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Table 3 Effect of self-definition keywords on best match lineages for E. coli

From: DarkHorse: a method for genome-wide prediction of horizontal gene transfer

 

Self-definition keywords

 

K12

83333

316407

562

Escherichia

Escherichia

Shigella

Escherichia

Shigella

Salmonella

Enterobacteria

4,203

4,063

3,640

3,173

Other bacteria

34

96

346

632

Phage

1

14

55

80

Eukaryotes

0

6

12

18

Archaea

0

0

2

3

Total matches

4,243

4,179

4,055

3,906

LPImax

0.993

0.984

0.950

0.918

LPImax matches

4,110

3,855

3,220

2,570

LPImax lineage

Bacteria;

Proteobacteria;

Gamma-proteobacteria;

Enterobacteriales;

Enterobacteriaceae;

Escherichia

Bacteria;

Proteobacteria;

Gamma-proteobacteria;

Enterobacteriales;

Enterobacteriaceae;

Shigella

Bacteria;

Proteobacteria;

Gamma-proteobacteria;

Enterobacteriales;

Enterobacteriaceae;

Salmonella

Bacteria;

Proteobacteria;

Gamma-proteobacteria;

Enterobacteriales;

Enterobacteriaceae;

Yersinia

  1. Filter threshold setting was 10%.