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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