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Detailed information for vg0204153194:

Variant ID: vg0204153194 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4153194
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


AATTCTTTTCCTATCATTAATTCATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCACAAAAGTTTTTAAATAAGACGAACGGTCAAA[C/T]
ATATGCTAAAAAGTCAACGGTGTCAAATATTTCGAAACGGAGGGAGTAGCTTGTGTGCTTAATGAAATTATGGACATACCTGAGCCGTTGGTTGGGGAGT

Reverse complement sequence

ACTCCCCAACCAACGGCTCAGGTATGTCCATAATTTCATTAAGCACACAAGCTACTCCCTCCGTTTCGAAATATTTGACACCGTTGACTTTTTAGCATAT[G/A]
TTTGACCGTTCGTCTTATTTAAAAACTTTTGTGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATGAATTAATGATAGGAAAAGAATT

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 78.90% 20.30% 0.74% 0.00% NA
All Indica  2759 73.80% 26.00% 0.25% 0.00% NA
All Japonica  1512 91.50% 6.70% 1.72% 0.00% NA
Aus  269 52.80% 46.80% 0.37% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 77.80% 21.90% 0.22% 0.00% NA
Indica III  913 59.50% 40.20% 0.33% 0.00% NA
Indica Intermediate  786 71.40% 28.20% 0.38% 0.00% NA
Temperate Japonica  767 97.40% 1.00% 1.56% 0.00% NA
Tropical Japonica  504 81.70% 16.10% 2.18% 0.00% NA
Japonica Intermediate  241 93.40% 5.40% 1.24% 0.00% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0204153194 C -> T LOC_Os02g07930.1 upstream_gene_variant ; 1950.0bp to feature; MODIFIER silent_mutation Average:87.081; most accessible tissue: Minghui63 root, score: 97.383 N N N N
vg0204153194 C -> T LOC_Os02g07940.1 upstream_gene_variant ; 3914.0bp to feature; MODIFIER silent_mutation Average:87.081; most accessible tissue: Minghui63 root, score: 97.383 N N N N
vg0204153194 C -> T LOC_Os02g07930-LOC_Os02g07940 intergenic_region ; MODIFIER silent_mutation Average:87.081; most accessible tissue: Minghui63 root, score: 97.383 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)
vg0204153194 C T -0.02 0.01 0.02 -0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204153194 NA 3.01E-06 mr1222_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
vg0204153194 NA 6.41E-06 mr1379_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
vg0204153194 1.98E-06 1.98E-06 mr1430_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
vg0204153194 NA 1.57E-06 mr1557_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
vg0204153194 NA 8.65E-06 mr1559_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