Table 2.

Indels and frameshifts with high or moderate impact and above the prevalence filter (>15%/<85%).

UniProt BLAST annotation		General information		PROVEAN	GO term			SnpEff annotation
Protein name	UniProt acc. no.	Prev.	% prot.	Prediction	No.	Asp.	Info	Variant	Cat.	Annotation (effect)	Put. imp.
Uncharacterized protein	A0A1G5IYU0	48%	87%	Neutral	No GO	–	–	p.Leu252_Glu253insAla	I	Disruptive_inframe_insertion	M
Gamma-glutamylputrescine oxidoreductase	A0A1F0J8L6	20%	1%	Neutral	GO:0016491	F	Oxido-reductase activity	p.Thr4_Ser5insProTyrPro	I	Conservative_inframe_insertion	M
			1%	na				p.Ser5fs	FS	Frameshift_variant	H

Cluster 2: 2 indels and frameshifts.

Only indels and frameshifts above the prevalence filter (prevalence in at least 15% of strains) are reported. Variant annotation was performed by SnpEff. Protein function prediction was performed by PROVEAN with a cutoff of −2.5 (default).

“% of protein” (general information) = percent of total protein length before frameshift or termination; “variant category” (SnpEff): manually assigned based on HGVS.c/HGVS.p annotation; “HGVS.c & HGVS.p” = variant using HGVS (Human Genome Variation Society) notation with 1- or 3-letter amino acid code. Note that in case the variant is not coding, HGVS.p (protein level) is given instead of HGVS.c (DNA level).

UniProt BLAST annotation: the best hit (by identity) is given in the table.

prev., prevalence; % prot., % of protein; asp., aspect; cat., category; put. imp., putative impact; na, not applicable; UniProt acc. no.; UniProt accession number; no., number; I, indel (category); FS, frameshift (category); M, moderate (putative impact); H, high (putative impact).