Table 1 Description of clinical isolates used in the study and basic statistics of the sequencing data

Isolation sites

CSF^a

CSF^a

FNAC^b

FNAC^b

Lymph node from biopsy

Total reads

3611330*2

3045593*2

13609758*2

7100266*2

3072728*2

Average read length

72

72

72

72

72

Total reads aligned after filtering

5572900

4656246

21378146

11116118

4672838

Total reference length

4411532

4411532

4411532

4411532

4411532

% Total reference covered

88.42

91.51

90.17

81.87

86.36

% Reads aligned with reference

96.32

83.78

95.81

94.82

96.72

Optimized average read depth

72.97

53.03

287.71

148.08

60.41