Table 8. Indels located in coding sequences.
| Position | Depth | Qual | Gene | SP | Frameshift | Sample | Allele frequency | Notes |
|---|---|---|---|---|---|---|---|---|
| 1,698 | 3,732 | 1.38E+04 | cox1 | C/CAAA | No | mRDI02, mRDI03 | 0.089, 0.85 | Insertion of 1 Lysine |
| 6,364 | 1,929 | 2.15E+09 | cytb | CT/C | Yes | fRDI04, mRDI05 | 0.80, 0.81 | Yields a shorter Cytb. Possible sequencing error due to the homopolymer CTTTTTTT |
| 10,449 | 1,780 | 2.15E+09 | nd5 | C/CT | Yes | fRDI01, fRDI04, fRDI05 | 0.11, 0.10, 0.11 | Yields a nd5 gene divided in 2 ORFs. Possible sequencing error due to the homopolymer CTTTTTT |
| 17,619 | 2,272 | 5.98E+03 | cox3 | AGCG/A | No | mRDI01 | 0.97 | Deletion of one Alanine |
| 17,621 | 2,188 | 9.99E+04 | cox3 | CG/C | Yes | mRDI01 | 0.99 | Always combined with SP_17624. Together change the last 35 amino acids |
| 17,624 | 2,287 | 5.98E+03 | cox3 | C/CAT | Yes | mRDI01 | 0.99 | Always combined with SP_17621. Together change the last 35 amino acids |
Note:
Depth, sequencing depth; Qual, quality of the called SP expressed in Phred score; Allele frequency, frequency of the alternative allele in each sample indicated in the “Sample” column.