Try this:
SELECT *, (IF(@schoolId=@schoolId:=A.schoolId, @s:=@s+1, @s:=1)) serial_number
FROM (SELECT SED.SchoolId, SAED.*
FROM StudentAnswerExamData SAED
INNER JOIN StudentEnrollmentDetails SED ON SED.StudentEnrollmentDetailsId = SAED.StudentEnrollmentDetailsId
WHERE SED.ExamCategoryId = 2 AND SED.ExamId = 2 AND SED.Standard = 5 AND
SED.CompanyId = 2
ORDER BY SED.SchoolId, SAED.Percentage DESC
) AS A, (SELECT @s:=1, @schoolId:=0) AS s;
Check this Link SQL FIDDLE DEMO
OUTPUT
| SCHOOLID | STUDENTANSWEREXAMDATAID | STUDENTID | STUDENTENROLLMENTDETAILSID | EXAMCATEGORYID | EXAMID | STANDARD | COMPANYID | UPLOADEDBYID | UPLOADEDDATETIME | MODIFIEDBYID | MODIFIEDDATETIME | MARKFORDELETE | SEATNO | NOOFCORRECT | NOOFINCORRECT | NOOFMISSING | MARKSSCORED | PERCENTAGE | SCHOOLRANK | DISTRICTRANK | STATERANK | NATIONALRANK | PROCESSEDSTATUS | FILEPATH | @S:=1 | @SCHOOLID:=0 | SERIAL_NUMBER |
|----------|-------------------------|-----------|----------------------------|----------------|--------|----------|-----------|--------------|--------------------------------|--------------|--------------------------------|---------------|------------|-------------|---------------|-------------|-------------|------------|------------|--------------|-----------|--------------|-----------------|----------|-------|--------------|---------------|
| 23 | 4 | 1546 | 2044 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1023052901 | 38 | 37 | 0 | 113 | 75.33 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 54 | 6 | 1557 | 2055 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1054052901 | 25 | 46 | 4 | 96 | 64 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 56 | 16 | 1550 | 2048 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1056052903 | 36 | 39 | 0 | 111 | 74 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 56 | 15 | 1549 | 2047 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1056052902 | 30 | 43 | 2 | 103 | 68.67 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 2 |
| 56 | 13 | 1548 | 2046 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1056052901 | 27 | 48 | 0 | 102 | 68 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 3 |
| 74 | 7 | 1551 | 2049 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1074052901 | 21 | 54 | 0 | 96 | 64 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 78 | 8 | 1558 | 2056 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1078052901 | 37 | 38 | 0 | 112 | 74.67 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 108 | 9 | 1547 | 2045 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1108052901 | 26 | 46 | 3 | 98 | 65.33 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 114 | 10 | 1555 | 2053 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1114052901 | 28 | 47 | 0 | 103 | 68.67 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 133 | 5 | 1556 | 2054 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1133052901 | 44 | 29 | 2 | 117 | 78 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 160 | 3 | 1552 | 2050 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1160052901 | 25 | 50 | 0 | 100 | 66.67 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 164 | 14 | 1553 | 2051 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1164052901 | 32 | 43 | 0 | 107 | 71.33 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 170 | 17 | 1554 | 2052 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1170052901 | 12 | 15 | 48 | 39 | 26 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 324 | 12 | 1560 | 2058 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1324052902 | 41 | 32 | 2 | 114 | 76 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 1 |
| 324 | 11 | 1559 | 2057 | 2 | 2 | 5 | 2 | 5 | January, 28 2014 15:01:13+0000 | 1 | January, 29 2014 11:19:35+0000 | 0 | 1324052901 | 29 | 33 | 13 | 91 | 60.67 | -1 | -1 | -1 | -1 | 1 | (null) | 1 | 0 | 2 |