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Table 3 PSE-HMM precision and recall are computed for a simulated dataset with 10× depth of coverage

From: PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities

  Real state
Heterozygous deletion Diploid Homozygous deletion Tandem duplication Sum Precision Recall
Predicted state Heterozygous deletions 1,146 660 97 0 1,903 0.60 1.00
Diploid 2 23,560 2 89 23,653 1.00 0.95
Homozygous deletions 0 279 1,221 1 1,501 0.81 0.93
Tandem duplications 3 363 0 2,577 2,943 0.88 0.97
sum 1,151 24,862 1,320 2,667 30,000   
  1. In columns 3 to 6, predicted state is shown versus the real state of the genomic segments, and number of segments is indicated in the corresponding cell. A total number of 30,000 genomic segments (4.5 million bp) are evaluated in this analysis