Os04g51690.1 downstream_gene_variant ; 1977.0bp to feature; MODIFIER silent_mutation Average:89.057; most accessible tissue: Minghui63 young leaf, score: 97.03 N N N N
vg0430619183 A -> G LOC_Os04g51680-LOC_Os04g51690 intergenic_region ; MODIFIER silent_mutation Average:89.057; most accessible tissue: Minghui63 young leaf, score: 97.03 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)
vg0430619183 A G 0.01 -0.05 -0.04 0.01 -0.01 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430619183 4.02E-15 NA mr1745 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
vg0430619183 3.38E-07 2.13E-09 mr1745 Jap_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
vg0430619183 6.77E-07 NA mr1064_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
vg0430619183 NA 3.66E-07 mr1167_2 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
vg0430619183 1.18E-20 NA mr1745_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
vg0430619183 9.16E-10 2.66E-13 mr1745_2 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