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Table 1 Streaming alignment statistics from nanopore data

From: Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Flowcell Time (m) Reads Bases Positions Missing bases Covered (%) True positive True negative False positive False negative Recall Precision Accuracy
Outbreak 60 920 5635627 7091 6463 8.86 10 617 0 2 0.83 1.00 0.09
Outbreak 120 2037 12853716 7091 4815 32.10 26 2237 7 7 0.79 0.79 0.32
Outbreak 180 3040 19297035 7091 3580 49.51 48 3436 13 15 0.76 0.79 0.49
Outbreak 240 3933 24900526 7091 2703 61.88 62 4291 17 19 0.77 0.78 0.61
Outbreak 300 4525 28614437 7091 2236 68.47 70 4736 25 25 0.74 0.74 0.68
Outbreak 360 5654 35848389 7091 1499 78.86 82 5454 26 31 0.73 0.76 0.78
Outbreak 420 6680 42498530 7091 1029 85.49 87 5914 25 37 0.70 0.78 0.85
Outbreak 480 7516 47950926 7091 749 89.44 94 6185 30 34 0.73 0.76 0.89
Outbreak 540 7913 50372188 7091 630 91.12 96 6300 29 37 0.72 0.77 0.90
Outbreak 600 8807 56254898 7091 463 93.47 103 6470 20 36 0.74 0.84 0.93
Outbreak 660 9666 61989423 7091 337 95.25 107 6588 22 38 0.74 0.83 0.94
Outbreak 720 10472 67171497 7091 267 96.23 111 6659 16 39 0.74 0.87 0.95
Outbreak 780 10833 69363106 7091 243 96.57 112 6686 16 35 0.76 0.88 0.96
Outbreak 840 11708 74625788 7091 191 97.31 117 6737 13 34 0.77 0.90 0.97
Outbreak 900 12479 79551399 7091 141 98.01 121 6780 16 34 0.78 0.88 0.97
Outbreak 960 13198 84228957 7091 120 98.31 124 6797 16 35 0.78 0.89 0.98
Outbreak 1020 13579 86600020 7091 107 98.49 125 6808 16 36 0.78 0.89 0.98
Outbreak 1080 14359 91437571 7091 90 98.73 126 6823 17 36 0.78 0.88 0.98
Outbreak 1140 15168 96646434 7091 74 98.96 124 6842 15 37 0.77 0.89 0.98
Outbreak 1200 15835 100970757 7091 70 99.01 123 6851 12 36 0.77 0.91 0.98
Outbreak 1260 16205 103367082 7091 63 99.11 124 6857 11 37 0.77 0.92 0.98
Outbreak 1320 16632 106040214 7091 60 99.15 125 6859 12 36 0.78 0.91 0.98
Outbreak 1380 17184 109618605 7091 56 99.21 125 6863 11 37 0.77 0.92 0.99
Outbreak 1440 17332 110500445 7091 55 99.22 124 6865 11 37 0.77 0.92 0.99
Non-outbreak 60 1268 5382184 7091 6372 10.14 1 717 2 0 1.00 0.33 0.10
Non-outbreak 120 2554 11567191 7091 4791 32.44 2 2284 15 0 1.00 0.12 0.32
Non-outbreak 180 3626 17058822 7091 3451 51.33 4 3607 29 1 0.80 0.12 0.51
Non-outbreak 240 4612 22004574 7091 2500 64.74 11 4545 32 4 0.73 0.26 0.64
Non-outbreak 300 5483 26582592 7091 1760 75.18 13 5281 35 3 0.81 0.27 0.75
Non-outbreak 360 6198 30340527 7091 1330 81.24 15 5705 40 2 0.88 0.27 0.81
Non-outbreak 420 6877 34040490 7091 985 86.11 16 6054 35 2 0.89 0.31 0.86
Non-outbreak 480 7522 37471113 7091 727 89.75 18 6306 37 4 0.82 0.33 0.89
Non-outbreak 540 8306 41387560 7091 552 92.22 18 6483 34 5 0.78 0.35 0.92
Non-outbreak 600 9032 45052523 7091 395 94.43 20 6643 28 6 0.77 0.42 0.94
Non-outbreak 660 9682 48325820 7091 304 95.71 20 6735 27 6 0.77 0.43 0.95
Non-outbreak 720 10262 51312827 7091 262 96.31 20 6783 21 6 0.77 0.49 0.96
Non-outbreak 780 10845 54417219 7091 202 97.15 21 6845 18 6 0.78 0.54 0.97
Non-outbreak 840 11346 57135819 7091 178 97.49 22 6870 16 6 0.79 0.58 0.97
Non-outbreak 900 11793 59514439 7091 145 97.96 23 6898 18 8 0.74 0.56 0.98
Non-outbreak 960 12192 61590631 7091 111 98.43 22 6932 19 8 0.73 0.54 0.98
Non-outbreak 1020 12571 63597395 7091 99 98.60 22 6944 19 8 0.73 0.54 0.98
Non-outbreak 1080 12926 65415215 7091 87 98.77 21 6959 18 7 0.75 0.54 0.98
Non-outbreak 1140 13263 67138579 7091 71 99.00 22 6976 15 8 0.73 0.59 0.99
Non-outbreak 1200 13594 68911549 7091 62 99.13 22 6985 15 8 0.73 0.59 0.99
Non-outbreak 1260 13881 70408443 7091 59 99.17 22 6992 11 8 0.73 0.67 0.99
Non-outbreak 1320 14186 72080944 7091 53 99.25 23 7001 8 7 0.77 0.74 0.99
Non-outbreak 1380 14471 73573256 7091 44 99.38 23 7008 10 7 0.77 0.70 0.99
Non-outbreak 1440 14683 74801565 7091 40 99.44 23 7012 10 7 0.77 0.70 0.99
  1. The columns show (from left to right): (1) the sample analysed; (2) the cumulative results at this time period (min); (3) the total number of two-direction reads; (4) the total number of nucleotide bases; (5) the total size of the alignment; (6) the number of bases in the alignment missing from the dataset; (7) the percentage of bases in the alignment that can be called; (8) the count of true positives; (9) the count of true negatives; (10) the count of false positives; (11) the count of false negatives; (12) the recall, that is, sensitivity, calculated as TP/(TP + FN); (13) the precision, calculated as TP/(TP + FP); (14) the accuracy, calculated as (TP + TN)/(P + N)