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Uncorrected mean genetic distances in COI between STUs were calculated in MEGA 5 [ 93] with all positions containing gaps or missing data removed.
These figures exclude the 3% of children on ART who were missing data for ART adherence at the pre-conflict visit and the 10% who were missing ART adherence data at the post-election visit; however, the analyses with missing data removed were no different than analyses assuming all those missing data were nonadherent.
The 13-taxon data set with sites containing missing data removed (13-taxon clean).
The eight-taxon data set with sites containing missing data removed (eight-taxon reduced then cleaned).
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Multiple filters were applied on the "merged allele file" by removing the loci where either of the parents have missing data, removing multi-alleleic loci and filtering out loci where more than 30% of the samples have missing data, resulting in a total of 57,863 loci.
The increase in diagnosed diabetes levels when patients with missing data are removed from the sample suggests that few people with diagnosed diabetes are removed.
Sequences with missing data were removed from the database by manual inspection using MEGA4 v4.1, and redundant sequences were removed using the NRDB program (http://pubmlst.org/perl/mlstanalyse/mlstanalyse.pl?site=pubmlst&page=nrdb&referer=pubmlst.org).org
SNPs with more than 5%% missing data were removed from our analysis, and the remaining missing genotypes were imputed using alleles of the highest frequencies across the population.
Entire locations enclosing gaps and missing data were removed.
All locations having gaps and missing data were removed from the data set using the complete-deletion option.
Finally, bad data such as outliers or missing data are removed using outlier detection, filters and smoothing of signal.
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