title: Minimal Glycolysis  ancestor S. cerevisiae CEN.PK102-12A
design: High quality genomic DNA of the strains CEN.PK102-12A and IMX372 (MG) was obtained using the Qiagen 100/G kit (Qiagen, Hilden, Germany) following manufacturer’s recommendations. Libraries of 300-bp insert were constructed and paired end sequenced (100 base pair reads) using an illlumina HISeq 2500 sequencer (Baseclear BV, Leiden, The Netherlands). A minimum data quantity of 950 Mb was generated, representing a minimum 80-fold coverage. The sequence reads were mapped onto CEN.PK113-7D genome using Burrows–Wheeler Alignment tool (BWA) and further processed using SAMtools. Single-nucleotide variations were extracted from the mapping 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 quality of at least 20 were kept (variant quality is defined as the Phred-scaled probability that the mutation call is incorrect, iii) mutations with a. depth of coverage below 10X were discarded and iv) the mutations found in CEN.PK102-12A were subtracted from the list sequence. Eventually, the single nucleotide variations were physically positioned and functionally annotated according to the CEN.PK113-7D sequence annotation.