Selected cases of misassembly. Orthologs were tracked across multiple sequencing depths, and selected examples are here showing some of the pitfalls of assembly. (A) The lengths of three proteins are shown (AlaRS, Alanyl-tRNA synthetase; 2-OGDH-E2, 2-oxoglutarate dehydrogenase subunit E2; EF2, Elongation factor 2), and the canonical protein length is indicated by a blue line. (B) Protein alignment view of the same three proteins compared to the Uniprot/Swissprot canonical protein, which is shown as the blue bar. A chimeric portion of AlaRS at 30 million reads is indicated by the red bar, where it contains a sequence from the putative mitochondrial alanyl-tRNA synthetase 2 protein (NP_941010), and corresponds to the red point at 30 in (A). For AlaRS and EF2, some alignments produced a few short gaps compared to the reference proteins.