A high school for Spanish speakers that most New Yorkers have probably never heard of earns the city’s highest overall score; an elementary school many parents strive to live near, P.S. 6 on the Upper East Side, earns just a B, and a school beloved by parents in the prospering Inwood section of Manhattan gets an F.

These eagerly awaited grades are among more than a thousand issued by the Department of Education to public schools across the city this morning. They will be used to determine a variety of rewards and punishments, from bonuses for principals and teachers to the shutdown of schools deemed beyond repair.

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At a press conference this morning, Mayor Bloomberg said the grades should serve as a “wake-up call” to teachers and principals at failing schools. “The school system is not run for the people that work in it,” he said. “The school system is run for the kids.”

He added, “Is this a wake-up call for the people that work there? You bet. That’s what we’re trying to do.”

Students at the 50 schools given F’s will have the opportunity to apply to transfer this spring.

Many of the grades defy public perceptions about the city’s best public schools. A well-regarded school on the Lower East Side, the NEST+m school, earned just a B, as did coveted elementary schools P.S. 321 in Park Slope, P.S. 87 on the Upper West Side, and P.S. 234 in TriBeCa.

School officials have been computing the grades, which analyze the 2005-2006 school year, for months, using a complicated formula that takes account of many factors but depends primarily on how students score on annual math and reading tests. How well students perform from one year to the next determines the largest portion of the grade, 55%, while absolute test scores make up 30%. The rest of the grade, 15%, is based on so-called environmental factors, including attendance figures and the survey results of parent, teacher, and student satisfaction.

The grading of high schools also weighs factors such as the percentage of students who graduate, how many students earn Regents diplomas, and how well students perform on the Regents exams.

Extra points are given to schools that close a gap between the performance of black and Hispanic students and the rest of the city’s students. The extra points are what helped push Manhattan Bridges High School to a score of 104.4, the highest in the city.

The highest-rated elementary school was P.S. 307, Eames Place in the Bronx. The top middle school in the city is M.S. 327, the Comprehensive Model School Project in the Bronx.

The highest-rated elementary school in Manhattan was P.S. 9, Sarah Anderson School, on the Upper West Side.

Overall scores range from 0 to 100 — with some schools, including the worst in the city, the middle school at the American Sign Language School, even dipping below zero. The letter grades were issued according a curve that aimed to give about 15% of schools D’s and F’s, and 15% A’s. But the final grades were higher, with 23% of schools receiving A’s and only 12% getting D’s and F’s. The city schools chancellor, Joel Klein, said extra-credit points given for closing a racial achievement gap pushed grades up.

Mr. Bloomberg said the report cards were a positive referendum on the changes he has made to the public schools in the last five years. He noted that more than one-third of schools given A’s were created under his administration, and that schools given extra freedoms over their budget and curriculum under a test program last year, known as “empowerment” schools, were graded especially well. All schools in the city this year follow the empowerment model.

The next step, Mr. Bloomberg said, is to use the grades to make decisions about schools’ futures. “Now that we have the information, we can start turning schools around,” he said.

Mr. Klein said that failing schools would be offered help. The best-ranked schools in the city, those that received A’s and a high rating on a second qualitative review by outside consultants, will be asked to become “demonstration schools” that can use extra funding to set up sites at their campuses to share ideas and strategies with other schools.

A new citywide data system that compiles the test scores of every school in the city, known as ARIS, will help principals research schools with similar populations to learn how they produced better results, Mr. Klein said.

Schools that seem unlikely to improve could be shutdown or see their principals fired. Mr. Klein said officials would study principals’ quality reviews, their track records, and their schools’ test score history before making decisions.

Principals at highly ranked schools can also receive bonuses at the end of the year tied to the grades, as can some teachers.

Mr. Bloomberg said one part of the new data was surprising: a finding that neither the length of a principal’s tenure nor the size of a school seemed to correlate to how well a school performed. He said many expected principals with longer careers to do better and small schools to outrank large ones. The Bloomberg administration has sought to break down large schools into smaller ones — a move, the mayor said, that is still a good idea.

Messrs. Bloomberg and Klein said that they are bracing for complaints over the grades.

Indeed, a parent advocate who has long argued against standardized tests, Jane Hirschmann, rose at the press conference this morning to complain about the report cards’ heavy emphasis on test scores.

She said that basing decisions on how to teach children on test results might push enriching subjects like art instruction out of the classroom. “Parents better rise up, because that is tantamount to child abuse,” she said.

Reversing a signature last line used by Mr. Bloomberg in press conferences, she added, “It’s a sad day for New York.”

Other findings in the review:

P.S. 9, Sarah Anderson, was the highest-ranked elementary school in Manhattan.

The West Side Collaboration Middle School in Manhattan was the highest-rated middle school, earning a score of 82.19.

A popular elementary school in Manhattan, P.S. 87, scored 52.79, earning a B.

A popular elementary school in TriBeCa, P.S. 234 scored 52.73, earning a B.

The highest rated school in the city, the Manhattan Bridges High School, got just a P for proficient on its quality review, two rankings below the top score, Outstanding.

P.S. 6 on the Upper East Side, Lillie D. Blake, scored a 63.31, earning a B. It got a P on its quality review.

P.S. 321 in Park Slope scored 55.35, earning a B. It got a W for well-developed on its quality review.

P.S. 107 in Park Slope scored a 70.03, earning an A.

P.S. 9 on the Upper West Side scored an 83.36, earning an A. It got a W on its quality review.

Muscota Middle School in Inwood received an F.

NEST elementary and middle school scored a 51.5, earning a B.

A popular elementary in Manhattan, P.S. 87, scored a 52.79, earning a B.

A popular elementary in TriBeCa, P.S. 234, scored a 52.73, earning a B.

P.S. 116 elementary in Manhattan, scored 73.96, earning an A.

P.S. 183 elementary in Manhattan, scored 64.65, earning an A.

Riverdale/Kinsgbridge elementary school earned a C.

Staten Island’s elementary and middle schools had the lowest percentage of A’s in the city, 2%.