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Detailed information for vg0324409104:

Variant ID: vg0324409104 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24409104
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGTCGCAAAATTTAGTTGGAGATTAGGCTTTTGTTTTTTGGTTCTCCTCCTGTACCCTGTCCCCTTCGCTTTGTCTTTTTGGCCCGCTTTGTACGTA[C/T]
ATTTATTCCTTCTTAATACAAAGATGTGCTCCTTGCGTATTCCAAAAAAAAAATCAACAACGGAAAATCTAGAGTAAATCAGCAAACGCCGATACTAGCA

Reverse complement sequence

TGCTAGTATCGGCGTTTGCTGATTTACTCTAGATTTTCCGTTGTTGATTTTTTTTTTGGAATACGCAAGGAGCACATCTTTGTATTAAGAAGGAATAAAT[G/A]
TACGTACAAAGCGGGCCAAAAAGACAAAGCGAAGGGGACAGGGTACAGGAGGAGAACCAAAAAACAAAAGCCTAATCTCCAACTAAATTTTGCGACCCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.20% 41.60% 0.15% 0.00% NA
All Indica  2759 95.40% 4.40% 0.22% 0.00% NA
All Japonica  1512 0.70% 99.30% 0.00% 0.00% NA
Aus  269 26.00% 74.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.20% 0.67% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 98.70% 1.20% 0.11% 0.00% NA
Indica Intermediate  786 89.90% 9.90% 0.13% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 40.00% 58.90% 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
vg0324409104 C -> T LOC_Os03g43660.1 downstream_gene_variant ; 390.0bp to feature; MODIFIER silent_mutation Average:72.085; most accessible tissue: Zhenshan97 panicle, score: 91.536 N N N N
vg0324409104 C -> T LOC_Os03g43660-LOC_Os03g43670 intergenic_region ; MODIFIER silent_mutation Average:72.085; most accessible tissue: Zhenshan97 panicle, score: 91.536 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)
vg0324409104 C T -0.01 -0.01 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324409104 2.38E-06 NA mr1593 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
vg0324409104 NA 3.52E-11 mr1713 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
vg0324409104 NA 8.31E-79 mr1718 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