Table 2 Number of false positive and false negative variants (SNPs and indels) identified in WGA-WGS samples when using the MAGMA pipeline for analysis of Illumina sequencing reads.
Positive control | dMDA processed samples | |||||
|---|---|---|---|---|---|---|
Amount of Mtb DNA used as input for the dMDA process (pg) | 0.1 | 0.5 | 1 | 5 | ||
Excluding complex regions | Total number of variants identified | 1290 | 917 | 1363 | 1294 | 1293 |
Number of SNPs | 1180 | 842 | 1252 | 1185 | 1180 | |
Number of indels | 110 | 75 | 111 | 109 | 113 | |
Number of false negative* variants (%) | 548 (59.76%) | 41 (3.01%) | 9 (0.70%) | 1 (0.08%) | ||
False negative SNPs | 501 (54.63%) | 34 (2.49%) | 6 (0.45%) | 1 (0.08%) | ||
False negative indels | 47 (5.13%) | 7 (0.51%) | 3 (0.23%) | 0 (0%) | ||
Number of false positive* variants (%) | 175 (19.08%) | 114 (8.36%) | 13 (1.00%) | 4 (0.31%) | ||
False positive SNPs | 163 (17.78%) | 106 (7.78%) | 11 (0.85%) | 1 (0.08%) | ||
False positive indels | 12 (1.31%) | 8 (0.59%) | 2 (0.15%) | 3 (0.23%) | ||
Including complex regions | Total number variants identified | 1655 | 1106 | 1688 | 1646 | 1657 |
Number of SNPs | 1503 | 1014 | 1544 | 1502 | 1503 | |
Number of indels | 152 | 92 | 144 | 144 | 154 | |
Number of false negative* variants (%) | 758 (68.54%) | 113 (6.69%) | 54 (3.28%) | 31(1.87%) | ||
False negative SNPs | 680 (61.48%) | 90 (5.33%) | 39 (2.37%) | 23 (1.39%) | ||
False negative indels | 78 (7.05%) | 23 (1.36%) | 15 (0.91%) | 8 (0.48%) | ||
Number of false positive* variants (%) | 209 (18.90%) | 146 (8.65%) | 45 (2.73%) | 33 (1.99%) | ||
False positive SNPs | 191 (17.27%) | 131 (7.76%) | 38 (2.31%) | 23 (1.39%) | ||
False positive indels | 18 (1.63%) | 15 (0.89%) | 7 (0.43%) | 10 (0.60%) | ||
