Fig. 4

Comparison of the new mitochondrial assemblies and the public sequences with the reference genome. The topmost track with CDS (annotations in red) is the reference genome, KP231180. Tracks 1–3: 6274 bp long C5, C8 and C10 assemblies respectively; tracks 4: 6229 bp long KP796149 [6] assembly; track 5–6: 6273 bp long CM003498 assembly split into two fragments by the alignment program to obtain collinearity. The fragment start-stop positions are given in the track name; track 7: 6184 bases long KP658101 [7] assembly. The three mitochondrion assemblies CM0003498, KP658101 and KP796149 along with the new C5, C8 and C10 sequences were compared with the reference genome evaluated in this study. The mapping and visualization were carried out using Geneious suite utilities to highlight SNPs. A synonymous transversion mutation was identified in all six assemblies in comparison with the reference. The alleles present in the query genomes with respect to the base in position 4415 of the reference genome are shown in the inset box. In addition, anomalous SNPs (marked by *) were observed in KP796149 and KP658101. The sequence integrity appears to be affected in the public sequences due to sequence shuffling (tracks 5–6 of CM0003498) and deletions indicated by blue triangles (tracks 4–7 for three genomes). The manually curated KP231180 [4] was used as the reference genome (topmost track with CDS annotations) for further analysis to avoid potential mis-assembly and propagation of false positive variants possible with other three genomes