The long line of voltage follwing the firing voltage is the firing time, which is the time elapsed when the spark is actually occurring. Differences in firing voltage and other parts of the waveform reflect conditions in the cylinder.
New school. Don't feel like looking up wiring diagrams or hooking stuff up? Simply use a GTC SmarTach+ COP tester. (See Figs. 9 and 10.) By placing its probe on the top of an ignition coil, it instantly gives an engine RPM, burn time and coil kV reading. So, instead of comparing waveforms, you simply comprare burn time and coil kV between coils.
This method can also be used to check misfirng cylinders on vehicles that use spark plug wires. The probe can be pointed at different spark plug wires. All the technician needs to do is compare results.
3. Swap coils and test again.
It is important to note that regardless of whether you are diagnosing ignition the old or new school way, ignition is always affected by conditions in a cylinder. So, low cylinder compression from a washed down cylinder can make a good coil look bad. (See Fig. 11.)
Simply swap a known "good" coil with the suspect one, and check again your readings. If the misfire changes cylinders, simply replace the suspect ignition coil. If it doesn't, the vehicle has a fuel or mechanical problem in that cylinder.
Presuming the reading does not change, the next step would be to remove the spark plug and do a compression test. If the vehicle does not have a dead misfire, it might be wise to check timing with a pressure transducer or do a cylinder leak down test. Now, if everything checks out, it is time to start testing the fuel injectors.
As for this 2006 Scion xB, the misfire changed cylinders, so it was fixed with a new coil.