Glossary

Term	Description
DNA	Deoxyribonucleic acid (DNA) is a type of nucleic acid, one of the four biological macromolecules contained in biological cells.
PCR	Polymerase chain reaction (PCR) is a molecular biology technique used to amplify specific DNA fragments. It can be regarded as special DNA replication outside the body. The biggest feature of PCR is that it can greatly increase the amount of DNA in a small amount.
Reads	A small sequenced fragment generated by a high-throughput sequencer.
Raw Reads	All raw data generated from a single sequencing run without any filtering.
Clean Reads	Raw Reads need to undergo a series of processing, such as removing sequencing adapters and primer sequences, filtering low-quality data, etc., and then obtaining high-quality reads are called Clean Reads.
Base Calling	Imaging first during sequencing, and then determining the type and quality score of bases based on the signal-to-noise ratio.
FASTQ	The first line begins with "@", followed by Sequence Identifier and an optional description. The second line is a series of single letters representing nucleotide sequence. The third line begins with "+" and an optional sequencing identifier. The last line is the corresponding quality value of the bases in the second line. The length of this line should be exactly the same as Line 2. The ASCII value corresponding to each character in the line minus 33/64 is the corresponding quality value.
Q30	Phred quality score, Q30 means the base call accuracy is 99.9%.
GC	GC content refers to the percentage of G and C bases in the total bases in Clean Data.
Mapping Ratio	The ratio of reads aligned to the genome to the total reads, the higher the value, the closer the relationship between the sequencing material and the genome.
Coverage	Sequencing coverage refers to the proportion of bases covered by sequencing reads on the reference genome, which is one of the indicators reflecting the randomness of sequencing. For good sequencing randomness, the bases on the genome should be evenly covered, and the depth is similar. Excessive local coverage depth may be caused by PCR bias.
Sequencing Depth	The ratio of the total number of bases (bp) obtained by actual sequencing to the actual genome size. In the case of good sequencing randomness, the base depth distribution on the genome should be normally distributed, and the peak should be near the target depth.
Insert Fragment	Fragments obtained by fragmentation of genomic DNA. Sequencing quality is not directly affected by the length of the insert fragment, but is determined by more complex systems and external factors such as reagents, sequencing chips, optical cameras, machine operation, laboratory environment (earthquake, exposure), etc.
SNP	Single nucleotide polymorphism mainly refers to the DNA sequence polymorphism caused by the variation of a single nucleotide at the genome level. It is the most common type of heritable variation in humans, accounting for more than 90% of all known polymorphisms. SNPs are widespread in the human genome, with an average of 1 in every 300 base pairs, and it is estimated that the total number can reach 3 million or more. SNP is a dimorphic marker, which is caused by the transition or transversion of a single base, and can also be caused by the insertion or deletion of bases. SNPs may be within the gene sequence or on non-coding sequences outside the gene.
INDEL	Insertion and deletion of small fragments within 50bp on the genome.
SV	SV refers to the sequence and position changes of large fragments (more than 50 bp in length) on the genome (Eichler, E.2015). The types include large fragment insertion or deletion (Big Indel), tandem duplication (Tandem Duplicate), chromosomal inversion ( Inversion), interchromosomal translocation (Translocation), copy number variation (CNV) and more complex chimeric variation.
CNV	Genomic copy number variation.
GATK	The Genome Analysis Toolkit, a software developed by Broad Institute for next-generation resequencing data analysis, contains many useful tools, mainly focusing on the identification of variants, genotyping, and attaches great importance to data quality assurance.
samtools	samtools is a commonly used software for processing high-throughput sequencing data, which is used to read/write/edit/index/view SAM/BAM/CRAM format files.
SnpEff	A software for annotating variants (SNPs, InDels) and predicting the impact of variants. According to the position of the variation site on the reference genome and the gene position on the reference genome, the region where the variation site occurs in the genome (intergenic region, gene region or CDS region, etc.), and the impact of the variation (synonymous and non-synonymous mutations, etc.).
Frameshift Mutation	Refers to the change of the reading frame of the DNA molecule due to the deletion or insertion of a certain base, resulting in a series of downstream code changes, so that the gene originally encoding a certain peptide chain becomes another completely different peptide chain sequence.
KEGG	KEGG is a database for systematic analysis of the metabolic pathways of gene products and compounds in cells and the functions of these gene products. It integrates data on genome, chemical molecule and biochemical system, including metabolic pathway (KEGG PATHWAY), drug (KEGG DRUG), disease (KEGG DISEASE), functional model (KEGG MODULE), gene sequence (KEGG GENES) and genome (KEGG GENOME). The KO (KEGG ORTHOLOG) system links the various KEGG annotation systems together. KEGG has established a complete KO annotation system, which can complete the functional annotation of the genome or transcriptome of newly sequenced species. See http://www.genome.jp/kegg/ for details.
GO	The database established by the Gene Ontology Consortium aims to establish a language vocabulary standard that is applicable to various species, defines and describes the functions of accumulated proteins, and can be updated with the deepening of research. GO is one of many biological ontology languages, which provides a systematic definition of three-level structures (molecular functions, biological pathways, and cellular components) to describe the functions of gene products.
COG	COG is the abbreviation of Clusters of Orthologous Groups of proteins.
NR	NR is the official protein sequence database of NCBI, which includes the protein coding sequence of GenBank gene, PDB (Protein Data Bank) protein database, SwissProt protein sequence and proteins from databases such as PIR (Protein Information Resource) and PRF (Protein Research Foundation) sequence. According to nr annotation information we can get GO functional annotation.
SwissProt	SwissProt is a database of annotated protein sequences maintained by the European Bioinformatics Institute (EBI). The database is composed of protein sequence entries, each entry contains protein sequence, cited literature information, taxonomic information, annotations, etc. Annotations include protein functions, post-transcriptional modifications, special sites and regions, secondary structures, quaternary structures, Similarity to other sequences, relationship between sequence defects and diseases, sequence variants and conflicts, etc. Redundant sequences have been reduced as much as possible in SwissProt, and cross-references have been established with more than 30 other data, including nucleic acid sequence libraries, protein sequence libraries, and protein structure libraries.