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第一种：sanger质量值
PHRED quality score of a base call, de?ned in terms of the estimated probability of error：
 

sanger质量值等于PHRED quality score：公式如下：

第二种：solexa质量值

The Solexa pipeline (i.e., the software delivered with the Illumina Genome Analyzer) earlier used a different mapping, encoding the odds ratio p/(1-p) instead of the probability p:

取值范围：

• Sanger format can encode a Phred quality score from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60, higher scores are possible in assemblies or read maps).
• Illumina 1.3+ format can encode a Phred quality score from 0 to 62 using ASCII 64 to 126 (although in raw read data Phred scores from 0 to 40 only are expected).
• Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)

换算关系：

• If the Phred quality is $Q, which is a non-negative integer, the corresponding quality character can be calculated with the following Perl code:

  $q = chr(($Q<=93? $Q : 93) + 33);  

  where chr() is the Perl function to convert an integer to a character based on the ASCII table.
• Conversely, given a character $q, the corresponding Phred quality can be calculated with:

  $Q = ord($q) - 33;  

  where ord() gives the ASCII code of a character.
• 同样的方法也可以应用于solexa数据
  

判断Sanger quality encoding或者solexa quality encoding：

The quickest way to distinguish Sanger Q-score encoding (ASCII-33) from Illumina (Solexa) Q-score encoding (ASCII-64) is to look for numerals [0-9] in the quality string. The numerals have ASCII values from 48-57 so it would be non-sensical to subtract 64 from them. If there are numerals in your quality string then the Q-score encoding is Sanger.

solexa质量值到sanger质量值的转化：

 

• given a character $q, the corresponding Phred quality value can be calculated with:

  $Q = ord($q) －64;  

  where ord() gives the ASCII code of a character.
• If the Phred quality is $Q, which is a non-negative integer, the corresponding quality character can be calculated with the following Perl code:

  $q = chr($Q + 33);  

• where chr() is the Perl function to convert an integer to a character based on the ASCII table.  

Conversion from ‘fastq-illumina’ to ‘fastq-sanger’ will be a common operation, and is very straightforward since both variants use PHRED scores but with di?erent o?sets. All that is required is to decrease the quality character codes by 31

参考资料：
1：http://en.wikipedia.org/wiki/FASTQ_format
2：Cock et al (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, doi:10.1093/nar/gkp1137
3：http://maq.sourceforge.net/fastq.shtml#intro