Table 1.

Sample ID, patient information, strain information and de novo assembly information.

Group	Strain/sample ID	Diagnose group	Sequence ID	Size (bp)2	Subtypec	Largest contig (bp)	N50 contig (bp)	M129 genome covered (%)d
1	M129	Reference	01	802,479	1	135,172	59,602	99.89
	FH	Reference	02	803,911	2	98,770	50,959	99.29
	R003	Reference	03	800,612	2	123,538	54,253	99.21
2	B174	Asymptomatic	11	805,944	1	135,177	53,512	99.83
	B247	Asymptomatic	12	801,799	1	96,961	66,934	99.63
	B406	Asymptomatic	14	804,626	2	98,962	51,557	99.06
3	A016	Upper RTI	04	800,489	2	123,550	54,265	99.18
	A058	Upper RTI	06	800,399	1	135,171	54,703	99.73
	C024	Upper RTI	15	809,160	1	135,170	59,355	99.85
	H030	Upper RTI	19	806,820	1	135,258	59,621	99.81
4	A035	Lower RTI	05	805,945	2	123,540	54,255	99.04
	A103	Lower RTI	07	821,841	1	92,532	45,886	99.73
	HAP111	Lower RTI	10	808,319	2	135,217	54,427	99.23
	HAP157	Lower RTI	09	800,436	1	92,731	51,728	99.73
	H010	Lower RTI	18	805,135	1	191,508	66,444	99.67
	H016	Lower RTI	20	805,824	1	135,161	59,300	99.77
	H026	Lower RTI	13	790,390	2	98,587	48,754	98.80
	C036-1a	Lower RTI	16	807,258	1	135,171	59,440	99.77
	C036-2a	Lower RTI	17	804,586	1	191,498	66,641	99.73
	HAP157FUP	Follow-up	08	802,814	1	191,496	66,615	99.75

^aMorphologically different M. pneumoniae colonies originating from the same patient sample. Both a large (C036-1) and a small colony (C036-2) were sequenced.

^bTotal assembly (bp). Contigs over 500 bp in length are considered in the assembly size.

^cSubtype 1 and 2 as described previously by Spuesens et al. (2013).

^dAll contigs, including contigs below 500 bp in length, were aligned to the M129 reference genome with MUMmer.