Table 2. Exome capture library statistics.
The ratio Z/W is the ratio of the read depth of the Z-linked regions (between 3.5–19.5 Mb and 23.5–31 Mb) over the read depth of the rest of the Z chromosome. We considered a ratio between 0.5 and 0.75 corresponding to females, and a ration over 0.75 to males. ND: not determined because the S. haematobium sexual chromosome is not identified in the current assembly.
| Library | Total reads | Mapped reads | % mapped reads | Paired reads | Singletons | Duplicates | % bait regions captured | Mean (median) read depth in bait regions | Mean (median) read depth in bait regions + adjacent 250 bp | ZW Ratio | Sex |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Sm.TZ_009.10.1 | 25798662 | 25419182 | 98 | 23340898 | 75658 | 778686 | 99.7 | 111.6 (50) | 29.46 (11) | 1.09 | M |
| Sm.TZ_009.1.1 | 10584471 | 8990428 | 84 | 8401922 | 30943 | 472062 | 99.61 | 41.13 (30) | 80.07 (17) | 1.1 | M |
| Sm.TZ_009.2.2 | 6322519 | 6285705 | 99 | 5908458 | 18458 | 108142 | 99.57 | 28.25 (22) | 20.44 (9) | 0.56 | F |
| Sm.TZ_009.4.2 | 14336010 | 13867259 | 96 | 12681806 | 44233 | 398843 | 99.45 | 61.84 (29) | 45.18 (11) | 0.7 | F |
| Sm.TZ_009.5.2 | 12072285 | 11756999 | 97 | 10697666 | 34578 | 270333 | 99.02 | 52.42 (24) | 38.6 (9) | 0.62 | F |
| Sm.TZ_009.6.1 | 6001101 | 5932580 | 98 | 5457864 | 19447 | 94657 | 99.52 | 25.97 (20) | 19.02 (8) | 1.15 | M |
| Sm.TZ_009.7.1 | 14570100 | 14433095 | 99 | 13250586 | 41663 | 245158 | 99.73 | 59.91 (45) | 43 (14) | 0.61 | F |
| Sm.TZ_009.8.2 | 7832169 | 7306500 | 93 | 6876540 | 20661 | 137371 | 99.6 | 32.86 (25) | 23.72 (10) | 1.08 | M |
| Sh.TZ_PEM0063.1 | 7029068 | 6464873 | 91 | 6040332 | 7279 | 179216 | 99.73 | 28.72 (22) | 20.55 (9) | ND | ND |
| Sh.TZ_PEM0076.1 | 11544736 | 11392803 | 98 | 9696738 | 67595 | 480559 | 99.92 | 41.62 (35) | 30.07 (12) | ND | ND |
| Sh.TZ_PEM0079.1 | 5557924 | 4998091 | 89 | 4672272 | 6737 | 127514 | 98.7 | 22.69 (14) | 16.72 (6) | ND | ND |
| Sh.TZ_PEM0089.2 | 18364494 | 17933751 | 97 | 16683002 | 20437 | 390640 | 99.85 | 71.88 (57) | 51.08 (17) | ND | ND |
| Sh.TZ_PEM0094.2 | 15443954 | 15214835 | 98 | 14091206 | 19001 | 317997 | 99.85 | 61.23 (52) | 44.06 (17) | ND | ND |
| Sh.TZ_PEM0099.2 | 7069391 | 6672191 | 94 | 6292150 | 7106 | 124974 | 99.78 | 28.88 (24) | 20.64 (9) | ND | ND |
| Sh.TZ_PEM0103.1 | 7958910 | 7809025 | 98 | 7293706 | 28039 | 487198 | 99.8 | 31.72 (26) | 22.86 (10) | ND | ND |
| Sh.TZ_PEM0104.1 | 5051982 | 4824636 | 95 | 4079848 | 40950 | 200550 | 99.77 | 17.83 (15) | 13.17 (6) | ND | ND |