Table 3 Statistical significance (p-values*) for generalized linear models in the association of assembly parameters (strategy, assembler, and sequencing depth) and a key metric of the 3 C criterion in the assessment of genome pan-assembly of four bacterial models.

From: Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness

Bacterial model

3 C metric

(response variable, Y)

Predictor (factors, Xi)

Strategy

Assembler

Depth for short-reads

Depth for long-reads

B. henselae

Contigs

5.72E-07

0.0007

0.3921

0.0090

N50

3.27E-05

0.0023

0.3786

0.0124

Mismatchs

1.09E-05

0.0144

0.1267

0.3386

Indels

2.95E-06

1.09E-05

0.1986

0.2241

CDS

2.79E-06

0.0591

0.8925

0.1900

BUSCO score

0.0011

2.12E-05

0.1749

0.3063

E. coli

Contigs

5.55E-06

0.0001

0.0729

0.0006

N50

4.59E-05

0.0008

0.0059

0.0003

Mismatchs

0.3936

0.0043

2.43E-06

0.1331

Indels

1.44E-07

4.14E-06

0.1184

0.0432

CDS

1.48E-09

0.0010

0.2439

0.0651

BUSCO score

3.00E-08

0.0081

0.0001

0.9368

P. aeruginosa

Contigs

1.92E-07

4.58E-05

0.0224

0.5472

N50

7.19E-08

0.0009

0.1138

0.4283

Mismatchs

2.36E-08

3.74E-06

0.3527

0.4355

Indels

1.33E-10

6.06E-07

0.2463

0.4424

CDS

2.13E-07

9.47E-05

0.2224

0.9103

BUSCO score

0.0004

3.79E-07

0.2384

0.2384

X. fastidiosa

Contigs

1.52E-08

4.15E-05

0.0318

0.0472

N50

2.14E-08

3.49E-06

0.0230

0.0069

Mismatchs

0.0424

7.59E-08

0.0002

0.1449

Indels

5.14E-07

1.31E-06

0.0004

0.3025

CDS

6.61E-08

0.0005

0.1496

0.4162

BUSCO score

5.09E-06

0.0026

5.26E-10

0.6539

  1. * Values with p < 0.01 (99% confidence) are presented with italics and bold font.
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