Table 3.
Illumina sequencing and mapping results of liver and gill samples
| Tissue (Specimen) | No. read | Retained reads |
Annotated transcriptome |
Reference transcriptome |
||||
|---|---|---|---|---|---|---|---|---|
| % Mapped | % Unmapped | % Ambiguous | % Mapped | % Unmapped | % Ambiguous | |||
| Liver (1) |
47,999,274 |
31,104,129 |
68.5 |
28.0 |
3.4 |
75.8 |
19.8 |
4.4 |
| Liver (2) |
60,009,042 |
39,254,065 |
61.9 |
34.5 |
3.5 |
70.9 |
24.4 |
4.7 |
| Liver (3) |
47,666,040 |
26,435,958 |
62.4 |
33.9 |
3.6 |
71.2 |
24.0 |
4.8 |
| Gill (1) |
71,817,060 |
42,149,816 |
50.4 |
2.1 |
2.1 |
64.7 |
31.6 |
3.7 |
| Gill (2) |
50,157,764 |
29,490,860 |
52.9 |
2.8 |
44.0 |
69.7 |
25.9 |
4.4 |
| Gill (3) | 59,998,042 | 35,620,006 | 43.8 | 1.9 | 54.2 | 61.4 | 34.9 | 3.7 |
Results from Illumina sequencing of liver and gill samples from P. borchgrevinki held at their natural water temperatures. Sequenced 100 nt reads were processed using the Fastx toolkit and processed to remove the adaptor sequence used in library construction, low quality sections of each read, and any reads of uniformly low quality. Retained reads were thus shorter (80 nt) but of higher quality and used for read mapping with the program Bowtie.