| Stop codon |
Any unambiguous stop codon (TGA, TAA, or TAG) |
| Bad inserts |
An insertion relative to the reference sequence that is not a
multiple of 3 bases, resulting in a frameshift |
| Bad deletion |
A deletion relative to the reference sequence that is not a
multiple of 3 bases, resulting in a frameshift |
| Too many mixtures |
>3.5% of nucleotides sequences called as mixtures |
| N count |
≥5 Ns (any base) in the sequence |
| Mark count |
≥100 positions marked as being potentially problematic |
| Single coverage |
>3 consecutive bases of single-read coverage with phred
scores of 40 |
| Low quality |
Any section where the quality of all coverage is too low to make
a call |
