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Detailed information for vg0524151064:

Variant ID: vg0524151064 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 24151064
Reference Allele: CAAlternative Allele: C
Primary Allele: CSecondary Allele: CA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGATCGGGCCAACGAATAGGCCCAAACAATCCTGTGTCCCACGATTTTCCGACCGATGGATTTGCTCCGAGATTCACGCCAAAAACCACGCGAGTCAAA[CA/C]
AAAAACTCAAAAAACTCTTTCGTCTTCCTCCTCGCGACTCCTCGCGCTCACCGCCATTGACGGCCACCTTTACCTCGGAAAAGGATTTGATCCCCGCTAA

Reverse complement sequence

TTAGCGGGGATCAAATCCTTTTCCGAGGTAAAGGTGGCCGTCAATGGCGGTGAGCGCGAGGAGTCGCGAGGAGGAAGACGAAAGAGTTTTTTGAGTTTTT[TG/G]
TTTGACTCGCGTGGTTTTTGGCGTGAATCTCGGAGCAAATCCATCGGTCGGAAAATCGTGGGACACAGGATTGTTTGGGCCTATTCGTTGGCCCGATCCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.20% 49.40% 0.36% 0.00% NA
All Indica  2759 73.10% 26.30% 0.62% 0.00% NA
All Japonica  1512 0.70% 99.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 80.80% 19.20% 0.00% 0.00% NA
Indica II  465 68.00% 31.20% 0.86% 0.00% NA
Indica III  913 70.80% 28.60% 0.66% 0.00% NA
Indica Intermediate  786 72.90% 26.20% 0.89% 0.00% NA
Temperate Japonica  767 0.00% 100.00% 0.00% 0.00% NA
Tropical Japonica  504 2.00% 98.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0524151064 CA -> C LOC_Os05g41240.1 downstream_gene_variant ; 2668.0bp to feature; MODIFIER silent_mutation Average:94.08; most accessible tissue: Callus, score: 98.48 N N N N
vg0524151064 CA -> C LOC_Os05g41240.3 downstream_gene_variant ; 2668.0bp to feature; MODIFIER silent_mutation Average:94.08; most accessible tissue: Callus, score: 98.48 N N N N
vg0524151064 CA -> C LOC_Os05g41240.2 downstream_gene_variant ; 2668.0bp to feature; MODIFIER silent_mutation Average:94.08; most accessible tissue: Callus, score: 98.48 N N N N
vg0524151064 CA -> C LOC_Os05g41230.1 intron_variant ; MODIFIER silent_mutation Average:94.08; most accessible tissue: Callus, score: 98.48 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)
vg0524151064 CA C -0.22 -0.27 -0.29 -0.14 -0.22 -0.24