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. Author manuscript; available in PMC: 2009 Aug 12.
Published in final edited form as: Bioinformatics. 2008 Jan 17;24(4):462–467. doi: 10.1093/bioinformatics/btm632

Table 3.

Sensitivity and specificity results of Figaro on Drosophila pseudoobscura shotgun reads

Max distance
m 		SNm
(%)		 SPm
(%)		 TPm FNm FPm
0 99.98 99.15 1 493 582 316 12 781
3 99.99 99.29 1 500 662 186 5831
5 ~100 99.72 1 502 428 67 4184
10 ~100 99.79 1 503 481 54 3144

Using a threshold of 30, Figaro is able to remove virtually all vector sequence and only overtrims a small proportion of reads by more than 3 bp. Note false positives and false negatives are computed only if they occur in the high-quality region of a read.