I have made graphs showing the coverage for the crp and cyaA genes for the supposedly cya mutants and two KW20 samples:
The cya graph shows that the whole gene is intact and there is no obvious interruption. The crp graph, however, shows that there is a dramatic interruption in the "cya" strains (and I have verified that this happens only in these strains).
This interruption occurs between position 1015189 and 1015190 in the reference sequence, giving us the following: CAAAATACATCAC[drop in coverage]GTCAAG
The coverage drops about 10x between the C and G, and drops another ~2x after the G. I can't say where exactly the insertion begins with this data is presented (it depends on the first base of whatever is inserted here and may be altered by mismatch tolerance during the alignment process) but it is pretty spot on to where Rosie had predicted in her previous post.
Anyway, what this data tells me is that all our "cyax" strains are actually only "crpx" strains. I'll keep you updated if there are any additional developments in this issue.