Table 1.

CryptoGenotyper warning messages and their explanations.

Gene target	Warning message	Explanation
SSU and gp60	Could not analyze chromatogram. Please check manually	Program cannot interpret the chromatogram file
	Poor Sequence Quality. Check manually	The sequence has low Phred score and cannot decipher the data
	No blast hits.	The sequence does not represent a Cryptosporidium gene target in the database
	NC	No comment
SSU specific	Average Phred Quality <10, could be other potential mixed seqs. Check manually	A Cryptosporidium species was identified, however due to low Phred quality, further mixed infections could be present.
gp60 specific	Not all bases in repeat region had Phred quality ≥ 20	The repeat region is not of the highest quality. Often a result of mixed peaks or sequencing artifacts.
	Could not classify repeat region. Check manually.	The program could not classify the repeat region with certainty. Most likely a cause of sequencing artifacts or the sequence was trimmed into the repeat region.
	BLAST percent identity is less than 99.1%. Check manually in case of new gp60 family	The program may have identified a new subfamily that is not described in the database. Check the sequence manually to confirm.