Table 5.

Mapping Statistics for alignments of sequencing data from enriched libraries to the Y. pestis CO92 reference genome (-n 0.01; MQ > 0).

(a)
IMO2 capture	# mapped reads without duplicates	# Reads > 30q	Mean MQ	C > T (5′ Pos. 1)	G > A (3′ Pos. 1)	Mean Cov	% 1X	% 2X	% 5X
Full reference	27,210	11,942	31.1	9.20%	9.30%	0.3319	14.87	2.84	0.5

(b)
IMO2 capture	# mapped reads without duplicates	# Reads > 30q	Mean MQ	Mean Cov	% 1X	% 2X	% 5X
Chromosome	26,171	11,048	18.6	0.33	14.4	2.7	0.5
pCD	501	426	32.3	0.45	34.1	8.7	0
pMT	286	244	31.9	0.19	16.8	2.2	0.1
pPCP	252	224	33.6	1.73	68.4	41.3	7.7

(a) Statistics for whole reference sequence and (b) statistics for each chromosome and plasmid separately.