One option is to put the subquery in a LEFT JOIN:
select sum ( t.graduates ) - t1.summedGraduates
from table as t
left join
(
select sum ( graduates ) summedGraduates, id
from table
where group_code not in ('total', 'others' )
group by id
) t1 on t.id = t1.id
where t.group_code = 'total'
group by t1.summedGraduates
Perhaps a better option would be to use SUM with CASE:
select sum(case when group_code = 'total' then graduates end) -
sum(case when group_code not in ('total','others') then graduates end)
from yourtable