Table 5. Illumina Nextera XT® VPRI P. leucotricha sequencing alignment results taken from vision alignment.
| Reads Raw | Reads Passed QC | PM ITS Raw | PM ITS | PM Mito1 Raw | PM Mito1 | PM Mito2 Raw | PM Mito2 | PM rRNA Raw | PM rRNA | Malus Mito Raw | Malus Mito | Malus Chloro Raw | Malus Chloro | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CheX | 3,301,690 | 2,125,386 | 142 | 0.01% | 2,395 | 0.11% | 1,603 | 0.08% | 3,382 | 0.16% | 1,915 | 0.09% | 2,956 | 0.14% |
| InuP | 7,172,861 | 5,266,236 | 837 | 0.02% | 13,406 | 0.26% | 10,011 | 0.19% | 5,696 | 0.11% | 4,223 | 0.08% | 5,210 | 0.10% |
| SDS | 6,913,188 | 3,950,749 | 477 | 0.01% | 7,518 | 0.19% | 5,551 | 0.14% | 1,805 | 0.05% | 5,479 | 0.14% | 6,237 | 0.16% |
| EznS | 919,376 | 746,040 | 80 | 0.01% | 1,544 | 0.21% | 1,120 | 0.15% | 806 | 0.11% | 59,470 | 7.97% | 164,254 | 22.02% |
| DnaZ | 6,236,108 | 2,948,446 | 21 | 0.00% | 457 | 0.02% | 304 | 0.01% | 72 | 0.00% | 3,060 | 0.10% | 10,743 | 0.36% |
| EznF | 5,911,120 | 4,799,780 | 408 | 0.01% | 1,773 | 0.04% | 1,353 | 0.03% | 1,849 | 0.04% | 20,072 | 0.42% | 24,437 | 0.51% |
| DneP | 5,999,284 | 3,837,027 | 88 | 0.00% | 403 | 0.01% | 350 | 0.01% | 494 | 0.01% | 7,692 | 0.20% | 10,775 | 0.28% |
| IspC | 241,089 | 195,337 | 99 | 0.05% | 635 | 0.33% | 412 | 0.21% | 1,013 | 0.52% | 23,867 | 12.22% | 29,683 | 15.20% |
| IspS | 140,095 | 110,579 | 16 | 0.01% | 87 | 0.08% | 71 | 0.06% | 334 | 0.30% | 5,711 | 5.17% | 5,737 | 5.19% |
| WizG | 4,517,829 | 3,631,938 | 72 | 0.00% | 161 | 0.00% | 120 | 0.00% | 1,657 | 0.05% | 14,064 | 0.39% | 25,543 | 0.70% |
| EznP | 6,256,598 | 5,063,754 | 142 | 0.00% | 481 | 0.01% | 360 | 0.01% | 1,494 | 0.03% | 35,642 | 0.70% | 67,163 | 1.33% |
| CTAB | 6,357,620 | 3,373,175 | 46 | 0.00% | 692 | 0.02% | 469 | 0.01% | 1,230 | 0.04% | 8,304 | 0.25% | 5,959 | 0.18% |
| DneP+ | 640,221 | 572,874 | 9 | 0.00% | 140 | 0.02% | 75 | 0.01% | 66 | 0.01% | 1,337 | 0.23% | 2,376 | 0.41% |
Total raw reads, QC reads and mapped raw reads and percentage of aligned sequence reads to reference genes: P. leucotricha ITS (PM ITS), P. leucotricha mitochondria 1 and 2 scaffolds (PM Mito 1/2), P. leucotricha rRNA scaffold (PM rRNA)s, Malus mitochondria and Malus chloroplast genomes. Extraction method abbreviations: Chelex®100 (CheX), innuPrep Plant DNA (InuP), sodium dodecyl sulphate (SDS), E.Z.N.A.® SP Plant (EznS), DNAzol™ (DnaZ), E.Z.N.A.® Forensic DNA (EznF), Qiagen DNeasy® Plant (DneP), Isolate II Plant DNA Lysis buffer PA1 C (IspC), Isolate II Plant DNA Lysis buffer PA2 S (IspS), Wizard® Genomic DNA Purification (WizG), E.Z.N.A.® Plant (EznP), Cetyl trimethyl ammonium bromide (CTAB) and Qiagen DNeasy® Plant plus PTB (DneP+).