. 2021 Mar 3;6(2):e01302-20. doi: 10.1128/mSphere.01302-20

TABLE 1.

Sequence data analysis of C. trachomatis gDNA from spiked serial dilutions of genotype D

Sample ID	ompA genotype	C_T ^a	Total no. of genome copies input	No. of:		Nonhuman read pair ratio	No. of:		% selected read pairs^b^,^c^,^d	Mean read depth^e	% of genome with coverage
Sample ID	ompA genotype	C_T ^a	Total no. of genome copies input	Raw read pairs	Nonhuman read pairs	Nonhuman read pair ratio	Total read pairs after QC^b^,^c	Selected read pairs^b^,^c^,^d	% selected read pairs^b^,^c^,^d	Mean read depth^e	≥5×	≥10×
D1	D	18.29	7,854,406	2,136,708	2,118,719	0.99	2,095,052	2,079,951	99.28	562.67	99.02	99.01
D2	D	22.01	942,398	1,482,054	1,382,594	0.93	1,335,421	1,318,461	98.73	359.60	99.02	99.01
D3	D	27.58	39,392	1,115,066	729,165	0.65	667,101	624,035	93.54	169.14	99.02	98.95
D4	D	29.055	16,945	1,117,188	277,491	0.25	237,908	155,934	65.54	42.22	98.69	97.66
D5	D	32.915	1,876	1,955,298	219,077	0.11	162,471	28,011	17.24	7.47	70.29	29.16
D6	D	36.345	265	1,509,294	189,690	0.13	159,750	2,132	1.33	0.57	0.73	0.006

C_T, cycle threshold based on C. trachomatis ompA RT-PCR (62). Cycle threshold is the cycle number at which the fluorescence generated within a reaction crosses the fluorescence threshold determined for the assay.

With a quality score of ≥15.

After quality control, i.e., deduplication and adapter trimming.

Selected for Chlamydia spp. and C. trachomatis read pairs.

With rRNA masked.