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A great deal of the studies [1, 5, 12, 17, 18, 37, 39, 41, 44, 46, 48] involve the application of structural techniques, which can be motivated by guidelines such as DO-178B [38], that requires minimum structural coverage assurances.
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And it has ceilings: treetops, structural coverage, or the sky.
In the sequence, section 'Structural coverage yielded by test sets across paradigms' brings novel results regarding objective (ii)—structural coverage of adapted test sets.
Beyond this, we measure the structural coverage that results from the applied test sets.
Currently, many of the considered proteins do not have a complete structural coverage of their sequences and the average structural coverage is 45 60%.
The resulting variant call format (VCF) file is then filtered for minimum coverage and minimum allele proportion.
VarScan parameters were as follows: minimum coverage, 1500; minimum supporting allele, 10; phred score, 30; variant frequency threshold, 0.1%.
Genomic variation was annotated using SnpEff (ver. 3.3; minimum coverage = 5X, minimum base quality = 20).
Single-base substitutions were detected based on minimum total coverage of 10 and minimum variant coverage of 3.
SNPs were only included for analysis with a minimum fragment coverage of 50 and minimum quality score of 20.
When conservation targets are satisfied with minimum cost in the minimum set coverage context, cost efficiency becomes maximised implicitly.
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