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Table 7 SNVs called by QQ-SNVHS-P80 on H1N1 clinical sample (all paired-end reads)

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

 

GAIIx

MiSeq

SNV identified in [12]

Positiona

Percentageb

P(SNV)c

Percentageb

P(SNV)c

406

nad

nad

0.09 %

0.99923

No

409

0.13 %

0.00110

0.10 %

0.00517

No

410

0.35 %

0.05514

0.28 %

0.60047

Yes

411

0.13 %

0.00016

0.09 %

0.00318

No

413

0.26 %

0.00482

0.14 %

0.98815

Yes

415

0.25 %

0.00207

0.16 %

0.98665

Yes

418

0.18 %

0.00011

0.09 %

0.00769

No

421

0.26 %

0.04058

0.16 %

0.94675

Yes

423

0.15 %

0.00012

0.08 %

0.02083

No

425

nad

nad

0.07 %

0.88219

No

  1. aNucleotide position in neuraminidase (NA) gene
  2. bObserved frequency of single nucleotide variant called by QQ-SNV
  3. cProbability that variant is a SNV, as predicted by QQ-SNV
  4. dNot classified as SNV by QQ-SNVHS-P80, P(SNV) ≤ 0.0001
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BMC Bioinformatics

ISSN: 1471-2105

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