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Everyday I open up my phone I have a picture of some type of pop up with a trojan virus or battery has been infected warning. I have tried malware scan, virus scans the phones own system scans, nothing works. I've tried the safe mode virus search and can't find it. These same pop ups also come two to three times a day.
Help???
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All of those are ads scaring you in browser.they trick you to install their software to fix but they are lying there are no viruses. its normal for every phone in browser.. im also frustrated when that happens because it vibrates.and says affected by watching porn.. only thing you do if you are rooted is download adblock .. if not then just click home the house icon it is located near in the url box
 
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As none of the anti-malware and antivirus utilities you tried were effective, there's a good chance some exploit has inserted itself into the operating system on your phone. There are several partitions in your phone's internal storage, a general user partition is where all your files and app settings are stored but there are also some restricted system partitions that are used only by the Android system that runs on your phone. Most malware only mess up things in that general user partition but recently some have evolved and are now able to infect the protected operating system.
Anti-malware and AV utilities installed as a general user are more effective on the general user partition but not as much when it involves the restricted system partitions. If your phone's operating system is compromised, a Factory Reset won't help in this case either, that only wipes the general user partition and an infected operating system will remain as is. To clean up a compromised system you'll have to reflash your phone with a factory ROM. Be sure to back up your personal data first.
http://www.androidrootz.com/2015/05/how-to-unroot-galaxy-s6-and-s6-edge.html
http://forum.xda-developers.com/galaxy-s6-edge/general/sm-g925f-s6-firmware-thread-t3078841
This is a last resort kind of thing so if others know of less drastic solutions please correct me and chime in.
 
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