Table 1.
Minority populations identified in Rv0678 when variant calling was performed on TDS data or whole genome sequencing data with variant calling either performed by a combination of GATK and visual inspection (using Tablet) or by the LoFreq variant caller
| Sample accession number European nucleotide archive | Rv0678 variant | Variant frequency % (number of mutant/total reads) | P-value | ||||
|---|---|---|---|---|---|---|---|
| TDS | WGS GATK/Visual | WGS LoFreq | TDS versus GATK/Visual | TDS versus LoFreq | GATK/Visual versus LoFreq | ||
| SAMEA5562524 | 192 G ins | 96.66% (17 551/18 158) | 100% (56/56) | 87.06% (74/85) | 0.31 | <0.0001 | 0.013 |
| SAMEA5562526 | 138 GA ins | 97.52% (13 299/13 638) | 100% (75/75) | 80.91% (89/110) | 0.31 | <0.0001 | 0.0002 |
| SAMEA5562527 | 138 G ins | 65.48% (9317/14 230) | 63% (45/71) | 55.21% (53/96) | 0.81 | 0.046 | 0.37 |
| 138 GA ins | 28.35% (4034/14 230) | 25% (18/71) | 19.79% (19/96) | 0.67 | 0.08 | 0.50 | |
| 192 G ins | 3.22% (461/14 230) | No MV detected: data missing | 4.49% (4/89) | 0.71 | |||
| SAMEA5562528 | 138 G ins | 91.68% (13 029/14 212) | 96% (79/82) | 81.55% (84/103) | 0.18 | 0.0004 | 0.004 |
| 138 GA ins | 5.86% (832/14 212) | No MV detected:data missing | 6.80% (7/103) | 0.85 | |||
ins = insertion; WGS = whole genome sequencing; TDS = targeted deep sequencing; MV = minor variant.