SharePoint 2013 - Not able to see Navigation Panel, Add an App, Site Permission settings

In SharePoint 2013, if you modify any thing in Master Page file, it may cause below issues:

1. Site Settings->navigations not appearing correctly as mentioned below.

2. Site Settings->Site Permissions, not able to find Grant Permission, Check permission tool bar as mentioned below.

3. Site Contents->Add an app, page should be blank.

The above issues are may be possible of having below scripts in Master Page.

<script type="text/javascript" src="/_layouts/15/init.js"></script>

If it exists, remove it and save and check the page.