Table 3 |
||||||
|
Percentage of undercovered microbial genome given 100× coverage |
||||||
|
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 |
|
|
|
||||||
|
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. |
||||||
|
Ross et al. Genome Biology 2013 14:R51 doi:10.1186/gb-2013-14-5-r51 |
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