Table 3.

Indels within coding regions.

Isolate	Indel	Reference Protein Length	Frameshift Length (bp change)	Query Protein Length	Locus	Annotation
Lab Culture	1	638 aa	29 aa (+C)	No stop codonb	BMAA1927	Hypothetical Protein
	2	154 aa	50 aa (-T)	75 aa	BMA1435	Hypothetical Protein
	3	145 aa	64 aa (-G)	85 aa	BMA2147	N utilization substance protein B
	4	711 aa	586 aa (+A)	No stop codonb	BMA2914	Oxidoreductase
Mouse spleen	1a	942 aa	No	938 aa	BMAA0680	Penicillin-binding protein
	2	357 aa	13 aa (+G)	321 aa	BMA0161	Rod shape-determining protein MreC
Horse Lung	1	787 aa	525 aa (+G)	721 aa	BMAA0367	Acetyltransferase, GNAT family
	2a	136 aa	No	138 aa	BMAA0623	Hypothetical protein
	3a	120 aa	66 aa	100 aa	BMA2996	Hypothetical protein
Human Liver	1a	659 aa	52 aa	62 aa	BMAA0729	Hypothetical protein
	2a	122 aa	69 aa	85 aa	BMA3028	Conserved domain protein
	3	No translation	49 aa (+A)	361 aa	BMAA1903	Conserved hypoth. protein
	4	685 aa	164 aa (+T)	328 aa	BMA0685	Vit. B12 receptor BtuB, putative
Human Blood	1a	122 aa	69 aa	85 aa	BMA3028	Conserved domain protein
	2a	193 aa	157 aa	No stop codonb	BMAA0789	Hypothetical protein
	3	No translation	49 aa (+A)	361 aa	BMA1903	Conserved hypoth. protein

^aCoding region indels within SSRs. Mouse spleen 1^a: repeat unit AACACCGAACCG; Horse lung 2^a: repeat unit GGTGCC, 3^a: repeat unit GAGCGGT; Human liver 1^a : repeat unit CGAGTCAT extra copy in reference, 2^a: repeat unit GCCGATT extra copy in query; Human blood 1^a: GCCGATT extra copy in query, 2^a: GCGCCTC two extra copies in reference.

^bReference protein lost the stop codon at the original position due to the frameshift; query protein has a new stop codon in a different position.