Skip to main content

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

From: A tandem simulation framework for predicting mapping quality

   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
  1. 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
  2. CID cumulative incorrect difference
  3. RCA relative change in area under CID
  4. RCE relative change in sum of squared errors
  5. SD standard deviation