Extended Data Fig. 10: Schematic of the method used to determine the S_p fraction by plasmid extraction and transformation, and of the method used to determine the copy number of transposons and plasmids in qPCR.

a, We used the Tet+ transposon and Kan+ plasmid as an example (Extended Data Fig. 3b) to show how we calculate the fraction of transposons on the plasmids. Three kinds of plasmids were extracted from the culture: originally empty plasmids (Kan+), plasmids with transposon insertions outside the kanR gene region (Kan+Tet+), and plasmids with transposons insertion inside the kanR gene region (Tet+). After transformation, plates with different antibiotic combinations were used to determine the total number of different plasmids from the original mixture. The detailed calculation process is in the method section. b, We used the Tet+ transposon and Kan+ plasmid as an example (Fig. 2c) to show how we calculate the copy of transposons or plasmids. During the chromosome integration process, a cmR gene was inserted into the chromosome together with but outside the transposon, so the probes for cmR gene can be used to represent the copy of chromosome. The transposon and the plasmid were marked with tetA and kanR gene respectively. We also constructed a DNA fragment with all three markers at 1:1:1 ratio, so this ca be used as a control to calculate the relative copies of different genes. For details of these calculations, see the Methods section.