As I know, e2e testing uses your files served by your web server, for unit test they are served directly by karma, e2e testing is mainly used to make sure your page works the way you expect, end-to-end testing of your server and client side . That's why you usually never expected to have 100% e2e coverage because they are more fragile.
This way people focus on the unit test (checking all edge cases) and they add the e2e test to make sure the page behavior works correctly.
You can use istanbul and create a coverage report with karma.
http://gotwarlost.imtqy.com/istanbul/
Or in this article: http://lkrnac.net/blog/2014/04/measuring-code-coverage-by-protractor/ summarize how to use the e2e protractor to generate a coverage report for your e2e tests. Using this tool: https://github.com/r3b/grunt-protractor-coverage
Hope this helps.
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