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Detailed information for vg0433207898:

Variant ID: vg0433207898 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33207898
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.81, C: 0.20, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GGATGAATTGCCACGTAAGCACCACGTCAATGCCACGTCAGATGAAGACCGAGTCAAATTAGCCACGTAGGCATCACATCATCCAAAACCGCCCTCAAAA[T/C]
CGCCGAGGGACTTAATCTGCACCGGTTTTGATAGTTGAAAGACCTGTTGTGTCTGGTTTTCTGGTTGAGGGACGAAAATCGAATTCGTTGACAAGTTAAG

Reverse complement sequence

CTTAACTTGTCAACGAATTCGATTTTCGTCCCTCAACCAGAAAACCAGACACAACAGGTCTTTCAACTATCAAAACCGGTGCAGATTAAGTCCCTCGGCG[A/G]
TTTTGAGGGCGGTTTTGGATGATGTGATGCCTACGTGGCTAATTTGACTCGGTCTTCATCTGACGTGGCATTGACGTGGTGCTTACGTGGCAATTCATCC

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 42.10% 13.00% 6.83% 38.13% NA
All Indica  2759 30.00% 2.20% 8.23% 59.48% NA
All Japonica  1512 69.00% 25.50% 2.45% 3.11% NA
Aus  269 19.30% 50.90% 8.18% 21.56% NA
Indica I  595 17.50% 0.50% 3.36% 78.66% NA
Indica II  465 22.60% 1.10% 3.87% 72.47% NA
Indica III  913 43.00% 3.90% 14.46% 38.55% NA
Indica Intermediate  786 28.90% 2.30% 7.25% 61.58% NA
Temperate Japonica  767 84.90% 11.30% 1.17% 2.61% NA
Tropical Japonica  504 51.60% 42.90% 1.59% 3.97% NA
Japonica Intermediate  241 54.80% 34.00% 8.30% 2.90% NA
VI/Aromatic  96 20.80% 14.60% 30.21% 34.38% NA
Intermediate  90 48.90% 16.70% 8.89% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0433207898 T -> C LOC_Os04g55770.1 upstream_gene_variant ; 3077.0bp to feature; MODIFIER silent_mutation Average:72.557; most accessible tissue: Minghui63 panicle, score: 94.477 N N N N
vg0433207898 T -> C LOC_Os04g55780.1 downstream_gene_variant ; 235.0bp to feature; MODIFIER silent_mutation Average:72.557; most accessible tissue: Minghui63 panicle, score: 94.477 N N N N
vg0433207898 T -> C LOC_Os04g55790.1 downstream_gene_variant ; 3472.0bp to feature; MODIFIER silent_mutation Average:72.557; most accessible tissue: Minghui63 panicle, score: 94.477 N N N N
vg0433207898 T -> C LOC_Os04g55780-LOC_Os04g55790 intergenic_region ; MODIFIER silent_mutation Average:72.557; most accessible tissue: Minghui63 panicle, score: 94.477 N N N N
vg0433207898 T -> DEL N N silent_mutation Average:72.557; most accessible tissue: Minghui63 panicle, score: 94.477 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)
vg0433207898 T C -0.02 -0.04 -0.04 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433207898 2.63E-07 2.63E-07 mr1361 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
vg0433207898 NA 2.84E-06 mr1708 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
vg0433207898 NA 9.76E-06 mr1800_2 Ind_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