Table 7.

Mapping of the amplicon sequences to associated genome references

Organism	Strain	PCR Assay	Amplicon Length (bps)	CIGAR*	Insertions	Deletions	SC left	SC right	Alignment Expected?	Expected PCR result	Observed PCR Result
B. anthracis	708	PRC_01	110	70M3D40M	0	3	0	0	Y	+	+
B. anthracis	708	PRC_04	182	155M4D27M	0	4	0	0	Y	+	+
B. anthracis	708	PRC_07	96	96 M	0	0	0	0	Y	+	+
Y. pestis	113	PRC_09	68	68 M	0	0	0	0	Y	+	+
Y. pestis	114	PRC_09	68	68 M	0	0	0	0	Y	+	+
Y. pestis	113	PRC_11	79	79 M	0	0	0	0	Y	+	+
Y. pestis	114	PRC_14	103	103 M	0	0	0	0	Y	+	–
Y. pestis	113	PRC_15	67	67 M	0	0	0	0	Y	+	+
Y. pestis	114	PRC_15	67	67 M	0	0	0	0	Y	+	+
F. tularensis	239	PRC_23	135	135 M	0	0	0	0	Y	+	+
F. tularensis	240	PRC_23	135	135 M	0	0	0	0	Y	+	+
F. tularensis	241	PRC_23	135	133M2S	0	0	0	2	Y	+	+
F. tularensis	239	PRC_28	171	90M1D81M	0	1	0	0	Y	+	+
F. tularensis	239	PRC_29	119	48S71M	0	0	48	0	N	–	–
F. tularensis	240	PRC_29	119	119 M	0	0	0	0	Y	+	–
F. tularensis	241	PRC_29	119	71M48S	0	0	0	48	N	–	–
F. tularensis	241	PRC_30	126	126 M	0	0	0	0	Y	+	+
B. mallei	164	PRC_49	100	100 M	0	0	0	0	Y	+	+
B. pseudomallei	197	PRC_49	100	no alignment**						–	+
B. pseudomallei	197	PRC_50	115	115 M	0	0	0	0	Y	+	+
B. pseudomallei	197	PRC_65	67	67 M	0	0	0	0	Y	+	+

Mapping of the amplicon sequences to the whole genome de novo sequence reference of the spiked strains to detect possible mismatches. All amplicon alignments match expected contig reference, however there are alignments with heavy soft clipping (SC). *Concise Idiosyncratic Gap Alignment Report; S - soft clipping, M - match, D - deletion, I - insertion. Soft-clipped parts of query sequence are ignored when calculating alignment mapping quality (consequence of local alignment). **Shown for completeness and comparison purposes