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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