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Table 2 Detection of human, mouse and rat piRNA clusters using proTRAC with different thresholds

From: proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

species thresholds* minimum piRNA density [hits/kb]** minimum loci/cluster cluster candidates tracked clusters (mono-, bi-, non-directional)*** p 0/≥2 mistakenly annotated clusters
  0.05/1.3 0.1 - 1.4 6 25402 368 (202, 120, 46) 0.001/0.992
human 0.01/2.0 0.6 - 2.4 8 14381 187 (139, 40, 8) 0.700/0.049
  0.001/3.0 1.5 - 3.5 11 4558 119 (99, 19, 1) 0.984/<0.001
  0.05/1.3 1.5 - 2.3 6 57260 242 (163, 63, 16) 0.133/0.595
mouse 0.01/2.0 2.5 - 3.4 8 51332 171 (129, 38, 4) 0.866/0.009
  0.001/3.0 3.7 - 4.7 11 37403 151 (123, 25, 3) 0.988/<0.001
  0.05/1.3 1.2 - 1.7 6 34069 186 (139, 43, 4) 0.334/0.293
rat 0.01/2.0 1.8 - 2.7 8 36402 168 (138, 28, 2) 0.926/0.003
  0.001/3.0 2.8 - 3.7 11 28576 162 (136, 26, 0) 0.994/<0.001
  1. *Significance level for increased hit density/minimum score for strand bias, enrichment of loci corresponding to infrequently mapped reads and enrichment of putative piRNA loci with 1T/10A. **depending on chromosomal piRNA density. ***mono-, bi-directional: >75% of mapped sequences located on the main strand.