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MySQL Mostrar el estado de la tabla, el incremento automático no es correcto

Es una característica... no un error.

Las estadísticas de la tabla se almacenan en caché. Para deshabilitar el caché y tener siempre la última versión, debe cambiar la variable del servidor que indica la duración del borrado de caché a 0:

SET PERSIST information_schema_stats_expiry = 0

El valor predeterminado de esta propiedad ha cambiado a 86400 (24 horas) en Mysql 8.x

Ejemplo:

SET PERSIST information_schema_stats_expiry = 86400
-- 86400 is the default value of mysql 8.x  if you have never changed this you don't need to set this


show variables like 'information_schema_stats_expiry';

+---------------------------------+-------+
| Variable_name                   | Value |
+---------------------------------+-------+
| information_schema_stats_expiry | 86400 |
+---------------------------------+-------+

create schema mytest;

create table `test` (
    `id` int(5) not null auto_increment,
    `name` varchar(256),
    PRIMARY KEY(`id`)
);

insert into test values(null,'name1')
insert into test values(null,'name2')
insert into test values(null,'name3')

show table status where name like 'test';
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| Name | Engine | Version | Row_format | Rows | Avg_row_length | Data_length | Max_data_length | Index_length | Data_free | Auto_increment | Create_time         | Update_time         | Check_time | Collation          | Checksum | Create_options | Comment |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| test | InnoDB |      10 | Dynamic    |    3 |           5461 |       16384 |               0 |            0 |         0 |              4 | 2018-10-09 15:32:15 | 2018-10-09 15:32:16 | NULL       | utf8mb4_0900_ai_ci |     NULL |                |         |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
-- The Auto_increment field is correctly set to 4.. but is now cached.

insert into test values(null,'name3');

show table status where name like 'test';
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| Name | Engine | Version | Row_format | Rows | Avg_row_length | Data_length | Max_data_length | Index_length | Data_free | Auto_increment | Create_time         | Update_time         | Check_time | Collation          | Checksum | Create_options | Comment |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| test | InnoDB |      10 | Dynamic    |    3 |           5461 |       16384 |               0 |            0 |         0 |              4 | 2018-10-09 15:32:15 | 2018-10-09 15:32:16 | NULL       | utf8mb4_0900_ai_ci |     NULL |                |         |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
-- The Auto_increment is still 4 (it was cached).

drop schema mytest

Ahora cambiamos la configuración:

SET PERSIST information_schema_stats_expiry = 0

y ejecutamos la misma prueba:

show variables like 'information_schema_stats_expiry'


+---------------------------------+-------+
| Variable_name                   | Value |
+---------------------------------+-------+
| information_schema_stats_expiry | 0     |
+---------------------------------+-------+

create schema mytest;
create table `test` (
    `id` int(5) not null auto_increment,
    `name` varchar(256),
    PRIMARY KEY(`id`)
);

insert into test values(null,'name1');
insert into test values(null,'name2');
insert into test values(null,'name3');

show table status where name like 'test';

+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| Name | Engine | Version | Row_format | Rows | Avg_row_length | Data_length | Max_data_length | Index_length | Data_free | Auto_increment | Create_time         | Update_time         | Check_time | Collation          | Checksum | Create_options | Comment |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| test | InnoDB |      10 | Dynamic    |    3 |           5461 |       16384 |               0 |            0 |         0 |              4 | 2018-10-09 15:32:49 | 2018-10-09 15:32:49 | NULL       | utf8mb4_0900_ai_ci |     NULL |                |         |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
--  Auto_increment is 4, but the result is not cached!

insert into test values(null,'name3');



show table status where name like 'test';


+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| Name | Engine | Version | Row_format | Rows | Avg_row_length | Data_length | Max_data_length | Index_length | Data_free | Auto_increment | Create_time         | Update_time         | Check_time | Collation          | Checksum | Create_options | Comment |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
| test | InnoDB |      10 | Dynamic    |    4 |           4096 |       16384 |               0 |            0 |         0 |              5 | 2018-10-09 15:32:49 | 2018-10-09 15:32:49 | NULL       | utf8mb4_0900_ai_ci |     NULL |                |         |
+------+--------+---------+------------+------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+--------------------+----------+----------------+---------+
-- The  Auto_increment field is now 5 (a correct, not cached value)

drop schema mytest;