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Table 1 Parameters of genetic diversity of the 13 nuclear regions using a nMLST approach

From: Genetic structure of Trypanosoma cruziin Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach

Gene fragment πa θb Number of polymorphic sites Genotypic diversity Number of genotypes Typing efficiencyc Ratio of NS to SN changesd
GPX 0.0897 0.20069 35 0.959 29 0.087 0.654
HMCOAR 0.00515 0.00828 16 0.792 11 0.736 0.659
PDH 0.00467 0.00713 20 0.766 14 0.833 0.127
GTP 0.02268 0.06233 38 0.941 24 0.163 0.223
STPP2 0.00439 0.00581 14 0.848 13 0.500 1.564
RHO1 0.01457 0.01656 26 0.959 28 0.771 1.759
SODA 0.00704 0.00979 19 0.893 14 0.377 0.427
SODB 0.01299 0.02177 28 0.763 8 0.208 0.369
LAP 0.00231 0.00290 7 0.424 6 0.857 0.0125
GPI 0.00001 0.00145 3 0.212 2 0.666 0.0698
LYT1 0.01722 0.02261 27 0.966 28 1.037 0.831
RB19 0.00873 0.00377 11 0.401 7 0.636 0.507
TR 0.00772 0.00357 10 0.383 7 0.700 1.352
  1. aπ is an index of nucleotide diversity. This measure is defined as the average number of nucleotide differences per site between any two DNA sequences chosen randomly from the sample population.
  2. bThe mutation parameter (θ) is defined as 4 Nm for autosomal loci of diploid organisms, where N is the effective population size (diploid individuals) and m is the neutral mutation rate (per gene or per base pair) per generation.
  3. cTyping efficiency is defined as the number of different genotypes described per polymorphic site.
  4. dSNPs in the coding region of a gene are of two types, synonymous (SN) and nonsynonymous (NS) SNPs. Synonymous SNPs do not affect the protein sequence while nonsynonymous SNPs change the amino acid sequence of protein.