FASTQ Format: Structure, Quality Scores & Examples

A FASTQ file is a text file in FASTQ format that stores nucleotide sequences along with their quality scores, which indicate the confidence of each base call. It is the standard format for storing sequencer output.

Common file extensions are ".fastq" and ".fq". These files are often gzip-compressed, resulting in extensions like ".fastq.gz" or ".fq.gz". Since next-generation sequencers (NGS) frequently produce paired-end reads, paired files are typically named with conventions such as "[sample_name]_1.fastq.gz" / "[sample_name]_2.fastq.gz" or "[sample_name]_1.fq.gz" / "[sample_name]_2.fq.gz" to clearly identify read pairs.

Files that contain only nucleotide sequences without quality scores use the FASTA format. For more details on FASTA files, see here.

In FASTQ format, every four consecutive lines form one record, representing a single sequence and its quality information.

Example of a FASTQ File

This example contains 8 lines, which means it holds two sequence records.

Each line in a record contains the following:

While there are several ways to encode quality, the Phred quality score is by far the most common.

The Phred quality score is defined by the following formula, where \(p_{err}\) is the probability that the base call is incorrect:

For example, Q10 indicates a 10% error probability, Q20 means 1%, Q30 means 0.1%, and Q40 means 0.01%.

In FASTQ files, each quality score is encoded as a single ASCII character.

The table below shows the mapping between quality scores and their corresponding characters.