Bah!

DROP   TABLE IF EXISTS temp_individual_genotype_a;
Query OK, 0 rows affected (0.02 sec)

CREATE TABLE           temp_individual_genotype_a
    -> (INDEX pk_ish (variation_id, population_id, allele_code_id))
    -> SELECT
    ->   variation_id, population_id, allele_code_id_1 AS allele_code_id,
    ->   `COUNT(*)` AS N
    -> FROM temp_individual_genotype_a1 LIMIT 6000000;
Query OK, 6000000 rows affected, 1 warning (6.08 sec)
Records: 6000000  Duplicates: 0  Warnings: 1

INSERT INTO  temp_individual_genotype_a
    -> SELECT
    ->   variation_id, population_id, allele_code_id_2 AS allele_code_id,
    ->   `COUNT(*)` AS N
    -> FROM temp_individual_genotype_a2 LIMIT 6000000;
Query OK, 6000000 rows affected, 1 warning (20.63 sec)
Records: 6000000  Duplicates: 0  Warnings: 1

OPTIMIZE TABLE temp_individual_genotype_a;
+---------------------------------------------------------------------+----------+----------+----------+
| Table                                                               | Op       | Msg_type | Msg_text |
+---------------------------------------------------------------------+----------+----------+----------+
| solanum_lycopersicum_variation_26_79_240.temp_individual_genotype_a | optimize | status   | OK       |
+---------------------------------------------------------------------+----------+----------+----------+
1 row in set (2.96 sec)

EXPLAIN
    -> SELECT *, COUNT(*), SUM(N) FROM temp_individual_genotype_a GROUP BY variation_id, population_id, allele_code_id;
+----+-------------+----------------------------+------+---------------+------+---------+------+----------+---------------------------------+
| id | select_type | table                      | type | possible_keys | key  | key_len | ref  | rows     | Extra                           |
+----+-------------+----------------------------+------+---------------+------+---------+------+----------+---------------------------------+
|  1 | SIMPLE      | temp_individual_genotype_a | ALL  | NULL          | NULL | NULL    | NULL | 12000000 | Using temporary; Using filesort |
+----+-------------+----------------------------+------+---------------+------+---------+------+----------+---------------------------------+
1 row in set (0.00 sec)