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Detailed information for vg1201304030:

Variant ID: vg1201304030 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 1304030
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGAGGGAGATGGCGTTGTGGTGACAACACCAACGATGGTGGATCTGCCTCCTCGCCCACCCATGTCTTAGCTTCCATTTTCCCGCACTATCAGAGCTC[G/A]
GGCCGTCTCCGCCGCTAGAGAGATAGAAAGATAGAGGTAGGAGAGACCCTTGCCTCATGCAACATTGCTGAACAAGGAGATGGCGGCGGCGGTAGCGACG

Reverse complement sequence

CGTCGCTACCGCCGCCGCCATCTCCTTGTTCAGCAATGTTGCATGAGGCAAGGGTCTCTCCTACCTCTATCTTTCTATCTCTCTAGCGGCGGAGACGGCC[C/T]
GAGCTCTGATAGTGCGGGAAAATGGAAGCTAAGACATGGGTGGGCGAGGAGGCAGATCCACCATCGTTGGTGTTGTCACCACAACGCCATCTCCCTCTTC

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 96.80% 2.50% 0.63% 0.00% NA
All Indica  2759 97.40% 2.40% 0.25% 0.00% NA
All Japonica  1512 95.10% 3.40% 1.52% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.67% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 94.20% 5.70% 0.11% 0.00% NA
Indica Intermediate  786 98.50% 1.40% 0.13% 0.00% NA
Temperate Japonica  767 90.90% 6.50% 2.61% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.40% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg1201304030 G -> A LOC_Os12g03340.1 upstream_gene_variant ; 3061.0bp to feature; MODIFIER silent_mutation Average:85.792; most accessible tissue: Zhenshan97 young leaf, score: 92.417 N N N N
vg1201304030 G -> A LOC_Os12g03350.1 upstream_gene_variant ; 742.0bp to feature; MODIFIER silent_mutation Average:85.792; most accessible tissue: Zhenshan97 young leaf, score: 92.417 N N N N
vg1201304030 G -> A LOC_Os12g03360.1 upstream_gene_variant ; 1109.0bp to feature; MODIFIER silent_mutation Average:85.792; most accessible tissue: Zhenshan97 young leaf, score: 92.417 N N N N
vg1201304030 G -> A LOC_Os12g03350-LOC_Os12g03360 intergenic_region ; MODIFIER silent_mutation Average:85.792; most accessible tissue: Zhenshan97 young leaf, score: 92.417 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)
vg1201304030 G A 0.02 0.01 0.01 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1201304030 7.75E-06 5.27E-07 mr1550 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
vg1201304030 1.22E-06 1.38E-10 mr1757 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
vg1201304030 NA 1.39E-07 mr1549_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
vg1201304030 NA 5.09E-07 mr1757_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