Table 2.
Coefficients (Coef.) of the generalized linear model (GLMs with quasi Poisson distribution and with overdispersion) comparing the parameters “identical alleles against circular reference genomes” (IAAR) with the parameters of interest “tested reference genomes” (REFERENCE), “successive platings” (PLATING) (B), “DNA extraction replicate” (DNA), “sequencing replicate” (SEQUENCING), read depth (DEPTH), read breadth (BREADTH), identified alleles against schema (IAAS) and cgMLST workflows (WORKFLOW) including BIGSdb (n = 420), INNUENDO (n = 336), GENPAT (n = 420), SeqSphere (n = 420), BioNumerics (n = 420) and MentaLiST (n = 420) applied to downsampled paired-end reads from 3 tested reference genomes of Listeria monocytogenes (i.e. ATCC19114, ATCC19115 and ATCCBAA679). Few parameters are not defined because of singularities
| Parameters | Coef. estimate | Coef. standard error | Coef. t value | Coef. P-value (>|t|) |
|---|---|---|---|---|
| WORKFLOW: MentaLiST | -1.9E-01 | 1.1E-02 | -1.7E+ 01 | 2.0E-16 |
| BREADTH | 5.6E-01 | 8.1E-02 | 6.9E+ 00 | 5.3E-12 |
| DEPTH | 8.1E-04 | 1.9E-04 | 4.3E+ 00 | 1.5E-05 |
| REFERENCE: ATCCBAA679 | −3.8E-02 | 1.1E-02 | −3.6E+ 00 | 3.5E-04 |
| SEQUENCING: NextSeq_B | −2.3E-02 | 7.0E-03 | −3.2E+ 00 | 1.3E-03 |
| REFERENCE: ATCC19115 | −3.0E-02 | 1.0E-02 | −3.0E+ 00 | 2.9E-03 |
| WORKFLOW: BioNumerics | −2.9E-02 | 1.2E-02 | −2.4E+ 00 | 1.7E-02 |
| PLATING: tenth_culture | −2.4E-02 | 1.1E-02 | −2.1E+ 00 | 3.3E-02 |
| WORKFLOW: INNUENDO | −2.0E-02 | 1.1E-02 | −1.8E+ 00 | 7.5E-02 |
| PLATING: fifth_culture | −1.8E-02 | 1.1E-02 | −1.6E+ 00 | 1.1E-01 |
| IAAS | 6.3E-04 | 5.1E-04 | 1.2E+ 00 | 2.2E-01 |
| DNA: extraction_A | −7.4E-03 | 8.4E-03 | −8.9E-01 | 3.7E-01 |
| DNA: extraction_B | −4.5E-03 | 8.3E-03 | −5.4E-01 | 5.9E-01 |
| WORKFLOW: GENPAT | 1.7E-04 | 1.1E-02 | 1.6E-02 | 9.9E-01 |
| WORKFLOW: SeqSphere | 4.5E-05 | 1.1E-02 | 4.3E-03 | 1.0E+ 00 |
| Model Intercept | −4.9E+ 01 | 8.1E+ 00 | − 6.1E+ 00 | 1.1E-09 |