I need to access the joomla user table jos_users for login checking from external php script [codeignitor].
joomla storing password like this
Joomla! uses PhPass.
root/libraries/phpass/PasswordHash.php
have a look here. you will see here how the password is generating.
The $2y is the default (and preferred) prefix on bcrypt hashes.
As for code, you'll want to look inside JUserHelper's hashPassword and verifyPassword methods to see how Joomla's working with things right now.
https://github.com/joomla/joomla-cms/blob/3.4.1/libraries/joomla/user/helper.php#L296-L387
https://docs.joomla.org/API15:JUserHelper/getCryptedPassword
https://docs.joomla.org/API15:JUserHelper/getSalt
Check the links, I hope you it will helpful :)