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Table 2 Quality validation of running LTRharvest on the D. melanogaster genome sequences (release 3)

From: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Chr Predictions References TP hTP FP FN
2L 91 66 64 1 26 1
2R 89 54 49 3 37 2
3L 96 59 51 7 38 1
3R 96 67 60 6 30 1
4 11 4 4 0 7 0
X 122 54 51 3 68 0
Total 505 304 279 20 206 5
  1. The used options are listed in Table 1 in column 'value D. mel.'. Column 'Predictions' gives the number of predicted and column 'References' the number of annotated 'full length' LTR retrotransposons for each chromosome. A prediction is classified as true positive (TP), if the maximum allowed distance between 5' and 3' coordinates of the prediction and the reference is at most 20 nucleotides. If only one of the two predicted boundary coordinates lies within the allowed distance of 20 nucleotides, the prediction is categorised as a half true positive (hTP). All other predictions are labelled false positive (FP). LTR retrotransposons that are missing in the prediction are labelled false negative (FN).