Table 1.

Summary Statistics and Characteristics of Cg Isolates

Isolate	Origin	Mapped Reads	%Used Reads	Read Depth	%Ns	SNPs	Genes
M.1001	Missouri, USA	Reference	—	—	9.21	—	12,006
i318	Nigeria	60,957,326	86.6	121×	9.83	9,170	12,004
i113173	Zimbabwe	58,434,572	69.8	120×	14.43	160,983	11,920
i47511	Michigan, USA	52,486,812	72.9	108×	13.9	141,118	11,929
iJAB2	Brazil	11,251,096	40.6	24×	25.24	155,561	11,900
i13649	Alabama, USA	46,081,744	89.7	93×	14.72	82,206	11,968
i63127	Germany	62,416,798	92.9	132×	19.79	115,695	11,925
i51134	Nagano, Japan	14,884,038	43.2	31×	19.53	139,134	11,952

Note.—Origin, region where the isolates were collected; mapped reads, the total number of effectively mapped reads from each isolate to the Cg M.1001 genome; %used reads, percentage of the number of sequenced reads effectively used for the assembly; read depth, the average per-base depth for each genome, taking into account only the unambiguous sites; SNPs, number of single nucleotide polymorphisms identified as compared with the Cg M.1001 reference genome; %Ns, for M.1001, the percentage of ambiguously called bases in the reference genome (non A, T, C, or G). For the sequenced isolates, the percentage of the genome with less than three reads coverage and therefore where SNPs were not called. Genes, number of M.1001 genes present in each isolate, considering a gene as “present” if the sequence contains more than 50% length with unambiguous bases.