Ancestor D39 isolate
To obtain a deep sequence coverage of the ancestor D39 strain, DNA was paired-end sequenced on an Illumina NextSeq 500 system using 150-bp read lengths by vertis Biotechnologie AG, Germany. These are the reads processed using Trim Galore (v0.4.4) with Cutadapt (v1.9.1) for paired-end reads, using default settings.