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

A FASTQ file normally uses four lines per sequence.

1. Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
2. Line 2 is the raw sequence letters.
3. Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
4. 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

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

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.

See also

• Biological sequence format
• Sequence Read Archive
• Phred quality score

References

FASTQ Resources
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