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Table 1 Sequencing performance for all samples

From: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

  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
  1. NEB treated with NEB repair kit, UT untreated, UA unamplified, MCT MCC samples, LP breast tumor samples, P pre-cancerous breast lesions