Table 1.
Sequencing read statistics by sequencing modality and bacterial species. Note for R.9.4/Kit10 four isolates were plexed and the total data output is a composite of the individual outputs; for the R10.3/Kit12 and R10.4/Kit12 evaluations each isolate extract was initially run separately. The same flowcell was washed and then re-used for the R10.4 evaluation for the S. aureus and then P. aeruginosa isolates. Finally, the four DNA extracts were also multiplexed on a single R10.4/Kit12 run
|
Species |
Sequencing modality/sub-group |
Total reads |
Total bases |
N50 |
Percentage of reads with a phred score of ≥20 |
|---|---|---|---|---|---|
|
Illumina |
3, 801,912 |
574,088,712 |
151 |
97.93 |
|
|
R9.4 (multiplexed run) |
353,317 |
2,364,469,570 |
11,705 |
67.1 |
|
|
R9.4 (multiplexed run; sup called) |
339, 077 |
2,242,222,750 |
11,535 |
70.03 |
|
|
R10.3 (single extract/run) |
1, 073,327 |
5,964,466,078 |
9,852 |
79.05 |
|
|
R10.3 (single extract/run; sup called) |
1, 072, 758 |
5,936,766,616 |
9,827 |
73.5 |
|
|
R10.4 (single extract/run; overall) |
1, 174, 227 |
6,124,985,330 |
10,507 |
66.2 |
|
|
R10.4 (single extract/run; sup called) |
1, 167, 782 |
6,131,556,595 |
10,562 |
79.09 |
|
|
R10.4 (single extract/run; sup called and duplex reads) |
52, 171 |
229, 801,689 |
7,274 |
98.21 |
|
|
R10.4 (multiplexed run) |
286, 239 |
671,853, 044 |
5,327 |
72.62 |
|
|
R10.4 (multiplexed run; sup called and duplex reads |
6,447 |
10, 999, 797 |
3,403 |
98.06 |
|
|
Illumina |
3,202,356 |
483,555,756 |
151 |
97.45 |
|
|
R9.4 (multiplexed run) |
377, 192 |
3,646,791,131 |
17,396 |
65.23 |
|
|
R9.4 (multiplexed run; sup called) |
361,657 |
3,458,646,526 |
17,157 |
68.59 |
|
|
R10.3 (single extract/run) |
789,562 |
7,772,922,913 |
19,228 |
77.29 |
|
|
R10.3 (single extract/run; sup called) |
774,119 |
765,899,2847 |
19,124 |
70.24 |
|
|
R10.4 (single extract/run; overall) |
869,853 |
7,481,444,246 |
18,612 |
65.83 |
|
|
R10.4 (single extract/run; sup called) |
865,400 |
7,495,921,601 |
18,697 |
79.79 |
|
|
R10.4 (single extract/run; sup called and duplex reads) |
54, 177 |
452,672,411 |
16,484 |
98.62 |
|
|
R10.4 (multiplexed run) |
224,555 |
1,667,146,081 |
15, 525 |
72.1 |
|
|
R10.4 (multiplexed run; sup called and duplex reads |
12,114 |
95,832,563 |
15,245 |
98.82 |
|
|
Illumina |
5,299, 866 |
800,279,766 |
151 |
97.25 |
|
|
R9.4 (multiplexed run) |
361,977 |
4,302,642,519 |
21, 597 |
66.49 |
|
|
R9.4 (multiplexed run; sup called) |
351,155 |
4,138,688,286 |
21,342 |
71.55 |
|
|
R10.3 (single extract/run) |
1,024,134 |
8,524,041,501 |
17,666 |
81.81 |
|
|
R10.3 (single extract/run; sup called) |
1,017,748 |
8,528,041,241 |
17, 683 |
76.05 |
|
|
R10.4 (single extract/run; overall) |
556,000 |
5,851,279,980 |
24,126 |
67.35 |
|
|
R10.4 (single extract/run; sup called) |
638,801 |
6,378,501,910 |
23,860 |
82.24 |
|
|
R10.4 (single extract/run; sup called and duplex reads) |
22,859 |
261,812,617 |
21, 432 |
98.58 |
|
|
R10.4 (multiplexed run) |
208,693 |
1,412,016,443 |
14,627 |
73.91 |
|
|
R10.4 (multiplexed run; sup called and duplex reads |
12,468 |
93,018,395 |
14, 095 |
98.83 |
|
|
Illumina |
9,033, 160 |
1,364,007,160 |
151 |
98.98 |
|
|
R9.4 (multiplexed run) |
40, 194 |
725,665, 757 |
33, 599 |
72.67 |
|
|
R9.4 (multiplexed run; sup called) |
39, 155 |
699,249,807 |
33,066 |
75.51 |
|
|
R10.3 (single extract/run) |
1,625,258 |
9,724,520,340 |
14, 338 |
82.06 |
|
|
R10.3 (single extract/run; sup called) |
1, 645,001 |
9,819,093,990 |
14,337 |
78.84 |
|
|
R10.4 (single extract/run; overall) |
950,361 |
7,371,346,901 |
23, 339 |
74.06 |
|
|
R10.4 (single extract/run; sup called) |
945,421 |
7,382,123,466 |
23,446 |
84.24 |
|
|
R10.4 (single extract/run; sup called and duplex reads) |
47, 087 |
334, 258,567 |
16,366 |
98.8 |
|
|
R10.4 (multiplexed run) |
80, 512 |
287, 957,484 |
14, 301 |
80.04 |
|
|
R10.4 (multiplexed run; sup called and duplex reads |
3,753 |
12, 755, 562 |
10,232 |
99.08 |