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Furthermore, because the present algorithm is derived from a physiological model of HVS, the meanings of tone mapping parameters are clear as in Section 2.3.
Hence, if the mapping parameters are too stringent some of the reads may not be mapped.
Alternatively, the link between error rates and sequencing coverage could also be an effect of imperfect mapping of reads with sequencing errors if mapping parameters are stringently set.
Such enrichment means that when only unique mapping parameters are considered, the X chromosome would be more likely to have reads excluded as compared to autosomes, skewing the estimates of RXE downward.
Our mapping parameters are selected to report only those reads with a mapping quality (MAPQ) score of 40 from the Sequence Alignment/Map (SAM) file, a value which signifies that the read was mapped uniquely.
Sequencing counts and mapping parameters are summarized in Table 1.> -wrap-foot> *B and D refer to C57BL/6J and DBA/2J strains that differ at 1,834,754 SNPs in 17,002 genes.
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For the first analyzed short read library (accession SRX759525), mapping parameters were set to a local alignment ("--very-fast-local") with multi-mapping allowed (value k = 10).
The choice of the exact mapping parameters is highly dependent on the polymorphism pattern and levels in the target organism.
Advice on mapping parameters is included in the documentation.
Mapping parameters were adjusted to map a maximum number of reads to the reference bacterial genomes.
High stringency mapping parameters were used, which allowed for a maximum of 2 mismatches.
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