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Detailed information for vg0819489414:

Variant ID: vg0819489414 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19489414
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCAAATCATTTTAGGGATTTTTCATGTAATAGCAAATCATTTTAGGAAGAAGGAGATGAGTCCCCCGTTAAATCTTGTTCTGGATCCGCCCCCGTTAA[C/T]
ACGCTCACAATTTCATATATTATTTCATAACTAAGTTTTTCTTGTTTTTTTTAAGTGGTGGGGGTGGTAGATTTTTAGTGTCACCACCACCGTCGTTGCC

Reverse complement sequence

GGCAACGACGGTGGTGGTGACACTAAAAATCTACCACCCCCACCACTTAAAAAAAACAAGAAAAACTTAGTTATGAAATAATATATGAAATTGTGAGCGT[G/A]
TTAACGGGGGCGGATCCAGAACAAGATTTAACGGGGGACTCATCTCCTTCTTCCTAAAATGATTTGCTATTACATGAAAAATCCCTAAAATGATTTGATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.90% 8.10% 0.02% 0.00% NA
All Indica  2759 95.90% 4.10% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 20.10% 79.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 91.30% 8.70% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 42.70% 1.04% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0819489414 C -> T LOC_Os08g31510.1 downstream_gene_variant ; 656.0bp to feature; MODIFIER silent_mutation Average:79.96; most accessible tissue: Minghui63 flag leaf, score: 97.564 N N N N
vg0819489414 C -> T LOC_Os08g31520.1 downstream_gene_variant ; 2743.0bp to feature; MODIFIER silent_mutation Average:79.96; most accessible tissue: Minghui63 flag leaf, score: 97.564 N N N N
vg0819489414 C -> T LOC_Os08g31480-LOC_Os08g31510 intergenic_region ; MODIFIER silent_mutation Average:79.96; most accessible tissue: Minghui63 flag leaf, score: 97.564 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)
vg0819489414 C T -0.04 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819489414 NA 2.25E-06 mr1344_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
vg0819489414 3.58E-06 NA mr1835_2 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