FASTQ Quality Score Convesion Table

In FASTQ format, the fourth line encodes the quality score of sequences in the second line. This scheme was initially used by the Phred base-calling program to use ASCII characters to encode the probability that the corresponding base call is wrong in traditional Sanger sequencing. The same format is also used by Illumina/Solexa sequencing, however the mapping from probability values to characters is slightly changed from the Phred score and also varies between different version of Solexa sequencer. The exact formula is given somewhere else. The following lists the conversion table for each platform and/or version. 

Range

  SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS.....................................................
  ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................
  ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................
  .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ......................
  LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL....................................................
  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
  |                         |    |        |                              |                     |
 33                        59   64       73                            104                   126

 S - Sanger        Phred+33,  raw reads typically (0, 40)
 X - Solexa        Solexa+64, raw reads typically (-5, 40)
 I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)
 J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40)
    with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) 
    (Note: See discussion above).
 L - Illumina 1.8+ Phred+33,  raw reads typically (0, 41)

Sanger sequencing score

   |------+-------+-------+--------------|
   | char | value | Phred |  Error-Prob. |
   |------+-------+-------+--------------|
   | !    |    33 |     0 | 1.0000000000 |
   | "    |    34 |     1 | 0.7943282347 |
   | #    |    35 |     2 | 0.6309573445 |
   | $    |    36 |     3 | 0.5011872336 |
   | %    |    37 |     4 | 0.3981071706 |
   | &    |    38 |     5 | 0.3162277660 |
   | '    |    39 |     6 | 0.2511886432 |
   | (    |    40 |     7 | 0.1995262315 |
   | )    |    41 |     8 | 0.1584893192 |
   | *    |    42 |     9 | 0.1258925412 |
   | +    |    43 |    10 | 0.1000000000 |
   | ,    |    44 |    11 | 0.0794328235 |
   | -    |    45 |    12 | 0.0630957344 |
   | .    |    46 |    13 | 0.0501187234 |
   | /    |    47 |    14 | 0.0398107171 |
   | 0    |    48 |    15 | 0.0316227766 |
   | 1    |    49 |    16 | 0.0251188643 |
   | 2    |    50 |    17 | 0.0199526231 |
   | 3    |    51 |    18 | 0.0158489319 |
   | 4    |    52 |    19 | 0.0125892541 |
   | 5    |    53 |    20 | 0.0100000000 |
   | 6    |    54 |    21 | 0.0079432823 |
   | 7    |    55 |    22 | 0.0063095734 |
   | 8    |    56 |    23 | 0.0050118723 |
   | 9    |    57 |    24 | 0.0039810717 |
   | :    |    58 |    25 | 0.0031622777 |
   | ;    |    59 |    26 | 0.0025118864 |
   | <    |    60 |    27 | 0.0019952623 |
   | =    |    61 |    28 | 0.0015848932 |
   | >    |    62 |    29 | 0.0012589254 |
   | ?    |    63 |    30 | 0.0010000000 |
   | @    |    64 |    31 | 0.0007943282 |
   | A    |    65 |    32 | 0.0006309573 |
   | B    |    66 |    33 | 0.0005011872 |
   | C    |    67 |    34 | 0.0003981072 |
   | D    |    68 |    35 | 0.0003162278 |
   | E    |    69 |    36 | 0.0002511886 |
   | F    |    70 |    37 | 0.0001995262 |
   | G    |    71 |    38 | 0.0001584893 |
   | H    |    72 |    39 | 0.0001258925 |
   | I    |    73 |    40 | 0.0001000000 |
   |------+-------+-------+--------------|

Solexa score (prior 1.3)

