STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

Table 1 Summary of STAT Human Sequence Removal Tool Results

	Human RNA_Seq: bronchoalveolar lavage fluid		SARS-CoV-2 Amplicon
Accession	SRR11092056	SRR11092057	SRR13402847	SRR13444106
Total spots	5239723	5184909	216859	471848
Total spots remaining	438796	501436	216720	470934
Total spots removed	4800927	4683473	139	914
Human spots remaining	26265	25384	20	2
Conserved lineage spots	27217	29507	70	13
Total length (kbp) of human spot alignments	3684	3508	< 3	< 1

Summary of results for SRA accessions subjected to STAT Human Sequence Removal Tool (see Human Contamination Identification and Removal in “Methods”). “Total Spots Remaining” is the count of spots found in the output (fastq) file and subtracting this count from the total determine “Total Spots Removed”
We define “Human Spots” as those where all hits (up to top five) are identified as human with eValue < 1e−10. “Conserved Lineage Spots” are those containing a human top hit (lowest eValue) though not the exclusive organism of hits with eValue < 1e−10, and where all spot hits have either identical eValue or the greatest has eValue < 1e−14. “Total Length of Human Spot Alignments” is the sum of all the top alignments for all human spots remaining

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