What is a FASTQ File and the FASTQ Format?

A FASTQ file is a file written in the FASTQ format, containing nucleotide sequences and their corresponding quality scores (confidence levels). It is commonly used to represent nucleotide sequences output from sequencers.

The file extensions are often ".fastq" or ".fq". They are also frequently gzip-compressed, with extensions like ".fastq.gz" or ".fq.gz". Additionally, the reads output from next-generation sequencers (NGS) often come in pairs, making it easier to identify paired files by naming them as "[sample_name]_1.fastq.gz", "[sample_name]_1.fq.gz", "[sample_name]_2.fastq.gz", or "[sample_name]_2.fq.gz".

Files that contain only nucleotide sequences without quality scores are called FASTA files. For a detailed explanation of FASTA files, please see here.

In the FASTQ format, four lines constitute one set, representing the nucleotide sequence and its quality.

Example of a FASTQ file

In this example, there are 8 lines, displaying information for two sequences.

The information for each line is as follows:

There are several ways to represent the quality score, but the Phred quality score is commonly used.

The Phred quality score is calculated using the following formula:

\(p_{err}\) represents the probability that the sequencing result is an error.

In other words, Q10 corresponds to a 10% probability of error, Q20 to 1%, Q30 to 0.1%, and Q40 to 0.01%.

In a FASTQ file, this quality score is represented by a single character.

Below is the table showing the correspondence between characters and scores.