   |------+-------+-------+--------------|
   | char | value | Phred |  Error-Prob. |
   |------+-------+-------+--------------|
   | ;    |    59 |    -5 | 0.7597469266 |
   | <    |    60 |    -4 | 0.7152527510 |
   | =    |    61 |    -3 | 0.6661394246 |
   | >    |    62 |    -2 | 0.6131368202 |
   | ?    |    63 |    -1 | 0.5573116338 |
   | @    |    64 |     0 | 0.5000000000 |
   | A    |    65 |     1 | 0.4426883662 |
   | B    |    66 |     2 | 0.3868631798 |
   | C    |    67 |     3 | 0.3338605754 |
   | D    |    68 |     4 | 0.2847472490 |
   | E    |    69 |     5 | 0.2402530734 |
   | F    |    70 |     6 | 0.2007600089 |
   | G    |    71 |     7 | 0.1663375308 |
   | H    |    72 |     8 | 0.1368068886 |
   | I    |    73 |     9 | 0.1118157698 |
   | J    |    74 |    10 | 0.0909090909 |
   | K    |    75 |    11 | 0.0735875561 |
   | L    |    76 |    12 | 0.0593509431 |
   | M    |    77 |    13 | 0.0477267210 |
   | N    |    78 |    14 | 0.0382865039 |
   | O    |    79 |    15 | 0.0306534300 |
   | P    |    80 |    16 | 0.0245033676 |
   | Q    |    81 |    17 | 0.0195623039 |
   | R    |    82 |    18 | 0.0156016622 |
   | S    |    83 |    19 | 0.0124327353 |
   | T    |    84 |    20 | 0.0099009901 |
   | U    |    85 |    21 | 0.0078806839 |
   | V    |    86 |    22 | 0.0062700123 |
   | W    |    87 |    23 | 0.0049868787 |
   | X    |    88 |    24 | 0.0039652856 |
   | Y    |    89 |    25 | 0.0031523092 |
   | Z    |    90 |    26 | 0.0025055927 |
   | [    |    91 |    27 | 0.0019912892 |
   | \\   |    92 |    28 | 0.0015823853 |
   | ]    |    93 |    29 | 0.0012573425 |
   | ^    |    94 |    30 | 0.0009990010 |
   | _    |    95 |    31 | 0.0007936978 |
   | `    |    96 |    32 | 0.0006305595 |
   | a    |    97 |    33 | 0.0005009362 |
   | b    |    98 |    34 | 0.0003979487 |
   | c    |    99 |    35 | 0.0003161278 |
   | d    |   100 |    36 | 0.0002511256 |
   | e    |   101 |    37 | 0.0001994864 |
   | f    |   102 |    38 | 0.0001584642 |
   | g    |   103 |    39 | 0.0001258767 |
   | h    |   104 |    40 | 0.0000999900 |
   |------+-------+-------+--------------|

Solexa score 1.3+

   |------+-------+-------+--------------|
   | char | value | Phred |   Error Prob |
   |------+-------+-------+--------------|
   | @    |    64 |     0 | 1.0000000000 |
   | A    |    65 |     1 | 0.7943282347 |
   | B    |    66 |     2 | 0.6309573445 |
   | C    |    67 |     3 | 0.5011872336 |
   | D    |    68 |     4 | 0.3981071706 |
   | E    |    69 |     5 | 0.3162277660 |
   | F    |    70 |     6 | 0.2511886432 |
   | G    |    71 |     7 | 0.1995262315 |
   | H    |    72 |     8 | 0.1584893192 |
   | I    |    73 |     9 | 0.1258925412 |
   | J    |    74 |    10 | 0.1000000000 |
   | K    |    75 |    11 | 0.0794328235 |
   | L    |    76 |    12 | 0.0630957344 |
   | M    |    77 |    13 | 0.0501187234 |
   | N    |    78 |    14 | 0.0398107171 |
   | O    |    79 |    15 | 0.0316227766 |
   | P    |    80 |    16 | 0.0251188643 |
   | Q    |    81 |    17 | 0.0199526231 |
   | R    |    82 |    18 | 0.0158489319 |
   | S    |    83 |    19 | 0.0125892541 |
   | T    |    84 |    20 | 0.0100000000 |
   | U    |    85 |    21 | 0.0079432823 |
   | V    |    86 |    22 | 0.0063095734 |
   | W    |    87 |    23 | 0.0050118723 |
   | X    |    88 |    24 | 0.0039810717 |
   | Y    |    89 |    25 | 0.0031622777 |
   | Z    |    90 |    26 | 0.0025118864 |
   | [    |    91 |    27 | 0.0019952623 |
   | \\   |    92 |    28 | 0.0015848932 |
   | ]    |    93 |    29 | 0.0012589254 |
   | ^    |    94 |    30 | 0.0010000000 |
   | _    |    95 |    31 | 0.0007943282 |
   | `    |    96 |    32 | 0.0006309573 |
   | a    |    97 |    33 | 0.0005011872 |
   | b    |    98 |    34 | 0.0003981072 |
   | c    |    99 |    35 | 0.0003162278 |
   | d    |   100 |    36 | 0.0002511886 |
   | e    |   101 |    37 | 0.0001995262 |
   | f    |   102 |    38 | 0.0001584893 |
   | g    |   103 |    39 | 0.0001258925 |
   | h    |   104 |    40 | 0.0001000000 |
   |------+-------+-------+--------------|

