Let's see if I can simplify this. Not sure what instrument you're interested in, so
The treble clef measure illustrates the "Melodic Drum" line. The first note is the note in question. The second note is one octave above. The third is one octave up from that. And the fourth one is 3 octaves up from the note you're wondering about -- a much more legible "E".
The bass clef measure illustrates the Taiko in a similar way. Walking up octave-by-octave, you can see it's a D. And actually, the D is only one whole step lower than the "Melodic Drum Line" E. These notes would've been much easier to read if the transcriber had avoided relying on so many ledger lines. He could've used 8vb / 15vb / etc, and maybe moved the "Melodic Drum" notation to the bass clef -- but I'm unfamiliar with percussion notation, so I can't say whether such notation would've been allowed.
I saw no lower notes in the score. The lowest note notated is D1, around 37Hz
according to this table. I haven't had a chance to listen critically to determine whether the performance is different from the score around 0:55 - 0:56, but I didn't hear anything obvious through my headphones.