Fig. 3

Identification of four repeats in the mitochondrion genome potentially affecting de novo assembly quality. A 45 bp deletion was observed in the terminal region of 6129 bp-long KP796149 assembly (greyed out sequence in the top track), which was investigated further. Four 15-mer repeats have been observed in the 6274 long KP231180 assemblies. Three of the four repeats were seen missing in the KP796149 assembly after alignment indicated by a blue triangle with a red bar (last track). Though the sequence from KP796149 appears to be aligned with the reads and KP231180, the colored and missing bases in the last track point to a forced misalignment. The C5 source-reads (used as a representative of all the three source-read datasets) mapped to this region in KP231180 and its assembly contained these repeats as expected (11 tracks in the middle). The presence of just one of the four repeats in KP796149 sequence [6] would result in improper mapping of the reads and render any dependent de novo assembly incomplete