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

BMC Bioinformatics

Table 6 Performance on H1N1 clinical sample

^a80^th percentile of the QQ-SNV_HS distribution of “error” frequencies was used as frequency cutoff to decrease the number of false positives obtained with QQ-SNV_HS
^bsens. is the percentage of SNVs as identified in [12] that were called as SNV by QQ-SNV in region 405–425 of NA gene in H1N1 BN3 sample
^cFP is the number of “non-variants” in [12] that were called as SNV by QQ-SNV
^dReads 1 of paired-end reads
^eReads 2 of paired-end reads (sequenced after paired-end turn)
^fAll paired-end reads
^gcomputation time in hours (h), minutes (m) and seconds (s)
^hWindows 7 64 bit, 8GB RAM, 3.2GHz
ⁱLinux Ubuntu 12.04.4, 57.6 GB RAM, one core (2.3GHz) used
^jLinux Ubuntu 12.04.4, 57.6 GB RAM, 8 cores (2.3GHz) used in parallel
^kNo result could be obtained for the ShoRAH/V-Phaser 2 algorithm due to failure of the ShoRAH/V-Phaser 2 software tool on our server

ISSN: 1471-2105