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Table 3 Single-nucleotide variant (SNV) F β scores for various β’s with original mapping qualities and with Qtip-generated qualities

From: A tandem simulation framework for predicting mapping quality

  Original Qtip Δ (Qtip − Orig)
β F β QUAL Q F β QUAL Q F β TP FP
0.250 0.9925 194 2 0.9924 213 2 -2.2e-05 +20,189 +1505
0.333 0.9906 150 3 0.9908 178 2 +2.6e-04 +16,001 +911
0.500 0.9872 87 3 0.9881 125 3 +8.3e-04 +15,143 +311
0.750 0.9843 10.6 3 0.9854 70.1 4 +1.1e-03 -413 -6537
1.000 0.9835 0.0158 3 0.9845 13.6 4 +9.4e-04 +3999 -2745
1.500 0.9846 1.79e-06 3 0.9856 0.000675 5 +1.0e-03 +4392 -1832
2.000 0.9860 5.06e-08 3 0.9870 1.38e-05 5 +1.0e-03 +3110 -5692
3.000 0.9880 1.16e-09 3 0.9889 8.64e-08 4 +8.6e-04 +2583 -7937
4.000 0.9892 1.06e-10 3 0.9899 6.58e-09 4 +7.1e-04 +1891 -13,600
  1. Paired-end reads from ERR194147, a female, were aligned with Bowtie 2 together with Qtip. SNV variants were called with Freebayes for chromosomes 1–22 and X. Variant-quality (QUAL) and mapping-quality (Q) thresholds yielding the greatest F β score are reported. Platinum variants were used as the true callset. Before calculating F β , calls outside Platinum Genomes high-confidence regions were excluded. The three rightmost columns show differences in F β , the number of true positive SNVs, and the number of false positive SNVs
  2. FP false positive
  3. SNV single-nucleotide variant
  4. TP true positive