Assembly and phylogeographical analysis of novel Taenia solium mitochondrial genomes suggest stratification within the African-American genotype

Table 1 Non-synonymous point mutations present in all African-American mitochondrial genomes with respect to the Chinese reference

Amino acid substitutions present in all the assembled African-American genomes are given per protein-coding gene. The Jensen–Shannon conservation and the Grantham score for each substitution are shown in parentheses. High Jensen–Shannon and Grantham scores indicate conserved positions and substitutions with a radically different amino acid, respectively. The threshold for classifying a position as conserved using the Jensen–Shannon score is calculated based on the top 30 positions with the highest scores in the protein sequence (see materials and methods). Threshold values per protein-coding gene are 0.74 (ATP6), 0.81 (COX1), 0.76 (COX2), 0.77 (COX3), 0.76 (CYTB), 0.73 (ND1), 0.77 (ND2), 0.73 (ND3), 0.8 (ND4), 0.74 (ND4L), 0.81 (ND5), and 0.74 (ND6). None of the non-synonymous mutations passed the conservation threshold. Substitutions with a Grantham score higher than 60 were considered to affect the physicochemical nature of the amino acid. These mutations are shown with an asterisk (*)

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