Solexa score 1.5+

   |------+-------+-------+--------------|
   | char | value | Phred |   Error Prob |
   |------+-------+-------+--------------|
   | C    |    67 |     3 | 0.5011872336 |
   | D    |    68 |     4 | 0.3981071706 |
   | E    |    69 |     5 | 0.3162277660 |
   | F    |    70 |     6 | 0.2511886432 |
   | G    |    71 |     7 | 0.1995262315 |
   | H    |    72 |     8 | 0.1584893192 |
   | I    |    73 |     9 | 0.1258925412 |
   | J    |    74 |    10 | 0.1000000000 |
   | K    |    75 |    11 | 0.0794328235 |
   | L    |    76 |    12 | 0.0630957344 |
   | M    |    77 |    13 | 0.0501187234 |
   | N    |    78 |    14 | 0.0398107171 |
   | O    |    79 |    15 | 0.0316227766 |
   | P    |    80 |    16 | 0.0251188643 |
   | Q    |    81 |    17 | 0.0199526231 |
   | R    |    82 |    18 | 0.0158489319 |
   | S    |    83 |    19 | 0.0125892541 |
   | T    |    84 |    20 | 0.0100000000 |
   | U    |    85 |    21 | 0.0079432823 |
   | V    |    86 |    22 | 0.0063095734 |
   | W    |    87 |    23 | 0.0050118723 |
   | X    |    88 |    24 | 0.0039810717 |
   | Y    |    89 |    25 | 0.0031622777 |
   | Z    |    90 |    26 | 0.0025118864 |
   | [    |    91 |    27 | 0.0019952623 |
   | \\   |    92 |    28 | 0.0015848932 |
   | ]    |    93 |    29 | 0.0012589254 |
   | ^    |    94 |    30 | 0.0010000000 |
   | _    |    95 |    31 | 0.0007943282 |
   | `    |    96 |    32 | 0.0006309573 |
   | a    |    97 |    33 | 0.0005011872 |
   | b    |    98 |    34 | 0.0003981072 |
   | c    |    99 |    35 | 0.0003162278 |
   | d    |   100 |    36 | 0.0002511886 |
   | e    |   101 |    37 | 0.0001995262 |
   | f    |   102 |    38 | 0.0001584893 |
   | g    |   103 |    39 | 0.0001258925 |
   | h    |   104 |    40 | 0.0001000000 |
   |------+-------+-------+--------------|

Solexa score 1.8+

   |------+-------+-------+--------------|
   | char | value | Phred |  Error-Prob. |
   |------+-------+-------+--------------|
   | !    |    33 |     0 | 1.000000e+00 |
   | "    |    34 |     1 | 7.943282e-01 |
   | #    |    35 |     2 | 6.309573e-01 |
   | $    |    36 |     3 | 5.011872e-01 |
   | %    |    37 |     4 | 3.981072e-01 |
   | &    |    38 |     5 | 3.162278e-01 |
   | '    |    39 |     6 | 2.511886e-01 |
   | (    |    40 |     7 | 1.995262e-01 |
   | )    |    41 |     8 | 1.584893e-01 |
   | *    |    42 |     9 | 1.258925e-01 |
   | +    |    43 |    10 | 1.000000e-01 |
   | ,    |    44 |    11 | 7.943282e-02 |
   | -    |    45 |    12 | 6.309573e-02 |
   | .    |    46 |    13 | 5.011872e-02 |
   | /    |    47 |    14 | 3.981072e-02 |
   | 0    |    48 |    15 | 3.162278e-02 |
   | 1    |    49 |    16 | 2.511886e-02 |
   | 2    |    50 |    17 | 1.995262e-02 |
   | 3    |    51 |    18 | 1.584893e-02 |
   | 4    |    52 |    19 | 1.258925e-02 |
   | 5    |    53 |    20 | 1.000000e-02 |
   | 6    |    54 |    21 | 7.943282e-03 |
   | 7    |    55 |    22 | 6.309573e-03 |
   | 8    |    56 |    23 | 5.011872e-03 |
   | 9    |    57 |    24 | 3.981072e-03 |
   | :    |    58 |    25 | 3.162278e-03 |
   | ;    |    59 |    26 | 2.511886e-03 |
   | <    |    60 |    27 | 1.995262e-03 |
   | =    |    61 |    28 | 1.584893e-03 |
   | >    |    62 |    29 | 1.258925e-03 |
   | ?    |    63 |    30 | 1.000000e-03 |
   | @    |    64 |    31 | 7.943282e-04 |
   | A    |    65 |    32 | 6.309573e-04 |
   | B    |    66 |    33 | 5.011872e-04 |
   | C    |    67 |    34 | 3.981072e-04 |
   | D    |    68 |    35 | 3.162278e-04 |
   | E    |    69 |    36 | 2.511886e-04 |
   | F    |    70 |    37 | 1.995262e-04 |
   | G    |    71 |    38 | 1.584893e-04 |
   | H    |    72 |    39 | 1.258925e-04 |
   | I    |    73 |    40 | 1.000000e-04 |
   | J    |    74 |    41 | 7.943282e-05 |
   |------+-------+-------+--------------|