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Table 1 Simulation study results

From: PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples

 

PathoID 1.0

PathoID 2.0

Organism

Default

Default

ThetaPrior (Low)

ThetaPrior (High)

Bacteroides fragilis 638R

4.00%

3.99%

3.99%

3.99%

Bifidobacterium bifidum BGN4

4.00%

3.99%

3.99%

3.99%

Clostridium perfringens ATCC 13124

3.99%

3.99%

3.99%

3.99%

Enterococcus faecalis V583

3.98%

3.99%

3.99%

4.00%

Escherichia coli 042

17.15%

4.01%

4.10%

4.02%

Escherichia coli 55989

0.57%

0.50%

1.51%

3.83%

Escherichia coli SE11

0.28%

10.10%

7.07%

3.74%

Escherichia coli SE15

0.71%

3.43%

3.73%

3.82%

Escherichia coli UMNK88

1.29%

1.95%

3.59%

4.16%

Haemophilus influenzae 10810

3.98%

3.99%

3.99%

3.99%

Neisseria meningitidis MC58

3.25%

3.99%

3.99%

3.92%

Pseudomonas aeruginosa DK2

4.00%

3.99%

3.99%

3.99%

Staphylococcus epidermidis ATCC 12228

3.97%

3.98%

3.98%

3.98%

Streptococcus mitis B6

2.94%

3.82%

3.87%

3.94%

Streptococcus mutans UA159

3.58%

3.99%

3.99%

3.99%

Stapylococcus aureus HO 5096 0412

0.31%

1.76%

2.48%

3.80%

Stapylococcus aureus JKD6008

0.05%

15.82%

13.40%

3.79%

Stapylococcus aureus MRSA252

0.69%

1.46%

2.14%

3.85%

Stapylococcus aureus N315

0.00%

0.68%

1.46%

1.01%

Stapylococcus aureus Newman

0.15%

0.33%

0.56%

3.48%

Streptococcus pneumoniae 670-6B

0.92%

3.28%

12.87%

4.43%

Streptococcus pneumoniae ATCC 700669

0.29%

0.99%

2.10%

4.23%

Streptococcus pneumoniae G54

0.16%

0.44%

1.17%

3.35%

Streptococcus pneumoniae Hungary 19A-6

19.42%

14.75%

2.58%

4.33%

Streptococcus pneumoniae Taiwan1 9 F-14

0.00%

0.66%

1.34%

2.83%

  1. Comparison of PathoID 1.0 to 2.0 using simulated data (see the section titled ‘Simulation study to evaluate improvements in PathoID 2.0’ for details).