Table 2. The estimated numbers (mean, 95% CI in parenthesis) of cases with genomes in the beginning and in the end of the pattern being from the same or different strain, for three different patterns in the Project CLEAR MRSA data, and the estimated proportion of the same strain cases.

	same strain/n	diff. strain/n	same strain prop.
STA → STA	199(199, 200)/224	24(24, 25)/224	0.89(0.84, 0.92)
STA → ∅ → … → STA	20(20, 21)/29	9(8, 9)/29	0.69(0.49, 0.84)
STA → STB → … → STA	12(12, 12)/18	6(6, 6)/18	0.65(0.41, 0.83)

“STA → STA” denotes the case where the ST does not change between two genomes at consecutive samples, “STA → ∅ → … → STA” is the pattern 1) where one or more negative samples are seen between the same ST and “STA → STB → … → STA” is the pattern 2) where a sample with different ST is observed between two samples of the same ST. n denotes the number of data points in each alternative.