Table 1 Mean and standard deviation of read depth of coverage estimated from BBMap (version February 13, 2020) or INNUca (version 4.2.2) with constant high read breadth of coverage (99.34 ± 0.07%) according to targeted read (Dr) and kmer (Dk) depth (X) from BBNorm downsampling (read length R = 150 and kmer size K = 30) of Listeria monocytogenes paired-end reads from tested reference genomes ATCC19114, ATCC19115 and ATCCBAA679 (n = 420)
From: In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes
Targeted depth of coverage | ATCC19114 | ATCC19115 | ATCCBAA679 | |||
|---|---|---|---|---|---|---|
BBMap | INNUca | BBMap | INNUca | BBMap | INNUca | |
Dr100-Dk75 | 101.6 ± 1.6 | 98.2 ± 1.5 | 101.9 ± 1.4 | 96.2 ± 1.8 | 101.0 ± 2.1 | 97.6 ± 2.6 |
Dr90-Dk68 | 91.9 ± 1.5 | 89.3 ± 1.7 | 92.3 ± 1.4 | 87.2 ± 2.3 | 92.0 ± 1.3 | 89.2 ± 2.1 |
Dr80-Dk60 | 80.9 ± 1.3 | 78.7 ± 1.8 | 81.3 ± 1.2 | 78.3 ± 1.7 | 81.4 ± 1.1 | 79.9 ± 2.2 |
Dr70-Dk53 | 71.4 ± 1.1 | 69.5 ± 2.0 | 71.7 ± 1.1 | 67.8 ± 1.6 | 72.0 ± 1.3 | 70.4 ± 1.7 |
Dr60-Dk45 | 60.5 ± 0.9 | 58.7 ± 2.0 | 60.7 ± 0.9 | 58.1 ± 1.5 | 61.1 ± 1.2 | 59.3 ± 2.2 |
Dr50-Dk38 | 50.9 ± 0.8 | 49.5 ± 1.2 | 51.1 ± 0.8 | 48.6 ± 1.6 | 51.5 ± 1.1 | 49.9 ± 2.0 |
Dr40-Dk31 | 41.3 ± 0.6 | 40.1 ± 1.0 | 41.5 ± 0.6 | 38.7 ± 1.3 | 41.9 ± 0.9 | 41.3 ± 1.7 |
Dr30-Dk23 | 30.7 ± 0.4 | 29.9 ± 1.6 | 30.8 ± 0.4 | 29.5 ± 1.1 | 31.1 ± 0.6 | 29.8 ± 1.1 |
Dr20-Dk16 | 21.5 ± 0.2 | 20.9 ± 0.9 | 21.5 ± 0.2 | 20.7 ± 0.9 | 21.7 ± 0.4 | 21.8 ± 0.8 |
Dr10-Dk8 | 10.9 ± 0.1 | 11.3 ± 0.1 | 10.9 ± 0.1 | 11.2 ± 0.1 | 11.0 ± 0.2 | 11.2 ± 0.2 |