PRJDB11994 SAMD00392805 Paired-end library WGS GENOMIC RANDOM TruSeq DNA PCR-Free Library Prep Kit: Paired-end libraries of ~800-bp insert size were prepared using the TruSeq DNA PCR-Free Library Prep kit (Illumina). Mate-pair libraries of ~8-kbp insert size were prepared using the Nextera Mate Pair Sample Preparation kit (Illumina) with gel-plus protocol according to the manufacturer's instruction. Each 300-bp of the libraries was sequenced on MiSeq with the MiSeq Reagent kit v3 (600 cycles; Illumina). Base-calling and demultiplexing of the reads were performed using Real-Time Analysis v1.18.54 and MiSeq Control Software v2.6.21. Correction of sequence errors based on a 17-mer frequency and removal of junction sequences of the mate-pair reads were performed using ShortReadManager v0.992, an accessary program of GenoFinisher v2.21 (Ohtsubo Y. et al. J Bacteriol 194:6970-1 (2012)). 300 0 Application Read Forward 1 1 Application Read Reverse 151 Illumina MiSeq PRJDB11994 SAMD00392805 Paired-end library WGS GENOMIC RANDOM Nextera Mate Pair Sample Preparation kit: Paired-end libraries of ~800-bp insert size were prepared using the TruSeq DNA PCR-Free Library Prep kit (Illumina). Mate-pair libraries of ~8-kbp insert size were prepared using the Nextera Mate Pair Sample Preparation kit (Illumina) with gel-plus protocol according to the manufacturer's instruction. Each 300-bp of the libraries was sequenced on MiSeq with the MiSeq Reagent kit v3 (600 cycles; Illumina). Base-calling and demultiplexing of the reads were performed using Real-Time Analysis v1.18.54 and MiSeq Control Software v2.6.21. Correction of sequence errors based on a 17-mer frequency and removal of junction sequences of the mate-pair reads were performed using ShortReadManager v0.992, an accessary program of GenoFinisher v2.21 (Ohtsubo Y. et al. J Bacteriol 194:6970-1 (2012)). 150 0 Application Read Forward 1 1 Application Read Reverse 76 Illumina MiSeq PRJDB11994 SAMD00392805 Mate-pair library WGS GENOMIC RANDOM Nextera Mate Pair Sample Preparation kit: Paired-end libraries of ~800-bp insert size were prepared using the TruSeq DNA PCR-Free Library Prep kit (Illumina). Mate-pair libraries of ~8-kbp insert size were prepared using the Nextera Mate Pair Sample Preparation kit (Illumina) with gel-plus protocol according to the manufacturer's instruction. Each 300-bp of the libraries was sequenced on MiSeq with the MiSeq Reagent kit v3 (600 cycles; Illumina). Base-calling and demultiplexing of the reads were performed using Real-Time Analysis v1.18.54 and MiSeq Control Software v2.6.21. Correction of sequence errors based on a 17-mer frequency and removal of junction sequences of the mate-pair reads were performed using ShortReadManager v0.992, an accessary program of GenoFinisher v2.21 (Ohtsubo Y. et al. J Bacteriol 194:6970-1 (2012)). 150 0 Application Read Forward 1 1 Application Read Reverse 76 Illumina MiSeq