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AS variants were categorized using the binary approach described by Nagasaki et al. [42].
The variants were categorized by their functional class and impact.
For each gene, variants were categorized into frequency bins as described above.
Abnormal paired-end reads were analyzed by clustering, and structural variants were categorized as insertions, tandem or dispersed duplications, deletions, and combinations of inversions and deletions.
For the qPCR analysis, cDNA harboring SMAD3 and SMAD4 variants were categorized as breast cancer cases with variants (BC-VAR) and controls with variants (CO-VAR).
Thirteen novel H3 variants were categorized into the H3.3 clade (Additional file 2: Figure S2B) and only H3 00036 was placed in the H3.1/H3.2 clade (Additional file 2: Figure S2C).
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Possibly they will result in a larger proportion of variants being categorized as uncertain significance.
After filtering common variants from a dataset, the remaining variants are categorized as rare (and consequently considered by many researchers as more likely to be causal for extremely rare phenotypes) [ 34].
The phylogenetic tree showed that the 14 novel mouse histone H3 variants are categorized into two well-delineated clades (H3.1/H3.2 clade and H3.3 clade) (Additional file 2: Figure S2A).
Therefore, it is preferable to carry out studies in a zebrafish strain in which the regions of invariant sequence are known with a high degree of confidence and all variants are categorized to allow for robust genomic mapping.
Each variant is categorized into one of the three groups.
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