TABLE 1.

Read and assembly statistics.

Strain IDs	Genome coverage (%)	Sequencing depth	# Mapped reads
3	99.03	523.604	308,387
12	99	377.339	216,691
18	98.78	272.294	175,050
57	98.81	1255.388	2,272,143
61	98.97	63.726	43,553
81	99.59	86.3	182,347
100A	98.68	848.073	1,460,162
196	98.2	22.6	143,725
240	99.59	86.3	70,185
274	98.88	240.667	180,375
285	98.31	129.085	116,342
298	98.67	219.616	212,198

The number of mapped reads for each genome was obtained using samtools flagstat and the genome assembly statistics were obtained using QUAST. The genome coverage was not affected by the number of reads or the sequencing depth. The genomes assembled from strains 81 and 196 had low sequencing depth and lower coverage in the genes surveyed in the study and were not used for further analysis. The strains 4 and 11 were identified to be N. meningitidis genomes from the ribosomal MLST analysis and were not analyzed further in the study (Supplementary Table 1).