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Detailed information for vg0311959727:

Variant ID: vg0311959727 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 11959727
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTTACTGCTTGGAGTGAAGGAAAAAAAAAATCCCGGGTGAGACGAAACGCGTGGTGTGGTGTGGGGTGCCTCGTGTCCATGGCGTGTGGGGTCCAGA[C/T]
CGGAGGAACGTTCTGGATGCTGGGCGTGATTACGTGATTACGGATGAGCTGTGTTGATTAGCGACGATCGGTTGGTTAAATGGAACCCATCTGTACCAAG

Reverse complement sequence

CTTGGTACAGATGGGTTCCATTTAACCAACCGATCGTCGCTAATCAACACAGCTCATCCGTAATCACGTAATCACGCCCAGCATCCAGAACGTTCCTCCG[G/A]
TCTGGACCCCACACGCCATGGACACGAGGCACCCCACACCACACCACGCGTTTCGTCTCACCCGGGATTTTTTTTTTCCTTCACTCCAAGCAGTAAATCA

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 99.20% 0.50% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 97.70% 1.70% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 93.50% 5.00% 1.59% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0311959727 C -> T LOC_Os03g21040.2 5_prime_UTR_variant ; 236.0bp to feature; MODIFIER silent_mutation Average:96.243; most accessible tissue: Zhenshan97 panicle, score: 99.772 N N N N
vg0311959727 C -> T LOC_Os03g21050.1 upstream_gene_variant ; 2786.0bp to feature; MODIFIER silent_mutation Average:96.243; most accessible tissue: Zhenshan97 panicle, score: 99.772 N N N N
vg0311959727 C -> T LOC_Os03g21040.3 upstream_gene_variant ; 162.0bp to feature; MODIFIER silent_mutation Average:96.243; most accessible tissue: Zhenshan97 panicle, score: 99.772 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)
vg0311959727 C T -0.04 -0.11 -0.1 -0.05 -0.02 -0.01