Table 1 Summary of the sequencing runs for in vitro DNA mixtures
From: Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes
Input amount | 10 ng | 20 ng | 40 ng | 80 ng | 10 ng | 80 ng |
|---|---|---|---|---|---|---|
LA cycles | 1 | 1 | 1 | 1 | 3 | 3 |
Total reads | 5,161,694 | 5,029,394 | 4,181,410 | 4,568,978 | 4,612,940 | 8,718,690 |
On-target reads | 4,449,285 | 4,226,778 | 3,528,081 | 4,051,939 | 3,591,578 | 7,704,936 |
On-target read pairs | 2,152,647 | 2,066,226 | 1,707,379 | 1,972,168 | 1,715,098 | 3,659,067 |
Median raw read depth | 9,263 | 8,558 | 6,454 | 6,915 | 7,701 | 16,275 |
Mean raw read depth | 10,514 | 10,096 | 8,332 | 9,628 | 8,271 | 17,635 |
% Bases >0.2x mean depth | 95 | 94 | 92 | 90 | 95 | 96 |
Median consensus read depth | 98 | 195 | 346 | 544 | 209 | 889 |
Mean consensus read depth | 98 | 187 | 336 | 530 | 208 | 839 |
Mean raw read/consensus read | 53 | 28 | 13 | 11 | 22 | 16 |
Median raw read/consensus read | 53 | 26 | 11 | 8 | 20 | 10 |
Bases in target region | 39,231 | 39,231 | 39,231 | 39,231 | 39,231 | 39,231 |
GIAB high confident region for NA12878 | 29,343 | 29,343 | 29,343 | 29,343 | 29,343 | 29,343 |
NA12878 unique SNVs | 134 | 134 | 134 | 134 | 134 | 134 |
Detected true positives | 17 | 40 | 76 | 93 | 39 | 114 |
Detected false positives | 0 | 2 | 3 | 5 | 4 | 3 |