title: IMX605 (endogenous SinLoG on chromosome V)
design: High quality genomic DNA of the strains of the strains IMX589, IMX605, IMX637, IMX645 was obtained using the Qiagen 100/G kit (Qiagen, Hilden, Germany) following manufacturer’s recommendations. Libraries of 300-bp inserts were constructed and paired-end sequenced (101 base pair reads) using an Illlumina HISeq 2500 sequencer (Baseclear BV, Leiden, The Netherlands). A minimum data quantity of 1GB was generated for each strain, representing a minimum 83-fold average coverage. Sequence reads of each strain were mapped onto the CEN.PK113-7D genome using the Burrows–Wheeler Alignment tool (BWA) and further processed using SAMtools. Single-nucleotide variations were determined using SAMtools’ varFilter. Default settings were used, except that the maximum read depth was set to 400X (-D400). To minimize false positive mutation calls, custom Perl scripts were used for further mutation filtering: i) mutation calls containing ambiguous bases in mapping consensus were filtered out, ii) only the single-nucleotide variations with a variant quality, defined as the Phred-scaled probability that the mutation call is incorrect, of at least 20 were kept and iii) mutations with a depth of coverage < 10X were discarded. Eventually, the single-nucleotide variations were positioned by their genomic locations, coding effects were predicted and functionally annotated according to the CEN.PK113-7D sequence annotation.