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Table 4 Performance on HIV plasmid mixture dataset 2

From: QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

 

QQ-SNVD

QQ-SNVHS-P80 a

LoFreq

ShoRAH

V-Phaser 2

Variant %

sens.b

sens.b

sens.b

sens.b

sens.b

 40.0 %

2/2

2/2

2/2

1/2

nah

 39.9 %

1/1

1/1

1/1

1/1

nah

 39.5 %

1/1

1/1

1/1

0/1

nah

 38.9 %

1/1

1/1

1/1

0/1

nah

 38.4 %

2/2

2/2

2/2

2/2

nah

 34.4 %

2/2

2/2

2/2

1/2

nah

 34.0 %

1/1

1/1

1/1

1/1

nah

 33.5 %

1/1

1/1

1/1

1/1

nah

 33.4 %

8/8

8/8

8/8

7/8

nah

 6.6 %

1/1

1/1

1/1

1/1

nah

 6.1 %

1/1

1/1

1/1

0/1

nah

 5.1 %

1/1

1/1

1/1

1/1

nah

 5.0 %

8/8

8/8

8/8

8/8

nah

 1.0 %

10/10

10/10

9/10

7/10

nah

 0.6 %

0/1

1/1

1/1

0/1

nah

 0.5 %

5/8

8/8

8/8

2/8

nah

 0.1 %

1/10

6/10

2/10

2/10

nah

 

FPc

FPc

FPc

FPc

FPc

 

0

1

0

3

nah

 

timede

timede

timedf

timedg

timedg

 

2h29m

2h29m

2d4h11m

57m45s

nah

  1. a80th percentile of the QQ-SNVHS distribution of “error” frequencies was used as frequency cutoff to decrease the number of false positives obtained with QQ-SNVHS
  2. bsens. is the percentage of true variants that were correctly called as SNV
  3. cFP is the number of variants incorrectly called as SNV
  4. dcomputation time in days (d), hours (h), minutes (m) and seconds (s)
  5. eWindows 7 64 bit, 8GB RAM, 3.2GHz
  6. fLinux Ubuntu 12.04.4, 57.6 GB RAM, one core (2.3GHz) used
  7. gLinux Ubuntu 12.04.4, 57.6 GB RAM, 8 cores (2.3GHz) used in parallel
  8. hNo results could be obtained for the V-Phaser 2 algorithm due to failure of the V-Phaser 2 software tool on our server
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BMC Bioinformatics

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