TABLE 4.

Quality control (QC) for SARS-CoV-2 sequencing data

QC bin	QC bin description	% genome uncovered (<10×)	Average coverage	Other observations	Submit to NCBI	Tag for SRA attribute: “quality_control_ determination”	Included in FDA dashboard
A	No QC issues evident	<5%	>1,000×	>50% reads are SARS-CoV-2	Yes	No quality control issues identified	Yes
B	Some QC issues, but variant calling likely OK	6%–40%	100×–1,000×		Yes	Minor quality control issues identified	Yes
C	Insufficient data for confidence in variant calling	40%–95%	10×–100×	Low fraction of lineage-specific mutations, (C-WAP reports)	Yes	Sequence flagged for potential quality control issues	No
F	Significant QC and/or study design issues	>95%	<10×	<5% reads SARS-Cov-2, suspected contamination (SNR low), low sequence quality, etc.	No	Sequence flagged for significant quality control issues	No

^a Four QC categories, or bins, were established based on thresholds set for various QC metrics. Sequence tags were developed to communicate these categories directly on the sequence file in an attribute called “quality_control_determination.” Only data with QC tagged in the A or B bin was visualized on the public FDA variant analysis dashboard.