Why default ‘mysql’ database created using MyISAM engine instead of InnoDB?

I am using MySQL version 5.6 which has the default MySQL engine as InnoDB, that is if you don’t specify an engine while creating tables, it is created using InnoDB.

But today, i noticed that the default mysql database is created using ‘MyISAM’ instead of InnoDB.

Any clue, why is it so?

Database changed
mysql> show tables;
+---------------------------+
| Tables_in_mysql           |
+---------------------------+
| columns_priv              |
| db                        |
| event                     |
| func                      |
| general_log               |
| help_category             |
| help_keyword              |
| help_relation             |
| help_topic                |
| innodb_index_stats        |
| innodb_table_stats        |
| ndb_binlog_index          |
| plugin                    |
| proc                      |
| procs_priv                |
| proxies_priv              |
| servers                   |
| slave_master_info         |
| slave_relay_log_info      |
| slave_worker_info         |
| slow_log                  |
| tables_priv               |
| time_zone                 |
| time_zone_leap_second     |
| time_zone_name            |
| time_zone_transition      |
| time_zone_transition_type |
| user                      |
+---------------------------+
28 rows in set (0.00 sec)

Here is my cnf file:

# For advice on how to change settings please see
# http://dev.mysql.com/doc/refman/5.6/en/server-configuration-defaults.html

[mysqld]
init-connect='SET NAMES utf8'
max_connections = 500
#
# Remove leading # and set to the amount of RAM for the most important data
# cache in MySQL. Start at 70% of total RAM for dedicated server, else 10%.
# innodb_buffer_pool_size = 128M
#
# Remove leading # to turn on a very important data integrity option: logging
# changes to the binary log between backups.
# log_bin
#
# Remove leading # to set options mainly useful for reporting servers.
# The server defaults are faster for transactions and fast SELECTs.
# Adjust sizes as needed, experiment to find the optimal values.
# join_buffer_size = 128M
# sort_buffer_size = 2M
# read_rnd_buffer_size = 2M
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock

# Disabling symbolic-links is recommended to prevent assorted security risks
symbolic-links=0

# Recommended in standard MySQL setup
#sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

Here is the mysqldump of one of these tables:

CREATE TABLE `columns_priv` (
  `Host` char(60) COLLATE utf8_bin NOT NULL DEFAULT '',
  `Db` char(64) COLLATE utf8_bin NOT NULL DEFAULT '',
  `User` char(16) COLLATE utf8_bin NOT NULL DEFAULT '',
  `Table_name` char(64) COLLATE utf8_bin NOT NULL DEFAULT '',
  `Column_name` char(64) COLLATE utf8_bin NOT NULL DEFAULT '',
  `Timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `Column_priv` set('Select','Insert','Update','References') CHARACTER SET utf8 NOT NULL DEFAULT '',
  PRIMARY KEY (`Host`,`Db`,`User`,`Table_name`,`Column_name`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_bin COMMENT='Column privileges';


mysql> show engines;
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
| Engine             | Support | Comment                                                        | Transactions | XA   | Savepoints |
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+
| MRG_MYISAM         | YES     | Collection of identical MyISAM tables                          | NO           | NO   | NO         |
| CSV                | YES     | CSV storage engine                                             | NO           | NO   | NO         |
| MEMORY             | YES     | Hash based, stored in memory, useful for temporary tables      | NO           | NO   | NO         |
| BLACKHOLE          | YES     | /dev/null storage engine (anything you write to it disappears) | NO           | NO   | NO         |
| MyISAM             | YES     | MyISAM storage engine                                          | NO           | NO   | NO         |
| FEDERATED          | NO      | Federated MySQL storage engine                                 | NULL         | NULL | NULL       |
| ARCHIVE            | YES     | Archive storage engine                                         | NO           | NO   | NO         |
| InnoDB             | DEFAULT | Supports transactions, row-level locking, and foreign keys     | YES          | YES  | YES        |
| PERFORMANCE_SCHEMA | YES     | Performance Schema                                             | NO           | NO   | NO         |
+--------------------+---------+----------------------------------------------------------------+--------------+------+------------+

Answer

14.5.4 Converting Tables from MyISAM to InnoDB

…

Important

Do not convert MySQL system tables in the mysql database (such as user or host) to the InnoDB type. This is an unsupported operation. The system tables must always be of the MyISAM type.

…

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Answer