Blue numbers above each point show the number of sites that fall within the decile; purple numbers below each point show the maximum total read depth for that decile (minimum total read depth is the maximum depth for the previous decile, or 300 for the lowest decile).
Their performance is compared with the aid of metaheuristic profiling and statistical analysis of the minimum total measured depth (TMD) found in multiple sequential runs.
The minimum total measured depth (TMD) located by all studied algorithms is similar (except for ACO), but the computation times and number of iterations taken by each one are different.
SNPs were identified and counted by VarScan (Koboldt et al., 2009), filtered by minimum base quality (≥25) and minimum total read depth (≥8).
We also required a minimum total read depth at exonic heterozygous sites of 300 reads (which should provide high power to detect modest ASE: Fontanillas et al., 2010), resulting in a total set of 2280 genes tested for ASE.
SNVs were called using Varscan v2.2.2 (ref. 18) with a minimum total coverage of 5 reads and a minimum variant read depth of 3. The mitochondrial variants were annotated using Annovar v.21-Feb-2013 (ref. 19) and its mtDNA-specific database files (hg19_MT_GRCh37).
h1 + h2 is the total depth.
Total depth of the beam, mm.
The optimal objectives of Scenario 1 are Pareto Optimality of minimum total energy consumption and minimum total CO2 emission.
Depth refers to the total depth of a diamond from table to culet, as a percentage of its total diameter.
