TABLE 1.
Alignment and genome coverage across various reference genomes within the genus Mycobacteria
| Reference genome species | Reference genome name | Accession no. | Reference | Reference genome length (bp) | % of reads successfully aligned to referencea (median [IQR]) | Genome coverage (median [IQR])b at: |
||
|---|---|---|---|---|---|---|---|---|
| ≥1× depth | ≥10× depth | ≥20× depth | ||||||
| Mycobacterium tuberculosis | ||||||||
| Lineage 4 | H37Rv | NC_000962.3 | 21 | 4,411,532 | 98.0 (97.9–98.1) | 98.9 (98.8–98.9) | 98.1 (98.0–98.3) | 97.2 (96.8–97.5) |
| Lineage 4 | CDC1551 | NC_002755.2 | 22 | 4,403,837 | 98.2 (98.1–98.3) | 99.3 (99.2–99.3) | 98.5 (98.4–98.7) | 97.6 (97.2–97.9) |
| Lineage 2 | CCDC5079 | CP001641 | 23 | 4,398,812 | 97.8 (97.7–97.9) | 98.8 (98.7–98.8) | 98.1 (97.9–98.2) | 97.1 (96.8–97.4) |
| Mycobacterium africanum | GN041182 | FR878060.1 | 24 | 4,389,314 | 97.5 (97.4–97.5) | 98.9 (98.8–98.9) | 98.1 (98.0–98.3) | 97.2 (96.8–97.4) |
| Mycobacterium bovis | AF2122/97 | NC_002945.3 | 25 | 4,345,492 | 97.6 (97.5–97.7) | 99.3 (99.2–99.3) | 98.5 (98.4–98.7) | 97.6 (97.2–97.9) |
| Mycobacterium canettii | CIPT 140010059 | NC_015848.1 | 26 | 4,482,059 | 96.5 (96.3–96.6) | 95.1 (95.0–95.1) | 94.3 (94.2–94.4) | 93.4 (93.0–93.8) |
| Mycobacterium kansasiic | ATCC 12478 | NC_022663.1 | 27 | 6,432,277 | 52.7 (51.6–53.4) | 34.5 (34.2–35.5) | 28.4 (27.8–29.1) | 25.5 (24.6–26.4) |
a
Calculated using SAMtools (flagstat) as (total mapped − secondary alignments − duplicate reads)/(total reads surviving trimming − duplicate reads).
b
QualiMap includes secondary alignments marked by BWA-MEM (range, 1% to 3% of total mapped), double counted in coverage calculations. Duplicates excluded.
c
pMK plasmid sequence not used for alignment.