Just to clarify, 49 is the unicode value for the character "1". Each character has its own number and that's whet you are seeing when you read an int from System.in.
For what it's worth, I've never used System.in.read() directly in over 10 years of programming Java. Macos's suggestion of using a Scanner is worth considering. BufferedReader is another option but that's a bit old fashioned these days.