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 |