Table 1.
Average analysis metrics for each sample category based on the mitochondrial DNA (mtDNA) analysis of the SweGen dataset. The passing category includes complete (all positions with at least 100X read depth) and nearly complete (one to four positions below 100X) haplotypes that met all quality control criteria. Incomplete haplotypes (five or more positions below 100X), possible mixtures and related samples were excluded from the analysis. The “% Mapped Reads” is the proportion of total reads that mapped to the GRCh37 and the “% mtDNA Reads” is the proportion of the mapped reads that aligned to the mtDNA reference genome.
| Category | Subclassification | Count | Total Reads | % Mapped Reads |
% mtDNA Reads |
Average Read Depth |
|---|---|---|---|---|---|---|
| Passing | Complete | 858 | 865,518,368.5 | 99.16% | 0.036% | 2365.9 |
| Nearly Complete | 59 | 833,866,169.5 | 99.20% | 0.010% | 652.5 | |
| Excluded | Incomplete | 17 | 784,241,829.7 | 99.32% | 0.010% | 592.0 |
| Mixed | 7 | 762,731,157.9 | 98.72% | 0.019% | 1191.1 | |
| Related | 1 | 869,537,450 | 99.52% | 0.029% | 1870.7 |