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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