Research Article
ExCNVSS: A Noise-Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data
Table 2
CNV detection performances using 10 real data sets. An artificial exome data set generated by Wessim was used as the control data set.
| | sample ID | ExCNVSS | ExCNVSS_noRatio | Excavator | Contra | ExomeCNV | Correctly detected
instances
(gain/loss) | FNR/FPR
(%) | Correctly
detected instances (gain/loss) | FNR/FPR
(%) | Correctly detected instances (gain/loss) | FNR/FPR
(%) | Correctly detected instances (gain/loss) | FNR/FPR
(%) | Correctly detected instances
(gain/loss) | FNR/FPR
(%) |
| | NA12843 | 99 | 26.67/ | 63 | 53.33/ | 61 | 54.81/ | 3 | 97.78/ | 100 | 25.93/ | | (51/48) | 12.39 | (27/36) | 14.99 | (54/7) | 4.43 | (0/3) | 0.05 | (54/46) | 43.35 | | NA12842 | 62 | 40.95/ | 39 | 62.86/ | 56 | 46.67/ | 0 | 98.10/ | 49 | 53.33/ | | (50/12) | 13.09 | (25/14) | 17.03 | (56/0) | 6.04 | (0/2) | 0.43 | (49/0) | 66.74 | | NA12748 | 59 | 41.58/ | 36 | 64.36/ | 63 | 37.62/ | 1 | 99.01/ | 56 | 44.55/ | | (50/9) | 13.21 | (24/12) | 14.47 | (54/9) | 5.46 | (0/1) | 0.04 | (56/0) | 55.38 | | NA12718 | 87 | 25.64/ | 76 | 35.04/ | 63 | 46.15/ | 7 | 94.02/ | 89 | 23.93/ | | (49/38) | 12.27 | (31/45) | 14.08 | (54/9) | 6.10 | (0/7) | 0.26 | (54/35) | 88.65 | | NA12275 | 57 | 41.84/ | 43 | 56.12/ | 56 | 42.86/ | 1 | 98.98/ | 56 | 42.86/ | | (49/8) | 11.53 | (33/10) | 13.74 | (56/0) | 6.09 | (0/1) | 0.27 | (54/2) | 91.48 | | NA12273 | 68 | 38.92/ | 40 | 64.60/ | 56 | 50.44/ | 4 | 96.46/ | 60 | 46.90/ | | (54/14) | 10.45 | (27/13) | 15.12 | (56/0) | 6.10 | (0/4) | 0.11 | (49/11) | 98.61 | | NA12272 | 58 | 41.41/ | 42 | 57.58/ | 64 | 35.35/ | 2 | 97.98/ | 65 | 34.34/ | | (48/10) | 11.31 | (31/11) | 13.86 | (57/7) | 6.08 | (0/2) | 0.23 | (54/11) | 97.54 | | NA11843 | 55 | 45.54/ | 37 | 63.37/ | 62 | 38.61/ | 1 | 99.01/ | 52 | 48.51/ | | (48/7) | 11.92 | (26/11) | 15.86 | (54/8) | 5.49 | (0/1) | 0.05 | (52/0) | 47.60 | | NA10847 | 58 | 38.95/ | 37 | 61.05/ | 63 | 33.68/ | 3 | 96.84/ | 52 | 45.26/ | | (55/3) | 11.15 | (36/1) | 16.24 | (63/0) | 6.06 | (1/2) | 0.5 | (52/0) | 92.17 | | NA06984 | 64 | 42.86/ | 46 | 58.93/ | 56 | 50.00/ | 4 | 96.43/ | 55 | 50.89/ | | (51/13) | 12.31 | (32/14) | 14.36 | (56/0) | 5.76 | (0/4) | 0.03 | (53/2) | 65.75 |
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