//Join node table with a field table and search for published nodes of a certain type with a specific field value:
SELECT node.nid AS node_id,
  LEFT(node.title, 10) AS node_title, field_data_field_reference_database_id.field_reference_database_id_value as ref_id
FROM node
LEFT JOIN field_data_field_reference_database_id
  ON node.nid = field_data_field_reference_database_id.entity_id
WHERE type='location'
  AND status='1'
  AND field_data_field_reference_database_id.field_reference_database_id_value IS NULL;