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Detailed information for vg0316216814:

Variant ID: vg0316216814 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16216814
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCGCATGTCTGTGGAAATGCTTCGATGGGCCCGAGAGTGGTGTTAATGTTAAAACCCATCGCAGGTGAACATAGAGGCCCGTTGCCCCGTTACAATCC[T/C]
TGCCCAGCCCACACTGGCGTACAAATGTGGCTGGAGACCAGACCAATCCAGGCTGCCCGTGCCAAGTGAACTTAAAGAGCAGTACCAAAGGCTTGATTAG

Reverse complement sequence

CTAATCAAGCCTTTGGTACTGCTCTTTAAGTTCACTTGGCACGGGCAGCCTGGATTGGTCTGGTCTCCAGCCACATTTGTACGCCAGTGTGGGCTGGGCA[A/G]
GGATTGTAACGGGGCAACGGGCCTCTATGTTCACCTGCGATGGGTTTTAACATTAACACCACTCTCGGGCCCATCGAAGCATTTCCACAGACATGCGGAT

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 87.60% 11.00% 1.44% 0.00% NA
All Indica  2759 99.30% 0.60% 0.07% 0.00% NA
All Japonica  1512 68.10% 27.60% 4.37% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 62.30% 29.10% 8.60% 0.00% NA
Tropical Japonica  504 76.20% 23.80% 0.00% 0.00% NA
Japonica Intermediate  241 69.30% 30.70% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 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
vg0316216814 T -> C LOC_Os03g28175.1 upstream_gene_variant ; 947.0bp to feature; MODIFIER silent_mutation Average:84.981; most accessible tissue: Callus, score: 95.231 N N N N
vg0316216814 T -> C LOC_Os03g28170.1 downstream_gene_variant ; 1356.0bp to feature; MODIFIER silent_mutation Average:84.981; most accessible tissue: Callus, score: 95.231 N N N N
vg0316216814 T -> C LOC_Os03g28180.1 downstream_gene_variant ; 3521.0bp to feature; MODIFIER silent_mutation Average:84.981; most accessible tissue: Callus, score: 95.231 N N N N
vg0316216814 T -> C LOC_Os03g28170-LOC_Os03g28175 intergenic_region ; MODIFIER silent_mutation Average:84.981; most accessible tissue: Callus, score: 95.231 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)
vg0316216814 T C -0.06 -0.06 -0.03 -0.02 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316216814 NA 4.57E-06 mr1531 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