Table 3 Number of reads mapped to original probe set (ddRAD loci) and assembly-based reference with corresponding levels of similarity threshold (*).
Species | N | Processed reads | Mapped reads to original probe set (%) | PCR duplicates (% over mapped reads) | Blast hits to original probe set** | Mapped reads to new assembly (%) |
|---|---|---|---|---|---|---|
J. edwardsii | 8 | 605,396 | 242,538 (40.06) | 97,952(40.39) | 910 | 331,505(42.91) |
J. frontalis | 8 | 286,288 | 28,360(9.91) | 5,403 (19.05) | 565 | 68,374(15.85) |
J. lalandii | 8 | 285,545 | 106,425(37.27) | 22,283(20.94) | 854 | 139,969(39.15) |
J. paulensis | 8 | 478,098 | 190,903(39.93) | 58,824 (30.81) | 875 | 264,249(52.33) |
J. tristani | 8 | 246,252 | 94,839(38.51) | 24,486(25.82) | 829 | 132,244(31.10) |
Total | 40 | 1,901,579 | 663,065(34.86) | 208,948 (31.51) | 925* | 936,241(49.23) |
