Hibernate native query does not create auto incremented primary key

Question

I have a table generated using liquibase as follows

       <createTable tableName="MyTable">
            <column name="id" type="BIGINT" autoIncrement="true">
                <constraints primaryKey="true" nullable="false"/>
            </column>
            <column name="a" type="VARCHAR(255)"/>
            <column name="b" type="VARCHAR(255)"/>
            <column name="c" type="BIGINT"/>
            <column name="fk_id" type="BIGINT"/>
        </createTable>

Then I have a native query that I use to persist this object

 EntityManager em = session.getEntityManagerFactory().createEntityManager();

        em.getTransaction().begin();
        em.createNativeQuery(
            "INSERT INTO MyTable (a, b, c, fk_id)"
                + " VALUES ( :a, :b, :c, :fk_id)")
            .setParameter("a", myObj.geta().toString())
            .setParameter("b", myObj.getb().toString())
            .setParameter("c", myObj.getc()))
            .setParameter("fk_id",
                myObj.getOtherObj().getId)
            .executeUpdate();
        em.getTransaction().commit();
        em.close();

I have set the JPA annotation to autoincrement this ID as follows

@Id
  @JsonProperty
  @GeneratedValue(strategy = GenerationType.IDENTITY)
  Long id;

Yet the ID is null in the database, what have I missed? I also tried inserting a null value in place of the primary key but it still does not auto increment it to a value?

Also tried changing it to

@Id
    @GeneratedValue(strategy = GenerationType.AUTO, generator = "native")
    @GenericGenerator(name = "native", strategy = "native")
    @Column(name = "id", updatable = false, nullable = false)
    private Long id;

That didnt seem to work

Also tried using GenerationType.Table and GenerationType.SEQUENCE

Here is the SQl that I see

Hibernate: 
    /* dynamic native SQL query */ INSERT 
    INTO
        MyTable
        (a, b, c, d, fk_id) 
    VALUES
        (?, ?, ?, ?, ?)

I then log the persisted entity to see if it gets an auto incremented ID

INFO  [2019-02-25 16:24:11,611] Successfully persisted myObj: 'null:FK_table{its values} other stuff gets saved' 

Notice that the ID column is null.

I also explicitly set the ID to null before executing the query but still no luck I tried executing the same query using a different mysql client and that seems to work