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We performed a CGH-like analysis obtaining the log-ratio between the normalised depth data from every affected individual and the control pool to confirm a homogenous distribution of the coverage along the candidate regions.
The mean log-ratio for the global data was −0.06 with a standard deviation of 0.55 (Table 2), showing a homogeneous distribution of the coverage between affected and control individuals.
The distribution of the coverage of protein coding regions was shown in Figure 4A.
Figure 2b shows distribution of the coverage for chromosome 20 (exemplary), which includes 39 767 SNP sites.
Figure 2C shows that the distribution of the coverage is smaller for test sample 1 compared to test sample 2 and NA06986 that was sampled down to a comparable mean coverage.
As the concentration of extracted DNA from purified schizonts in ChitongoZ2 strain was lowest, we suspect that the whole-genome amplification procedure for this strain caused biased amplification, resulting in an uneven distribution of the coverage; however, this did not affect SNPs detection.
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Despite the fact that The Gambia has reported consistently high national immunization coverage for many years, this study highlights room for improvement, both with overall immunization coverage in some parts of the country and the distribution of this coverage.
The distribution of the bin coverage sum obtained for all randomly chosen regions was used to define a threshold with p-value < 0.005.
The distribution of the mapping coverage percentage (MCP) and the mapped read depth (MRD) in bins of 0.5 Mbp over the entire length of the concatenated reference sequence is shown as heat maps in Figures 2A and 2B, respectively.
(C) Density distribution of the alignment coverage of curated uniprot, S. cerevisiae, and B. cinerea proteins matching proteins in the V1 and V2 T. minima predicted proteomes (BLASTP, e -value < 1e−6 ).
In order to retrieve the best fit to the distribution of the WSSD coverages, a maximum likelihood fit was done.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com