FASTQ format

Four lines define each entry in a FASTQ file

@AY01234       # sequence-ID (and description)

GCATCTCGA...   # FASTA-like (nucleotide) sequence

+              # quality header line (optional: repeated sequence-ID, usually empty)

BF7'F<0&F...   # →Quality values of each sequence position


Illumina FASTQ format

FASTQ example 

Three entries of forward read sequences (Illumina R1 FASTQ file):

@A0216:173:HJNFKDSX:3:1101:2745:1016 1:N:0:TTACGCAC+AGATGGTC

GGGAGACGAGCGTCACGTTCATGAGCGCCTCCTCGACCTCGTCGACGGAGTCGAAATTACGCGCCACCCACAGCGGAAATTCGAACGTGGCGACGTTTTCC

+

BBBFBFFFFFFFBF<FBB0B<BF<FFFFFIIII'<<FF7BF<'7<BBBBB<<BBBBBBBBBBBBBBBBBBBBBB<7BB<<B<BFB<BBBB77<BB<BBBBB

@A0216:173:HJNFKDSX:3:1101:3884:1016 1:N:0:TTACGCAC+AGATGGTC

GCTTCGCCTTGCCGCCCGCACCAAACACCGTGTCATAGTGGTAGCCGCGCGGAGTAACCAAGATGGTCTCCCCATATGAGAAACTCCAGTCGAGATTACGG

+

BBBFFFFFFFFFFFFFIBFFIIIFFIIBBF0BFFF0BF<BF<BBFFBFFB<BBFBBBF0<BBFFFBBBFBBFFFBBBF<<BBBBFFFFB<BBFFFBBBB07

@A0216:173:HJNFKDSX:3:1101:4010:1016 1:N:0:TTACGCAC+AGATGGTC

TATTTTTATGCATTTGCTTAATTTTAATAGCTGCAAAAGTTAATAAAATAAAACCAATTGCTACAAAAAAAGAAGTGCAGCTTCAAGAAGATGTAAAACTG

+

<<<<<0<00000<BB7BBBB000BB0<7BB000B<0BB'<<<'0'0'<0<00'07BB'77''07<7''0000'7<<0'0<<''7<'7'77'000'77'''7

Meaning of Illumina sequence names

@instrumentID:run:lane:tile:xPos:yPos  direction(R1 or R2):quality(N=ok filtered):index sequence pairs

→ Illumina FASTQ file format


Read more

→ wikipedia FASTQ format

→ Phred quality scores

→ Paired-end reads explained by Torsten Seemann

→ Sanger FASTQ file format

→ awk: How to add "/1" and "/2" to FASTQ sequence-IDs

→ FASTA file format