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Table 1 General and BUSCO benchmark statistics for homology grouping performed under setting D1 to D8

From: The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool

Clustering setting

Minimum sequence similarity

Homology groups

Single copy groups

Correct groups a

True Positives

False Positives

False Negatives

Recall

Precision

F-score

D1

95%

49,290

812

395

128,085

14

3905

0.9704

0.9999

0.9849

D2

85%

28,896

1615

629

131,795

24

195

0.9985

0.9998

0.9992

D3

75%

24,650

1690

638

131,952

35

38

0.9997

0.9997

0.9997

D4

65%

22,347

1699

640

131,975

38

15

0.9999

0.9997

0.9998

D5

55%

20,636

1683

639

131,975

44

15

0.9999

0.9997

0.9998

D6

45%

19,234

1653

633

131,985

245

5

0.9981

0.9981

0.9991

D7

35%

17,908

1612

623

131,985

508

5

0.9962

0.9962

0.9981

D8

25%

16,486

1486

607

131,986

7002

4

1.0000

0.9496

0.9741

  1. a Correct groups are defined as the number of groups that correctly organize one out of 670 ‘complete’ and ‘non-duplicated’ Enterobacteriaceae BUSCO genes. Calculations of recall, precision, and F-score explained in Methods