Table 2. Transcriptome assembly statistics for the three species examined in this study.
“Main transcripts” refers to the primary transcripts predicted by EvidentialGenes; “alternate transcripts” refers to predicted alternative splice variants of the main transcripts; and “all transcripts” refers to the merged set of main and alternate transcripts. Only SNPs in the main transcripts were counted in the last row (i.e., alternate transcripts were excluded), to avoid potential pseudo-replication caused by SNPs found in multiple splice variants of the same transcript.
| T. pusillus | H. riparius | T. rathkei | |
|---|---|---|---|
| Main transcripts | 34,920 (35.2 Mb) |
25,408 (34.7 Mb) |
33,881 (38.8 Mb) |
| Alternate transcripts | 58,041 (64.9 Mb) |
36,684 (63.7 Mb) |
82,444 (114.3 Mb) |
| All transcripts | 92,961 (100.1 Mb) |
62,092 (98.4 Mb) |
116,325 (153.1 Mb) |
| Complete single-copy BUSCOs (all transcripts) | 248 (24.5%) | 243 (24.0%) | 148 (14.6%) |
| Complete duplicated BUSCOs (all transcripts) | 705 (69.6%) | 757 (74.7%) | 844 (83.3%) |
| Fragmented BUSCOs (all transcripts) | 32 (3.2%) | 8 (0.8%) | 10 (1.0%) |
| Missing BUSCOs (all transcripts) | 28 (2.7%) | 5 (0.5%) | 11 (1.1%) |
| Complete single-copy BUSCOs (main transcripts) | 879 (86.8%) | 929 (91.7%) | 935 (92.3%) |
| Complete duplicated BUSCOs (main transcripts) | 37 (3.7%) | 37 (3.7%) | 37 (3.7%) |
| Fragmented BUSCOs (main transcripts) | 40 (3.9%) | 13 (1.3%) | 17 (1.7%) |
| Missing BUSCOs (main transcripts) | 57 (5.6%) | 34 (3.3%) | 24 (2.3%) |
| Total SNPs/biallelic SNPs with genotype data in all samples (number of samples) | 134,485/5,401 (5) | 53,613/12,676 (4) | 32,542/17,684 (2) |