Table 2.
Variants detected in nine HT-29 cells sequenced using the eWGA protocol according to the following thresholds: depth of 30 reads and minimum allele frequency of 3%.
| Variant | inWGS | inWES | IsInBulk | mAF_WGS | mAF_WES | mAF_Bulk |
|---|---|---|---|---|---|---|
| m.73A > G | 5 | 1 | 1 | 1.00 | 1.00 | 1.00 |
| m.73A > T | 5 | 1 | 1 | 1.00 | 1.00 | 1.00 |
| m.114C > T | 5 | 2 | 1 | 1.00 | 1.00 | 1.00 |
| m.263A > G | 6 | 3 | 1 | 1.00 | 1.00 | 1.00 |
| m.310T > C | 4 | 1 | 0 | 0.38 | 0.68 | 0 |
| m.497C > T | 5 | 2 | 1 | 0.99 | 0.99 | 1.00 |
| m.750A > G | 7 | 2 | 1 | 1.00 | 0.98 | 1.00 |
| m.1189T > C | 5 | 2 | 1 | 1.00 | 0.97 | 1.00 |
| m.1352C > T | 2 | - | 0 | 0.06 | - | 0 |
| m.1413T > C | 6 | 2 | 1 | 1.00 | 1.00 | 1.00 |
| m.1438A > G | 6 | 2 | 1 | 1.00 | 1.00 | 1.00 |
| m.1811A > G | 9 | 2 | 1 | 1.00 | 1.00 | 1.00 |
| m.2706A > G | 9 | 3 | 1 | 1.00 | 0.91 | 1.00 |
| m.3480A > G | 9 | 3 | 1 | 1.00 | 0.99 | 1.00 |
| m.4769A > G | 4 | 1 | 1 | 1.00 | 1.00 | 1.00 |
| m.5591G > A | 2 | - | 0 | 0.08 | - | 0 |
| m.7028C > T | 4 | 1 | 1 | 1.00 | 1.00 | 1.00 |
| m.8860A > G * | 4 | 1 | 0 | 1.00 | 1.00 | 1.00 |
| m.9055G > A | 9 | 6 | 1 | 1.00 | 1.00 | 1.00 |
| m.9510T > C * | 6 | 4 | 0 | 0.31 | 0.36 | 0.37 |
| m.9698T > C | 8 | 4 | 1 | 0.99 | 0.99 | 0.97 |
| m.10398A > G * | 9 | 2 | 0 | 0.99 | 1.00 | 1.00 |
| m.10550A > G | 9 | 3 | 1 | 0.99 | 1.00 | 1.00 |
| m.10978A > G | 7 | 4 | 1 | 0.99 | 0.98 | 1.00 |
| m.11145C > A | 3 | - | 0 | 0.06 | - | 0 |
| m.11299T > C | 9 | 7 | 1 | 1.00 | 0.99 | 1.00 |
| m.11467A > G | 9 | 5 | 1 | 1.00 | 1.00 | 1.00 |
| m.11470A > G | 9 | 5 | 1 | 1.00 | 1.00 | 1.00 |
| m.11719G > A | 8 | 3 | 1 | 1.00 | 1.00 | 1.00 |
| m.11914G > A | 7 | 3 | 1 | 1.00 | 1.00 | 1.00 |
| m.12308A > G | 7 | 2 | 1 | 1.00 | 1.00 | 1.00 |
| m.12372G > A * | 7 | 4 | 0 | 1.00 | 1.00 | 0.96 |
| m.12954T > C | 5 | 6 | 1 | 1.00 | 1.00 | 1.00 |
| m.13831C > A * | 5 | 5 | 0 | 0.37 | 0.34 | 0.22 |
| m.14167C > T | 7 | 9 | 1 | 1.00 | 1.00 | 1.00 |
| m.14766C > T | 9 | 4 | 1 | 1.00 | 0.99 | 1.00 |
| m.14798T > C | 8 | 6 | 1 | 1.00 | 0.99 | 0.96 |
| m.15289T > C | 2 | - | 0 | 0.08 | - | 0 |
| m.15326A > G | 9 | 3 | 1 | 1.00 | 1.00 | 1.00 |
| m.15924A > G | 9 | 3 | 1 | 1.00 | 1.00 | 1.00 |
| m.16224T > C | 7 | 6 | 1 | 0.99 | 1.00 | 1.00 |
| m.16234C > T | 7 | 6 | 1 | 1.00 | 1.00 | 1.00 |
| m.16311T > C | 8 | 5 | 1 | 1.00 | 1.00 | 1.00 |
| m.16519T > C | 5 | 1 | 1 | 1.00 | 0.97 | 1.00 |
Variant: type and genomic location of each variant in the format m.[POS][REF] > [ALT] (m: chrM; POS: genomic position; REF: reference base; ALT: alternative base); inWGS: number of cells sequenced by WGS in which the variant is detected; inWES: number of cells sequenced by WES in which the variant is detected; IsInBulk: a flag indicating if a variant is detected (1) or not detected (0) in the bulk; mAF_WGS: mean allele frequency in cells sequenced by WGS; mAF_WES: mean allele frequency in cells sequenced by WES; mAF_Bulk: allele frequency in the bulk (reported also for sites supported by less than 30 reads). mAF_Bulk values of 0 indicate that the site is not covered by reads. * indicates variants apparently not supported by the bulk because covered by less than 30 reads.