Table 4 Mapping efficiency of PBjelly2’s mapping step. The percentages in brackets give the percentage of the total number of reads (CYP, TUR or CYP + TUR). The line “# covered scaffolds” gives the number of scaffolds in which at least one read was mapped. Here, the number in brackets gives the percentage of the total number of scaffolds
SetupPacBio vs. v2.5PacBio vs. vAMMinION vs. v2.5MinION vs. v2.6
# mapped TUR reads198,675 (86.9%)198,629 (86.9%)14,098 (45.6%)15,886 (51.4%)
# mapped CYP reads131,976 (86.6%)131,942 (86.6%)
# total reads mapped330,651 (86.8%)330,571 (86.8%)14,098 (45.6%)15,886 (51.4%)
# unmapped reads50,371 (13.2%)50,451 (13.2%)16,837 (54.4%)15,049 (48.6%)
# scaffolds input genome3,1662,9903,1662,895
# covered scaffolds2,971 (93.8%)2.804 (93.8%)1.689 (53.3%)1.429 (49.4%)