FASTQ

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

Description[edit | edit source]

A FASTQ file normally uses four lines per sequence.

Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
Line 2 is the raw sequence letters.
Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.

A FASTQ file carrying n sequences will have 4n lines.

Quality[edit | edit source]

The quality scores are in the Phred quality score, which logarithmically relate to error probabilities. The character '!' represents a score of 0 and the character '~' a score of 93. The ASCII value of a character in the quality string minus 33 gives the quality score of the corresponding base call.

Variations[edit | edit source]

There are several variations of the FASTQ format which can be distinguished by their methods of encoding quality scores. The original Sanger format and the Solexa/Illumina format. The Sanger format encodes a Phred quality score from 0 to 93 using ASCII 33 to 126, while the Solexa/Illumina format encodes a Solexa quality score from -5 to 62 using ASCII 59 to 126.

References[edit | edit source]

FASTQ Resources
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