You can probably get better support for SqlLite through SqlLite support:
http://sqlite.org/support.html.
If the JavaScript version of SqlLite interface is not available, but the C# version is, then you could create a Windows Runtime component written in C#, add the SqlLite specific code to the C# project and then call the C# class/function from the WinJS app
to do the SQLLite specific work for you.
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