So I've checked the mean length of my reads here:
Great!
Next, how long is the amplicon you sequenced?
Then calculate the overhead as shown here!
It is common for reverse reads to show a decrease in the quality of the reads?
Yes, though it's usually not this bad. Take a look at this example from the Atacama soils tutorial.
Because my last two sequencings my analyses were conducted by a single-end approach, due to bad quality of the reverse reads.
Maybe a problem with the PCR, or the sequencing core, or something spooky! 