Analyzing base-pair coverage of BDGPTrans annotations in the IR and RIR sets
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IR set |
RIR set |
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| Chr arm |
Chr length (Mb) |
Cumulative length of BDGP TEs (kb) |
Cumulative length of RIR set (kb) |
TruePos (kb) |
FalsNeg (kb) |
FalsPos (kb) |
Recall (%) |
Precision (%) |
TruePos (kb) |
FalsNeg (kb) |
FalsPos (kb) |
Recall (%) |
Precision (%) |
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| X | 22.2 | 833.0 | 799.5 | 546.3 | 253.2 | 50.5 | 68.33 | 91.54 | 611.3 | 188.5 | 89.2 | 76.43 | 87.27 | ||||||||
| 2L | 22.4 | 879.5 | 818.7 | 590.1 | 228.6 | 38.9 | 72.08 | 93.82 | 660.7 | 158.0 | 64.1 | 80.7 | 91.15 | ||||||||
| 2R | 20.8 | 861.5 | 816.8 | 647.4 | 169.4 | 138.4 | 79.26 | 82.39 | 712.2 | 104.8 | 202.7 | 87.17 | 77.84 | ||||||||
| 3L | 23.8 | 939.5 | 874.1 | 664.6 | 209.5 | 55.4 | 76.03 | 92.31 | 735.8 | 138.6 | 87.2 | 84.15 | 89.4 | ||||||||
| 3R | 27.9 | 868.3 | 820.8 | 637.1 | 183.8 | 14.1 | 77.61 | 97.83 | 696.0 | 124.9 | 16.9 | 84.79 | 97.62 | ||||||||
| 4 | 1.3 | 128.1 | 86.8 | 44.3 | 42.5 | 86.8 | 51.03 | 78.65 | 54.4 | 32.4 | 206.7 | 62.64 | 72.45 | ||||||||
| Total
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118.4
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4509.9
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4216.7
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3129.8
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1087
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384.1
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74.22
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89.07
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3470.4
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747.2
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668.6
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82.28
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87.83
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We consider “positive findings” to be those regions in the IR and RIR sets that overlapped with BDGPTrans annotations. The positive set columns (4 and 9) show the number of base pairs from the BDGPTrans set that were in our positive findings. Recall is a measure of sensitivity and reports the percent of true positive base pair annotations out of all the base pairs annotated in the “gold truth” BDGPTrans set. Precision is a measure of specificity and reports the percentage of true positive base pairs out of all the base pairs our method annotated as TE component.
