Table 5.
Comparison of mt-tRNA gene predictions with NCBI RefSeq annotations. About 73 674 annotated mt-tRNA genes in 3345 mitochondrial genomes from NCBI RefSeq (24) were used as references for comparison. ‘Consistent’ represents the count and percentage of predicted mt-tRNA genes that are the same or nearly the same as RefSeq annotations (may include up to a 15-nt difference in start and/or end positions). ‘Isotype mismatch’ represents the number and percentage of predicted mt-tRNA genes that have conflicting isotype classification. ‘Position mismatch’ represents the number and percentage of predicted mt-tRNA genes that had conflicting strand or start/end positions beyond ±15 nts. ‘Novel’ represents the predicted mt-tRNA genes that were not found in RefSeq annotations. ‘Not detected’ is the count of RefSeq annotations that were not detected by the prediction algorithm.
| Prediction algorithm | Predicted mt-tRNAs | Consistent | Isotype mismatch | Position mismatch | Novel | Not detected |
|---|---|---|---|---|---|---|
| tRNAscan-SE 2.0 (vertebrate mito mode) | 73 671 | 72 920 (99.0%) | 35 (0.05%) | 527 (0.7%) | 189 (0.3%) | 192 |
| ARWEN | 80 617 | 70 677 (87.7%) | 211 (0.3%) | 551 (0.7%) | 9178(11.4%) | 2235 |
| MiTFi | 73 685 | 72 796 (98.8%) | 96 (0.1%) | 528 (0.7%) | 265 (0.4%) | 254 |