Guitar intonation is important and can make a big difference to your instrument if it is set up correctly
Sometimes your guitar will be out of tune even after you tune it, which means your intonation is out. You can tell when your intonation is out if an open string harmonic at the 12th fret A�(lightly touch string at the 12th fret and pluck it) A�and the fretted note one octave higher (hold the string down at the 12th fret and pluck it) are not the same. Guitar intonation tuning is making the notes of each fret of a string equal to the chromatic reference pitches, or the natural musical scale temperaments by adjusting string lengths at the saddles. The chromatic musical scale and natural musical scale are similar, so tuning the natural musical scale of the brass instruments is preferred. This makes the twelfth fret note of a string theoretically be about one octave higher than its corresponding open string note pitch, and the seventh fret note octave pitch similar as the corresponding seventh fret harmonic pitch.
To rectify this:-
Depending on your saddle, the intonation can be adjusted by filing an angle on the saddle specific to the string in question to adjust the string length.
If the note on the 12th fret is sharp, the saddle for that string needs to be moved back away from the headstock.
If the note on the 12th fret is flat, the saddle for that string needs to be moved forward toward the headstock.
Compare the twelfth fret note to the corresponding twelfth fret harmonic pitch with electronic tuner for meter. This is decent intonation tuning for notes between nut and twelfth fret range
If the angle already there is incorrect and correction could affect your action negatively, then, this may require fitting a new saddle.