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Table 2 Relative change in area under CID (RCA) and relative change in sum of squared error (RCE) for various aligners and reference genomes, expressed as percentage change

From: A tandem simulation framework for predicting mapping quality

    100 nt 250 nt
    RCA RCE RCA RCE
    Mean SD Mean SD Mean SD Mean SD
Unpaired GRCh37 Bowtie 2 −11.22 1.08 −24.43 0.66 −15.02 0.39 −28.37 0.38
   BWA-MEM −14.49 2.29 −49.54 0.43 −9.14 2.09 −52.31 0.38
   SNAP −15.94 0.32 −36.86 0.23 −9.53 3.88 −28.57 0.47
  GRCh38 Bowtie 2 −7.43 1.82 −18.53 2.61 −16.82 2.01 −19.97 0.44
   BWA-MEM −15.49 0.58 −47.42 0.37 −15.78 0.57 −51.14 0.31
   SNAP −19.58 0.18 −36.58 0.47 −14.74 0.27 −25.47 0.32
  Mouse Bowtie 2 −5.60 0.24 −17.19 0.45 −7.05 0.33 −17.73 0.37
   BWA-MEM −13.50 0.15 −46.25 0.27 −16.39 0.38 −51.12 0.30
   SNAP −9.02 0.17 −31.07 0.33 −10.61 0.20 −31.78 0.43
  Zea mays Bowtie 2 −6.63 0.32 −19.56 0.25 −17.09 0.38 −25.89 0.44
   BWA-MEM −19.26 0.11 −58.32 0.26 −25.14 0.19 −66.76 0.23
   SNAP −13.02 0.24 −38.48 0.53 −24.01 0.43 −53.80 0.42
Paired GRCh37 Bowtie 2 −25.86 0.33 −30.26 0.50 −36.31 2.16 −38.29 0.60
   BWA-MEM −13.33 0.23 −45.70 0.27 −10.08 0.75 −47.58 0.31
   SNAP −56.53 1.99 1.39 2.34 −42.89 7.63 13.17 3.95
  GRCh38 Bowtie 2 −15.80 1.29 −21.79 0.33 −38.22 0.31 −33.63 0.30
   BWA-MEM −14.19 0.16 −41.35 0.19 −12.36 0.46 −42.78 0.29
   SNAP −51.36 0.98 −11.16 1.12 −51.32 1.45 4.34 2.29
  Mouse Bowtie 2 −10.10 0.26 −18.93 0.31 −19.03 0.21 −29.07 0.32
   BWA-MEM −11.86 0.12 −36.18 0.37 −13.30 0.19 −39.91 0.21
   SNAP −29.90 0.67 −17.04 0.76 −30.16 0.30 −15.79 0.47
  Zea mays Bowtie 2 −17.92 0.21 −26.95 0.27 −43.19 0.18 −51.69 0.38
   BWA-MEM −17.04 0.15 −47.48 0.29 −21.45 0.20 −56.58 0.08
   SNAP −36.28 0.55 −17.08 0.79 −26.45 4.44 −20.05 0.52
  1. The experiments used 100 or 250 nt reads, and unpaired or paired-end reads, 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