The school ranks highly on the progress pupils make
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Many secondary schools have plummeted down league tables after the ministers raised the bar for expected achievement.
Schools are now judged on how many pupils achieve a good set of GCSE passes including English and maths.
Before, the measure was good grades in any five GCSEs (A* to C).
The change has been a blow to Grange Secondary School in Oldham, Lancashire, which has a high proportion of children who do not speak English at home.
The school ranks high on the new contextual value-added measure, meaning that pupils who go there achieve more than similar children at other schools.
But it has dropped down from a position near the top of the local league table - when all GCSEs were counted - to the bottom.
While 69% of pupils passed five GCSEs at good grades this year, only 15% managed to get five good GCSE passes including English and maths.
Across England, 46% of pupils achieved five good GCSEs including England and maths, while about 59% passed five GCSEs of any subject at good grades.
Ministers insist it is right to give parents a fuller picture of a school's achievement and to expose schools which do not do well in English and maths.
But secondaries - such as Grange School - which serve many very deprived children who struggle with English - say this should be taken into account.
Grange's head teacher Graeme Hollinshead, said: "Our pupils are coming to our school with levels in English and maths which are lower than the national average.
"It takes some of them a bit longer to get to the level of C or above."