Contacts missing in icloud and Iphone

Just did a backup to icloud for first time and most of the contacts are not on icloud and some are now gone from the phone. What happened and how do I get them all to transfer to icloud.

Sounds like you have some contacts in the From My Mac groups that are not in iCloud; they may have been synced to your phone at some point.  On your iPhone, go to Settings>iCloud, turn Contacts to Off and choose Delete from My iPhone.  Then check you contacts to confirm that some are still there.  If so, check a few against your contacts on icloud.com to confirm they are not on icloud.com. 
If you still have contacts on your phone that are not on icloud.com at this point you can add them to iCloud by doing the following:
If you haven't already done so, go to Settings>iCloud on your phone, turn Contacts off and choose Delete from My iPhone.
Download the app My Contacts Backup.  (If there are 500+ contacts remaining on your phone you will need the Pro version.)  Use this app to backup the remaining contacts on your phone as a vCard attachment to an email and send it to yourself.  Confirm that you have received the email on your phone.
Go to Settings>Mail,Contacts,Calendars>Default Account (in the Contacts section) and confirm this is still set to iCloud.
Open the My Contacts Backup email and tap the attachment to import the contacts from the On My Mac groups to iCloud.  Go to icloud.com to confirm that they appear there.
If the On My Mac contacts are still on your phone, go to Settings>iCloud, turn Contacts off and choose Delete from My iPhone.  Open the My Contacts Backup app, tap the gear-shaped icon the bottom right.  In the window that opens, scroll to the bottom and tap Remove All Contacts.  Then go to Settings>iCloud and turn Contacts back on.  The duplicate contacts from the On My Mac groups should now be gone from your phone and they should all be in iCloud.

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