How to compute merkle root without coinbasetxn? How do you build a merkle root without a coinbase transaction? I compute the merkle root without the coinbase portion and I get a different root then the submitter.
What pool are you using? As an example, if you hit (POST a request to) eligius pool (http://gbt.mining.eligius.st:9337) with the body as 

{"id": 0, "method": "getblocktemplate", "params": [{"capabilities": ["coinbasetxn", "workid", "coinbase/append"]}]}

as taken from https://en.bitcoin.it/wiki/Getblocktemplate you will get a coinbasetxn field returned in the json.