Table 1.
Sequencing performance for all samples
| MCT6-NEB-UA | MCT6-NEB-WGA | MCT6-UT-UA | MCT6-UT-WGA | MCT6-20 ng | MCT6-5 ng | MCT4-NEB-UA | MCT4-NEB-WGA | MCT4-UT-UA | MCT4-UT-WGA | MCT4-20 ng | MCT4-5 ng | LP S1 | LP S2 | LP S3 | LP S4 | P1 | P2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mean coverage | 1.34 | 0.14 | 1 | 0.18 | 1.96 | 2.23 | 1.53 | 0.19 | 1.24 | 0.22 | 2.25 | 2.13 | 2.66 | 1.68 | 1.8 | 2.1 | 1.98 | 0.75 |
| Total reads (millions) | 62.4 | 16.4 | 48.5 | 17.9 | 90.2 | 104.9 | 72.1 | 19.2 | 59.3 | 19.9 | 101.7 | 101.9 | 119.9 | 81.3 | 88.3 | 96.1 | 88.4 | 40.3 |
| Mapped reads (millions) | 61.7 | 14.0 | 47.0 | 15.4 | 88.5 | 102.5 | 71.2 | 15.9 | 57.7 | 17.1 | 101.1 | 100.9 | 119.0 | 80.8 | 87.7 | 95.5 | 87.7 | 39.5 |
| Reads mapped (%) | 98.96 | 85.57 | 96.97 | 85.85 | 98.04 | 97.66 | 98.73 | 83.18 | 97.35 | 86.17 | 99.4 | 99.1 | 99.28 | 99.39 | 99.29 | 99.32 | 99.23 | 98.09 |
| Reads duplicates (%) | 4.89 | 35.67 | 5.73 | 26.73 | 4.13 | 5.74 | 5.14 | 28.8 | 5.73 | 20.65 | 4.54 | 8.28 | 5.14 | 7.26 | 10.56 | 5.38 | 4.18 | 12.66 |
| Total reads minus duplicates (millions) | 59.4 | 11.4 | 45.8 | 13.8 | 86.5 | 99.0 | 68.4 | 14.6 | 55.9 | 16.3 | 97.1 | 93.5 | 113.8 | 75.5 | 79.1 | 90.9 | 84.7 | 35.3 |
| Target bases (%) > = onefold coverage | 58.26 | 9.17 | 48.53 | 11.41 | 67.97 | 71.54 | 61.91 | 11.45 | 56.48 | 14.2 | 74.44 | 72.15 | 80.14 | 62.94 | 65.31 | 73.84 | 72.33 | 33.37 |
| Target bases (%) > = tenfold coverage | 0.14 | 0.01 | 0.07 | 0.01 | 0.48 | 0.78 | 0.19 | 0.01 | 0.11 | 0.02 | 0.6 | 0.52 | 0.83 | 0.26 | 0.3 | 0.31 | 0.25 | 0.06 |
| Median fragment length | 124 | 80 | 120 | 85 | 111 | 110 | 113 | 88 | 124 | 98 | 120 | 111 | 124 | 96 | 101 | 119 | 122 | 79 |
| Tissue age (years) | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 5 | 2 | 7 | 2 | 9 | 7 | 11 |
NEB treated with NEB repair kit, UT untreated, UA unamplified, MCT MCC samples, LP breast tumor samples, P pre-cancerous breast lesions