Table 7 Quality control criteria of interest for all datasets. Depth of coverage is calculated as bases(MB)*1,000,000/total base pairs. Mean (minimum value; maximum value) reported.

From: Four European Salmonella Typhimurium datasets collected to develop WGS-based source attribution methods

Data N50 No. contigs Total base pairs of assembly Depth of coverage
DK human 274,445 (148,864; 490,821) 63 (35; 151) 4,932,862 (4,730,908; 5,217,740) 90 (46; 296)
DK food and animal 280,405 (151,473; 507,939) 60 (36; 184) 4,945,037 (4,769,818; 5,254,474) 104 (65; 154)
DE human 299,886 (188,812; 393,902) 61 (33; 326) 4,937,911 (4,682,559; 5,162,175) 103 (45; 276)
DE food and animal 137,544 (19,719*; 377,001) 112 (35; 466) 4,937,743 (4,730,293; 5,240,180) 79 (33; 173)
UK human 211,889 (53,936; 550,741) 69 (36; 170) 4,941,438 (4,723,064; 5,284,498) 74 (36; 178)
UK food and animal 267,335 (143,510; 464,171) 68 (31; 125) 5,037,113 (4,804,529; 8,982,655**) 83 (31; 215)
FR enviromental 263,923 (143,153; 356,020) 64 (42; 101) 4,939,325 (4,771,190; 5,090,477) 236 (56; 473)
FR animal 261,383 (143,153; 356,020) 64 (42; 89) 4,935,805 (4,810,678; 5,084,053) 215 (56; 431)
  1. *This sequence was included despite its relatively low N50 value because the number of contigs and total base pairs were acceptable.
  2. **This sequence was included despite its large size because the associated number of contigs and N50 value were acceptable and no contamination was observed from a kmer analysis using KmerFinder freely available from the Center for Genomic Epidemiology (www.genomicepidemiology.org).