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Detailed information for vg0210369537:

Variant ID: vg0210369537 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10369537
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.26, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TATTATATCATCATTAGCCGATTGCTTTTTATATCATTATCTACATGGGACATATAGCCGATTGCTTAAATCCCATCGCTATCGGCTGGTATTGGTATCG[G/A]
CATCAGCTATTATCGGCTATCGGCTGGAACTACTCCATCGGCTTGTCAGCCGATCGGCTGTTTTGATCTACTATTTGCATATCTTGTCAGTTGCAGGATC

Reverse complement sequence

GATCCTGCAACTGACAAGATATGCAAATAGTAGATCAAAACAGCCGATCGGCTGACAAGCCGATGGAGTAGTTCCAGCCGATAGCCGATAATAGCTGATG[C/T]
CGATACCAATACCAGCCGATAGCGATGGGATTTAAGCAATCGGCTATATGTCCCATGTAGATAATGATATAAAAAGCAATCGGCTAATGATGATATAATA

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 78.70% 19.90% 1.40% 0.00% NA
All Indica  2759 74.60% 25.30% 0.11% 0.00% NA
All Japonica  1512 89.50% 6.70% 3.77% 0.00% NA
Aus  269 51.30% 47.20% 1.49% 0.00% NA
Indica I  595 86.60% 13.40% 0.00% 0.00% NA
Indica II  465 70.10% 29.70% 0.22% 0.00% NA
Indica III  913 68.70% 31.20% 0.11% 0.00% NA
Indica Intermediate  786 75.10% 24.80% 0.13% 0.00% NA
Temperate Japonica  767 83.80% 10.00% 6.13% 0.00% NA
Tropical Japonica  504 98.80% 0.40% 0.79% 0.00% NA
Japonica Intermediate  241 88.00% 9.50% 2.49% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 85.60% 12.20% 2.22% 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
vg0210369537 G -> A LOC_Os02g17910.1 upstream_gene_variant ; 1483.0bp to feature; MODIFIER silent_mutation Average:64.509; most accessible tissue: Minghui63 flag leaf, score: 83.412 N N N N
vg0210369537 G -> A LOC_Os02g17900.1 downstream_gene_variant ; 4001.0bp to feature; MODIFIER silent_mutation Average:64.509; most accessible tissue: Minghui63 flag leaf, score: 83.412 N N N N
vg0210369537 G -> A LOC_Os02g17900-LOC_Os02g17910 intergenic_region ; MODIFIER silent_mutation Average:64.509; most accessible tissue: Minghui63 flag leaf, score: 83.412 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)
vg0210369537 G A -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210369537 4.71E-06 4.71E-06 mr1317 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
vg0210369537 8.29E-07 8.29E-07 mr1897_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
vg0210369537 1.32E-06 1.32E-06 mr1914_2 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
vg0210369537 1.37E-07 1.37E-07 mr1927_2 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