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When we download a .FTF or ROM file as a stock ROM, is there a way to verify that it is really the stock ROM and is not modified by someone?
Yes, you can check the SHA1 or MD5 checksum.
You didn't specify which ROM you are downloading. Let's have a look at the Nexus stock ROMs:
There is a download link and a version number and checksums listed like that:
To verify a checksum you can do it via command line:
$ md5sum mantaray-jdq39-factory-d79f489e.tgz
$ openssl sha1 mantaray-jdq39-factory-d79f489e.tgz
If it matches with the one stated at the google page, you can assume the file is not corrupted or modified.
The terminal commands only work out of the box in MacOS or Linux. To verify checksums in Windows there is a tool by Microsoft called Checksum Integrity Verifier.
Thanks. Is there somewhere to find md5sums for sony(xperia z) official ROMs? I have downloded Xperia_Z_C6602_10.3.A.0.423_Generic US
Well, Sony is neither offering direct download links nor telling anything about file integrity. The only thing you can do is doing it like described here: Download via official Sony Software. In future, don't buy Sony devices :p