Table 2. QC metrics.

QC metrics are shown with their thresholds, which bioinformatics tool we used, and the QC category.

No.	QC Metrics	Cutoff	Tool (version)	Category
1	total reads	NC	FastQC	Step 1: Fastq quality check
2	read length	NC	FastQC	Step 1: Fastq quality check
3	average phred score	>25	FastQC	Step 1: Fastq quality check
4	mean depth per nucleotide (MDN)	>10	Samtools	Step 2: Depth check
5	standard deviation for MDN	NC	Samtools	Step 2: Depth check
6	coefficient of variation for MDN	NC	Samtools	Step 2: Depth check
7	number of nucleotides with depth <10 (for Illumina)	<3000	Samtools	Step 2: Depth check
8	number of nucleotides with depth <20(for nanopore)	<3000	Samtools	Step 2: Depth check
9	number of paired-end reads	NC	Titan 1.4.4	Step 3: Bioinformatics workflow check
10	assembly total length	>29400	Titan 1.4.4	Step 3: Bioinformatics workflow check
11	ambiguous Ns	<10%	Titan 1.4.4	Step 3: Bioinformatics workflow check
12	assembly mean coverage	>25	Titan 1.4.4	Step 3: Bioinformatics workflow check
13	% mapped to the Wuhan reference	>65%	Titan 1.4.4	Step 3: Bioinformatics workflow check
14	VADR alert number	<=1	Titan 1.4.4	Step 3: Bioinformatics workflow check
15	nextclade_aa_dels	NC	Titan 1.4.4	Step 3: Bioinformatics workflow check
16	nextclade_aa_subs	NC	Titan 1.4.4	Step 3: Bioinformatics workflow check
17	nextclade_version	NC	Titan 1.4.4	Step 3: Bioinformatics workflow check
18	pango_lineage	NC	Titan 1.4.4	Step 3: Bioinformatics workflow check
19	pangolin_version	NC	Titan 1.4.4	Step 3: Bioinformatics workflow check

Notes.

NC

not a criterion

These values are reported but not used as criteria for passing or failing a sample.