Within ST mixed infection.

Analysis for mixed infections with two lineages of the same sequence type is shown in 24 donors/recipients without mixed sequence type infection. The number of variable sites within each sequence type contributing to the analysis is shown together with the number of unique sequences of the sequence type present in the database. A likelihood ratio statistic was used to compare the maximum likelihood obtained under the mixed infection model, with the likelihood of the data without mixed infection.
Samples with a −2 log likelihood statistic ≥19.4 were considered mixed (see calibration set results). The probability of each possible dominant/minor sequence pair from the database being the true pair was calculated, and pairs arranged in descending probability. The number of pairs accounting for ≥95% probability is shown in the penultimate column, with the range of SNPs present between the most likely dominant-minor pairs (within 95% cumulative probability) in the last column. This can be compared to the estimated divergence between dominant and minor sequences which is estimated independently and provides a check on whether the pairs identified within the database are consistent with the divergence between the dominant and minor sequences.