Table 3.
L. monocytogenes sequence data used for assessing the reproducibility by hqSNP analysis.
| Strain ID | Sequence Read Archive number | DNA extraction operator (DEO)a | Sequencing operator (SO)b | Sequencing laboratories (SL)c | Accession number for PacBio sequence used as referenced |
|---|---|---|---|---|---|
| PIR00542 | *SRR6347440 | DEO1 | SO1 | SL1 | CP025222 |
| SRR6347433 | DEO1 | SO2 | SL1 | ||
| SRR6347434 | DEO1 | SO3 | SL2 | ||
| SRR6347435 | DEO2 | SO1 | SL1 | ||
| SRR6347436 | DEO2 | SO2 | SL1 | ||
| SRR6347430 | DEO2 | SO3 | SL2 | ||
| PIR00544 | *SRR6347431 | DEO1 | SO1 | SL1 | CP025562, CP025563, CP025564, CP025565 |
| SRR6347459 | DEO1 | SO2 | SL1 | ||
| SRR6347458 | DEO1 | SO3 | SL2 | ||
| SRR6347457 | DEO2 | SO1 | SL1 | ||
| SRR6347456 | DEO2 | SO2 | SL1 | ||
| SRR6347463 | DEO2 | SO3 | SL2 | ||
| PIR00547 | *SRR6347462 | DEO1 | SO1 | SL1 | CP025219 |
| SRR6347461 | DEO1 | SO2 | SL1 | ||
| SRR6347460 | DEO1 | SO3 | SL2 | ||
| SRR6347455 | DEO2 | SO1 | SL1 | ||
| SRR6347454 | DEO2 | SO2 | SL1 | ||
| SRR6347526 | DEO2 | SO3 | SL2 |
a
Two different operators performed the DNA extractions (DEO1 and DEO2).
b
Three different sequencing operators (SO1, SO2, and SO3) sequenced the DNA at
c
two different sequencing laboratories (SL1 and SL2).
d
For each analysis two references were used and evaluated: de novo assembled Illumina reads of isolate (*) and PacBio contigs.