Table S1. Summary of assembly characteristics of 20 ESBL-negative CMY-2-positive E.coli isolates. N50 = largest scaffold length N, such that 50% of the assembled genome size is contained in scaffolds with a length of at least N. A species-specific minimum and maximum reference genome size were based upon the assembled genomes used by Kluytmans et al. to create species-specific wgMLST schemes. Isolate no Sequencer Number of Reads, n Number of Matched Reads, n Average Length of Reads (base count), n Average Length of Reads (base count), n Percentage reads matched, % N50 (base count), n Number of Scaffolds, n Maximum Scaffold Length (base count), n Total scaffolds base counts, n Average Coverage (mean depth), n Average Coverage Matched Reads, n Percentage of expected min ref genome size, % Percentage of expected max ref genome size, % ref ≥15,000 ≤1,000 ≥50,000 ≥20 ≥20 >90% <115% 1 HiSeq 2689989 2184501 97.63 98.23 81.21 92869 125 235223 5153917 50.96 41.64 113.05 98.32 2 HiSeq 3052370 2524911 94.85 95.71 82.72 169171 124 381463 5160328 56.10 46.83 113.19 98.44 3 HiSeq 2591258 2136036 95.95 96.56 82.43 188856 107 385860 4970841 50.02 41.49 109.03 94.83 4 MiSeq 1795657 1734949 151.45 153.90 96.62 74848 210 182193 5598647 48.57 47.69 122.81 106.80 5 HiSeq 2435466 1892845 97.17 97.53 77.72 43319 237 130321 5004132 47.29 36.89 109.77 95.46 6 MiSeq 2191597 2154474 210.21 212.20 98.31 257099 65 613545 5235212 88.00 87.33 114.83 99.87 7 MiSeq 1251167 1215241 140.71 141.04 97.13 86556 151 299258 4997853 35.23 34.29 109.63 95.34 8 MiSeq 1438343 1398268 168.84 170.24 97.21 82298 126 296509 4808959 50.50 49.50 105.48 91.74 9 MiSeq 1285931 1234773 114.97 117.77 96.02 36648 272 115045 5159584 28.65 28.18 113.17 98.43 10 HiSeq 3243522 2703474 96.07 96.64 83.35 142409 99 330072 4835565 64.44 54.03 106.07 92.25 11 MiSeq 750105 733057 232.06 234.93 97.73 265504 45 516628 4735908 36.76 36.36 103.88 90.35 12 HiSeq 3206359 2518175 95.48 96.23 78.54 60862 201 226117 5225597 58.59 46.37 114.62 99.69
RkJQdWJsaXNoZXIy MTk4NDMw