Table 2.
Comparison of 15 MiSeq run metrics according to the 5 MiSeq instruments
| MiSeq instrument (n=) | |||||
|---|---|---|---|---|---|
| A (n = 136) | B (n = 125) | C (n = 67) | D (n = 51) | E (n = 107) | |
| Cluster density | 929.1 ± 31.7 | 886.8 ± 35.8 | 1,032.1 ± 37.1a, b | 1,048.3 ± 43.5 a, b | 828.5 ± 32.5 a, c, d |
| Clusters PF | 86.9% ± 0.8% | 82.1% ± 1.6% a | 90.2% ± 1.2% a, b | 84.4% ± 1.3%c | 86.5% ± 0.8%b, c |
| %≥Q30 (Overall) | 81.6% ± 0.6% | 73.8% ± 1.1% a | 78.9% ± 1.4%b | 76.4% ± 1.7%a | 78.5% ± 0.7%a, b |
| %≥Q30 (R1) | 88.1% ± 0.4% | 82.7% ± 1.0%a | 85.2% ± 1.4%a | 82.0% ± 1.8% a | 85.6% ± 0.6%a, b |
| %≥Q30 (IR1) | 93.8% ± 0.6% | 88.2% ± 1.7% a | 94.7% ± 1.2% b | 93.5% ± 1.2%b | 90.1% ± 1.0%a, c, d |
| %≥Q30 (IR2) | 90.5% ± 0.8% | 82.5% ± 1.8% a | 92.1% ± 1.1% b | 89.1% ± 1.5%b | 82.9% ± 1.2%a, c, d |
| %≥Q30 (R2) | 75.7% ± 0.6% | 64.1% ± 1.4% a | 72.1% ± 1.5%a, b | 70.4% ± 1.7%a, b | 71.4% ± 0.9%a, b |
| Total yield | 7.5 ± 0.2 Gb | 7.0 ± 0.3 Gb | 9.0 ± 0.3 Gb a, b | 8.3 ± 0.3 Gba, b | 6.6 ± 0.2 Gb a, c, d |
| q30 yield | 6.1 ± 0.2 Gb | 5.2 ± 0.2 Gb a | 7.2 ± 0.3 Gb a, b | 6.4 ± 0.3 Gbb | 5.2 ± 0.2 Gb a, c, d |
| Total reads | 1.7 × 107 ± 5.4 × 105 | 1.6 × 107 ± 6.4 × 105 | 2.0 × 107 ± 6.9 × 10 b | 1.9 × 107 ± 7.9 × 10b | 1.5 × 107 ± 5.9 × 10 c, d |
| Reads PF | 1.5 × 107 ± 4.2 × 105 | 1.3 × 107 ± 5.5 × 105 | 1.8 × 107 ± 6.2 × 10 b | 1.6 × 107 ± 6.5 × 10b | 1.3 × 107 ± 4.6 × 10 c, d |
| Prephasing (R1) | 0.055% ± 0.002% | 0.111% ± 0.008%a | 0.113% ± 0.031% | 0.119% ± 0.037% | 0.074% ± 0.004%a, b |
| Prephasing (R2) | 0.116% ± 0.006% | 0.171% ± 0.016%a | 0.169% ± 0.028% | 0.179% ± 0.037% | 0.131% ± 0.007%b |
| Phasing (R1) | 0.074% ± 0.005% | 0.096% ± 0.008% a | 0.092% ± 0.017% | 0.072% ± 0.003% b | 0.087% ± 0.005%d |
| Phasing (R2) | 0.150% ± 0.007% | 0.174% ± 0.012% | 0.172% ± 0.008%a | 0.162% ± 0.007% | 0.172% ± 0.008%a |
“n” is equal to the number of MiSeq runs performed per sequencer. Values represent the means ± SE. Values that are deemed statistically significant are indicated by the corresponding symbol according to the figure legend below. The best and worst values based on manufacturer recommendations for each variable are indicated with underline and bold, respectively
a
Significant compared to MiSeq A.
b
Significant compared to MiSeq B.
c
Significant compared to MiSeq C.
d
Significant compared to MiSeq D.