Table 3.
Sequencing and Alignment Statistics
| Product | Center | Normalized read counts | Average insert | Insert sd | Aligned | Failed to align | Suppressed (ambiguous) | Remainder | Potential PCR duplicate | PCR duplicate-free count | Total reduction |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Agilent SureSelect rep 1 | Stowers | 23,928,746 | 205.9 | 62.2 | 95.71% | 2.13% | 2.16% | 22,902,203 | 16.65% | 19,088,986 | 20.23% |
| Agilent SureSelect rep 2 | Stowers | 23,928,746 | 216.2 | 58.2 | 95.53% | 1.85% | 2.63% | 22,859,132 | 13.67% | 19,734,289 | 17.53% |
| Agilent SureSelect rep 1 | Michigan | 23,928,746 | 207.9 | 63.3 | 95.47% | 2.26% | 2.26% | 22,844,780 | 15.87% | 19,219,313 | 19.68% |
| Agilent SureSelect rep 2 | Michigan | 23,928,746 | 217.3 | 58.1 | 95.79% | 1.79% | 2.42% | 22,921,352 | 14.30% | 19,643,599 | 17.91% |
| NimbleGen array rep 1 | Stowers | 23,928,746 | 158.3 | 23.3 | 94.00% | 1.76% | 4.23% | 22,493,023 | 33.79% | 14,892,631 | 37.76% |
| NimbleGen array rep 2 | Stowers | 23,928,746 | 158.3 | 23.3 | 94.05% | 1.73% | 4.23% | 22,504,988 | 31.46% | 15,424,919 | 35.54% |
| NimbleGen array rep 1 | Michigan | 23,928,746 | 158.8 | 23.2 | 94.26% | 1.73% | 4.01% | 22,555,244 | 34.77% | 14,712,785 | 38.51% |
| NimbleGen array rep 2 | Michigan | 23,928,746 | 158.7 | 23.2 | 94.26% | 1.70% | 4.04% | 22,555,244 | 32.16% | 15,301,478 | 36.05% |
| NimbleGen solution rep 1 | Stowers | 23,928,746 | 94.5 | 20.3 | 92.96% | 2.12% | 4.92% | 22,244,166 | 29.28% | 15,731,074 | 34.26% |
| NimbleGen solution rep 2 | Stowers | 23,928,746 | 94.1 | 20.3 | 92.80% | 2.14% | 5.07% | 22,205,881 | 28.92% | 15,783,940 | 34.04% |
| NimbleGen solution rep 1 | Michigan | 23,928,746 | 94.3 | 20.3 | 92.53% | 2.42% | 5.05% | 22,141,278 | 28.49% | 15,833,228 | 33.83% |
| NimbleGen solution rep 2 | Michigan | 23,928,746 | 94.5 | 20.3 | 92.77% | 2.21% | 5.03% | 22,198,708 | 28.61% | 15,847,658 | 33.77% |
For each replicate, various statistics from the alignment were recorded. These included the average DNA template size, the percent alignment, the number of reads suppressed for ambiguity, percent PCR duplicates, and final aligned read counts. Stowers, Stowers Institute for Medical Research; Michigan, University of Michigan.