So basically I have noticed this weird problem which happens on any ROM or stock and even custom or stock kernel. Whenever I fully discharge my phone from 100% to 0 till it you know completely shuts off and then recharge it I can get decent battery life of about 6 to 7 hours on screen time however if say I started re charging my phone from 2 or 5 or 10 % and then use it my SOT time seems to decrease to about 3 to 4 hours which sucks. Does anyone know what might be causing this ?
Historically this was a rough way to calibrate your battery although with lithium it's actually detrimental to the longevity of it.
From the years I've had mobile phones (early 90s) and the tests I've done over those years I've come to find that is how you use your phone that effects battery the most, en more so the content on your phone, so if you've got Twitter, Facebook. Snapchat, WhatsApp all running as well as apps which have push ads and live widgets, then your device will suffer for it.
Keeping the device light with only apps that you need and by not allowing it to completely die not over charging your battery will provide the best and longest experience.
I average 2 days battery with around 8-9 hours SOT, with some tweaks and a push I can get over 10 hours with 10 hours 50 minutes being my longest.
There should be no reason why charging from 0 or 10% would have a difference on your SOT.
Lighten the load, use a stock kernel and about overcharging your device and see how you get on