Table 1.

The results of whole-genome sequencing for each sample

Strain ID	CLR susceptibility testing	Total reads (clean reads)	Mapping to genome reads	Covered length	Coverage (%)	Average depth	Total SNVs	Total InDels
S1	Ra	9,815,508	8,780,946	1,517,430	90.98	545.66	67,219	106
S2	S b	10,573,646	9,813,458	1,534,369	91.99	601.38	68,671	95
S3	S	10,269,810	9,529,590	1,527,013	91.55	565.38	70,135	101
S4	R	9,931,112	8,921,164	1,553,847	93.16	522.64	67,929	132
S5	R	9,965,800	8,012,304	1,522,585	91.29	459.11	67,580	134
S6	S	8,326,490	7,203,062	1,537,013	92.15	528.19	68,032	99
S7	S	8,023,030	7,541,380	1,536,514	92.12	549.71	68,496	112
S8	R	7,687,812	7,171,310	1,522,399	91.28	535.58	69,891	104
S9	S	11,190,968	9805694	1,522,469	91.28	731.93	68,658	67
S10	S	12,167,520	11,643,382	1,539,435	92.3	888.02	70,933	94
S11	R	9,756,502	8,630,028	1,517,874	91.01	532.33	67,285	112
S12	R	6,575,708	6,090,808	1,521,421	91.22	378.89	67,231	177

S2 and S3 (italic values) indicates the phenotype-susceptible strains with mutant in A2143G of 23S rRNA gene

^aR indicated the strain was resistant to clarithromycin

^bS indicated the strain was susceptible to clarithromycin