Table 1.
Genome properties. Reads were either mapped to the Cryptosporidium parvum IowaII reference genome or assembled de novo using Spades
| Total sequence (Mbp) | Read length (bp) |
Mapped reads (%) | Fraction of genome covered (%) | Sequencing coverage (X-fold +/− SD) |
De Novo Genome Assembly Statistics | MDA statistics | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Size (% of reference) | Longest contig (bp) | NG50 | Ct (h)a | Effic-iencyb | Yield (AU)c | ||||||
| Cell 1 | 920 | 2 × 300 | 99.8 % | 94.7 % | 90.3 ± 157 | 91.8 % | 225 980 | 57 459 | 2.3 | 70 | 0.85 |
| Cell 2 | 1366 | 2 × 300 | 99.9 % | 93.8 % | 127 ± 225 | 90.7 % | 227 055 | 64 805 | 3.0 | 65 | 0.74 |
| Cell 3 | 2013 | 2 × 300 | 99.8 % | 87.8 % | 169 ± 540 | 80.6 % | 147 412 | 20 114 | 3.0 | 123 | 1.69 |
| Cell 4 | 341 | 2 × 300 | 99.6 % | 69.4 % | 30.6 ± 79.4 | 60.0 % | 67 943 | 1 513 | 2.8 | 99 | 0.69 |
| Cell 5 | 1218 | 2 × 300 | 99.8 % | 74.9 % | 105 ± 307 | 66.3 % | 119 204 | 4 309 | 3.3 | 91 | 0.56 |
| Cell 6 | 1460 | 2 × 300 | 99.9 % | 68.4 % | 111 ± 509 | 57.1 % | 73 330 | 1 398 | 2.3 | 97 | 2.17 |
| Cell 7 | 1470 | 2 × 300 | 99.8 % | 78.8 % | 90.3 ± 304 | 67.6 % | 203 151 | 5 364 | 2.8 | 102 | 0.60 |
| Cell 8 | 1460 | 2 × 300 | 99.8 % | 85.5 % | 112 ± 284 | 77.5 % | 117 185 | 11 229 | 2.3 | 192 | 1.52 |
| Cell 9 | 1360 | 2 × 300 | 99.8 % | 94.9 % | 118 ± 194 | 91.6 % | 547 655 | 65 774 | 3.3 | 44 | 0.50 |
| Cell 10 | 1877 | 2 × 300 | 99.8 % | 66.9 % | 115 ± 767 | 49.6 % | 57 954 | 687 | 3.5 | 72 | 0.60 |
| Meta-genome | 6273 | 2 × 250 | 84.2 % | 97.8 % | 535 ± 829 | 94.4 % | 95 102 | 7 076 | N.A. | N.A. | N.A. |
aThe number of hours to reach above the background fluorescence threshold
bThe exponential amplification of DNA in the exponential amplification phase where a value of 100 % represents a doubling in DNA concentration every 15 min
cThe total DNA fluorescence (arbitrary fluorescence units) at the end of the 16 h MD