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All replicate data sets were pooled after normalizing and before analysis with the exception of coverage analysis on specific genome loci (presented as box plots, Figure 4i & 4ii) where each replicate was analyzed and shown independently.
APHRC's communications team mostly tracks coverage of stories that directly relate to the institution's work (with the exception of coverage of research presented in its conferences or awards that are issued), yet the strategy goes beyond APHRC's staff and research work.
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It is found that, with the exception of the coverage variable, the results reported above reflect within-country rather than cross-country differences.
With the exception of training coverage, which is an administrative estimate, the other programme indicators are collected from surveys of households or health facilities.
Default parameters were used with the exception of minimum coverage for the germ-line sample that was set to 10, minimum variant frequency was changed to 0.01 and tumour purity was set to 0.5.
Conversely, the fraction of true variants among singly-called variants was significantly lower, and decreased with increasing coverage, both for SNPs (with the exception of very low coverage; <50 % above 30× coverage) and especially for indels (<15 % above 30× coverage).
Coverage of found genes was around 50%, with the exception of the low coverage for PGD.
Because the care for these conditions does not end with childhood, these exceptions and terminations of coverage are particularly disturbing.
In the channels defined as private, IMS coverage of outlets (i.e., number of outlets sampled divided by estimated total number of these outlets) ranged from 1 20%, with the exception of >80% coverage in South Africa and in one of the two relevant channels in Pakistan.
With the exception of Ghana where coverage of CHI is relatively high, enrolment levels have remained low in the rest of sub-Saharan African countries, thus raising concerns about sustainability of such schemes.
During the assembly step in dnaPipeTE, Trinity (version r20140717) was used with default parameters for single-end reads, with the exception of the minimum coverage to join k-mer contigs set to 1 to retain contigs from low copy repeats (Haas B, personal communication).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com