Table 3 The pangenome composition of ST131 clades and subclades showed stable core, soft core and shell genomes with open pangenomes (alpha).

From: An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

Clades

All

A

B

C

C1_6

C2_4

C2_9

#isolates

4,071

414

433

3,200

1,113

384

1,651

alpha

0.823

0.807

0.762

0.806

0.755

0.696

0.822

Average alpha

0.812

0.780

0.796

0.766

0.749

0.754

0.799

Total genes

26,479

12,163

16,323

21,304

16,490

10,322

15,485

Core genes

3,712

3,798

3,771

3,916

3,843

4,109

4,019

Soft core genes

242

292

281

334

424

380

354

Shell genes

1,018

764

1,437

731

571

642

566

Cloud genes

21,507

7,309

10,834

16,323

11,652

5,191

10,546

  1. The average alpha was determined for sample sizes from 30 to the maximum per group (see Fig. 6): for all ST131 this was 0.812 ± 0.024 (mean ± standard deviation); for A 0.780 ± 0.045; B 0.796 ± 0.046; C 0.766 ± 0.031; C1_6 0.749 ± 0.017; C2_4 0.754 ± 0.077; and C2_9 0.799 ± 0.038. The groups’ cloud gene rates correlated with sample size following a power law model. B0 (n = 13) was included with B. Eight C1_10 and 16 C2_6/C2_10 isolates not assigned to clear Fastbaps clusters were not examined.
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