Table 2.
Barcode combination experiment. (Basic results before and after enrichment for mtDNA of 4 × 4 libraries with all possible barcode combinations. For the assessment after enrichment, we downsampled all reads to 125 406, to facilitate comparability across samples. Italicized numbers represent the number of reads that aligned to the mitochondrial (mt) genome.)
| before enrichment |
after enrichment |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P5 barcode | P7 barcode | all reads | reads aligning to hg19 (mt) | % endogenous (%) | all reads | reads aliging to mt genome | % of reads aligning to mt genome (%) | unique reads aligning to mt genome | median length in bp | damage rate in terminal bases (%) | % of unique reads aligning to mt genome (%) | duplication rate (%) | average mt coverage |
| ATCGATT | GACTTAT | 44 884 | 1256 (3) | 2.80 | 125 406 | 90 118 | 71.9 | 17 455 | 62 | 8.72 | 13.9 | 80.6 | 71.6 |
| ATCGATT | TCGAACA | 45 866 | 1287 (8) | 2.81 | 125 406 | 88 429 | 70.5 | 17 395 | 65 | 9.37 | 13.9 | 80.3 | 73.2 |
| ATCGATT | AGTCCGC | 35 813 | 935 (2) | 2.61 | 125 406 | 88 335 | 70.4 | 18 253 | 64 | 9.70 | 14.6 | 79.3 | 76.6 |
| ATCGATT | CTAGGTG | 29 091 | 870 (4) | 2.99 | 125 406 | 86 795 | 69.2 | 13 970 | 59 | 8.05 | 11.1 | 83.9 | 55.3 |
| CAGTCAA | GACTTAT | 34 104 | 888 (1) | 2.60 | 125 406 | 90 026 | 71.8 | 19 122 | 65 | 9.46 | 15.2 | 78.8 | 81.2 |
| CAGTCAA | TCGAACA | 38 693 | 1060 (3) | 2.74 | 125 406 | 89 294 | 71.2 | 15 242 | 64 | 8.14 | 12.2 | 82.9 | 62.8 |
| CAGTCAA | AGTCCGC | 37 276 | 996 (5) | 2.67 | 125 406 | 88 251 | 70.4 | 18 240 | 64 | 9.17 | 14.5 | 79.3 | 77.0 |
| CAGTCAA | CTAGGTG | 29 494 | 952 (2) | 3.23 | 125 406 | 85 767 | 68.4 | 11 060 | 60 | 6.98 | 8.8 | 87.1 | 43.5 |
| GCTAGCC | GACTTAT | 24 227 | 707 (2) | 2.92 | 125 406 | 86 112 | 68.7 | 16 948 | 63 | 8.90 | 13.5 | 80.3 | 71.3 |
| GCTAGCC | TCGAACA | 40 675 | 1157 (1) | 2.84 | 125 406 | 83 702 | 66.7 | 14 922 | 59 | 9.63 | 11.9 | 82.2 | 59.4 |
| GCTAGCC | AGTCCGC | 38 108 | 1191 (3) | 3.13 | 125 406 | 85 471 | 68.2 | 16 518 | 61 | 8.39 | 13.2 | 80.7 | 67.6 |
| GCTAGCC | CTAGGTG | 33 780 | 1092 (3) | 3.23 | 125 406 | 89 368 | 71.3 | 13 421 | 63 | 7.72 | 10.7 | 85.0 | 54.0 |
| TGACTGG | GACTTAT | 54 050 | 1555 (12) | 2.88 | 125 406 | 89 679 | 71.5 | 18 298 | 65 | 9.56 | 14.6 | 79.6 | 77.9 |
| TGACTGG | TCGAACA | 27 733 | 790 (2) | 2.85 | 125 406 | 87 788 | 70.0 | 16 149 | 62 | 8.52 | 12.9 | 81.6 | 66.1 |
| TGACTGG | AGTCCGC | 35 675 | 1097 (4) | 3.07 | 125 406 | 86 835 | 69.2 | 18 303 | 63 | 9.23 | 14.6 | 78.9 | 76.9 |
| TGACTGG | CTAGGTG | 36 744 | 1102 (2) | 3.00 | 125 406 | 88 364 | 70.5 | 13 550 | 59 | 7.15 | 10.8 | 84.7 | 53.4 |