gistfile1.txt

SELECT t.`id`, t.`reference_id`, t.`tenant_id`, t.`amount`,
    (
    SELECT SUM(t.`amount`)
        FROM `transaction` t 
    ) AS total
FROM `transaction` t
WHERE total > 0
GROUP BY t.`reference_id`;

SELECT t.id, t.reference_id, t.tenant_id, t.amount
FROM transaction t
WHERE total =
(
SELECT total
FROM (
SELECT SUM(t.amount) as total
FROM transactions t
) t
GROUP BY t.reference_id
WHERE total > 0 ) t

SELECT t.id, t.reference_id, t.tenant_id, t.amount, SUM(t.amount) total
FROM transaction t
GROUP BY t.reference_id
HAVING total > 0

SELECT t.id, t.reference_id, t.tenant_id, t.amount,
(
SELECT SUM(t.amount)
FROM transaction t
WHERE t.deleted_at IS NOT NULL
) AS total
FROM transaction t
GROUP BY t.reference_id
HAVING total > 0