FASTQ and FASTA are two common file formats used to store biological sequences like DNA, RNA, or proteins. Here are the general features of each:

FASTQ:

$1.$ Contains both sequence and quality score information.

$2.$ Each sequence entry consists of four lines:

a$.$ Line $1$: Begins with $\text{'}$@$\text{'}$ followed by a sequence identifier.

b$.$ Line $2$: Contains the sequence.

c$.$ Line $3$: Begins with $\text{'}+\text{'}$ and can optionally contain the sequence identifier or other information.

d$.$ Line $4$: Quality scores corresponding to each base in the sequence.

$3.$ Quality scores are typically encoded using ASCII characters and represent the confidence level of base calling at each position in the sequence.

FASTA:

$1.$ Contains only the sequence information.

$2.$ Each sequence entry consists of two lines:

a$.$ Line $1$: Begins with $\text{'}>\text{'}$ followed by a sequence identifier.

b$.$ Line $2$: Contains the sequence.

Quality scores in a FASTQ file relate to the confidence level of base calling at each position in the sequence. These scores are crucial for assessing the reliability of the sequenced data. Lower quality scores indicate higher uncertainty in base calling, which may imply sequencing errors or variations in sequencing quality at different positions in the sequence. During bioinformatics analysis, these quality scores are used to filter and trim low$-$quality regions of the sequence data to improve the accuracy of downstream analyses.