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Hollow, Bonky E String

Hey gang, I have a complaint about my mim j. I have never been real stoked on the bass, there Is a massive dead spot on the 5th and 6th fret on g that totally chokes the note out. Well a few months ago I put DA Chrome Flats on it, and I've started noticing lately, my low E string is tubby and thin sounding. Loud finger attack, but thin and quiet tone, not much sustain. I didnt notice it before, but that doesn't mean it wasn't bad. Now the open e is fine, so it's not a nut issue. I believe it's a string or wood issue. My pup heights are correct, btw. Also, it's not quite as bad with the neck pup soloed as the neck, so I don't know what's up.
 
Might be a fret job too , recheck everything on the bass , sometime we forget the obveous , **** happen right . Or did you get your bass to a repair man , he might/must find what s the problem on your bass . Also happened to have defect new strings , good luck with this