Orth_POR2
Sequencing was carried out using the Nextera XT kit (Illumina), followed by a single-end 150 cycle, high-output sequencing on the NextSeq (Illumina) at the Tufts core facility (www.tucf.com). The resulting 39-56 million reads, with a coverage of >1100, were used for a de novo genome assembly on the POR2 reads using CLC Genomics Workbench software (v11) (Qiagen). This yielded 95 contigs greater than 300 bp in size, for a total genome size of 5,083,670 bp. The reads from the VopC deletion and complemented strain were then mapped to the POR2 contigs. The mapping files were then put through the Basic Variant Detection algorithm in CLC Genomics Workbench.