Table 1.

Relative change in area under CID (RCA) and relative change in sum of squared error (RCE) when running Qtip and Bowtie 2 on Mason-simulated Illumina-like samples of various lengths

		End-to-end				Local
		RCA		RCE		RCA		RCE
	Read length	Mean	SD	Mean	SD	Mean	SD	Mean	SD
Unpaired	50	−9.03	0.26	−24.61	0.19	−2.49	0.47	−15.30	0.57
	100	−7.43	1.82	−18.53	2.61	−10.26	1.52	−27.87	1.59
	150	−9.11	1.15	−16.22	0.62	−14.77	2.15	−29.27	1.03
	250	−16.82	2.01	−19.97	0.44	−22.51	1.77	−28.85	0.62
	500	−33.77	0.60	−27.26	0.37	−37.75	1.32	−31.65	1.01
Paired	50	−13.11	0.44	−19.60	0.44	−18.60	0.28	−33.63	0.24
	100	−15.80	1.29	−21.79	0.33	−36.84	0.69	−45.42	0.53
	150	−22.39	1.74	−25.94	0.28	−46.87	0.54	−52.76	0.56
	250	−37.65	0.97	−33.48	0.22	−58.39	0.91	−58.75	1.38
	500	−54.59	0.58	−44.91	0.34	−68.54	0.95	−70.37	3.45

Relative change is expressed as a percentage. Each sample consists of 4 million reads/pairs. Samples are either unpaired or paired-end, and Bowtie 2 is run in either end-to-end or local alignment mode as indicated. Results are means and standard deviations over ten random trials, repeated starting from the input modeling step

CID cumulative incorrect difference

RCA relative change in area under CID

RCE relative change in sum of squared errors

SD standard deviation