First of all, you have to configurate your drone properly, I have seen that you are with the default parameters, so you must follow this guide https://ardupilot.org/copter/docs/tuning-process-instructions.html or press ALT+A in Mission Planner and follow the steps. You haven’t got a power module which tells you the voltage and current of the battery, and for me, that is mandatory.
The PWM of your motors is not equal while hovering, so you probably have your motors tilted.
You have problem with vibes, as soon as your motors increase rpm, you have a lot of vibes. Check your motors and propellers, maybe you have to balance them.
And I think that is the problem of your negative altitude, with such high vibes, the IMU cannot estimate the altitude properly. And of course neither the roll and pitch.
The second compass is being interfered by power cables close to your Pixhawk, since it depends on your throttle, so try to move them away. But your first compass is good.
So finally I think that you crashed mainly for the high vibes. After you follow the guide and you solve all the problems, make another flight only hovering in AltHold about 2 or 3 minutes and post that log.