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Table 3 Percentage of undercovered microbial genome given 100× coverage

From: Characterizing and measuring bias in sequence data

Data set Relative coverage thresholds (% of genome)
Sample # Sequencing platform = 0 ≤0.1 ≤0.25 ≤0.5
P. falciparum 3D7 1 Illumina MiSeq 0.010 0.18 3.7 24
  2 Ion Torrent PGM 2.6 14 22 33
  3 Pacific Riosciences RS 0.012 0.13 0.33 2.7
  1+2 Illumina + Ion Torrent 0.0096 1.1 12 30
  2+3 Ion Torrent + Pac Bio 0.0062 0.097 1.6 17
  3+1 Pac Bio + Illumina 0.0051 0.040 0.33 7.9
E. coli K12 MG1655 4 Illumina MiSeq 0.00022 0.0019 0.019 0.54
  5 Ion Torrent PGM 0.00047 0.013 0.046 0.27
  6 Pacific Biosciences RS 0 0.00075 0.030 0.36
  4+5 Illumina + Ion Torrent 0 0.0012 0.0053 0.075
  5+6 Ion Torrent + Pac Bio 0 0.00037 0.0018 0.054
  6+4 Pac Bio + Illumina 0 0.00026 0.0012 0.061
R. sphaeroides 2.4.1 7 Illumina MiSeq 0.00094 0.045 0.39 2.7
  8 Ion Torrent PGM 0.88 19 36 47
  9 Pacific Biosciences RS 0.000048 0.0021 0.0071 0.067
  7+8 Illumina + Ion Torrent 0.0038 0.23 1.8 19
  8+9 Ion Torrent + Pac Bio 0.000024 0.00058 0.14 16
  9+7 Pac Bio + Illumina 0.00012 0.0018 0.017 0.49
  1. The percentage of each microbial genome left completely uncovered as well as ten-fold, four-fold, and two-fold undercovered given 100× (randomly downsampled) coverage of Illumina MiSeq, Ion Torrent PGM, and Pacific Biosciences RS data (data sets in italics; Table 2). Also included are the same statistics from data sets that combine 50× coverage from each pair of sequencing technologies.