Skip to main content
Fig. 2 | BMC Genomics

Fig. 2

From: Improvement in detection of minor alleles in next generation sequencing by base quality recalibration

Fig. 2

Recalibrated base quality scores generated from different methods for simulated data. For each method the recalibrated scores are compared to the empirical scores; the ideal (diagonal) line is shown in each plot. The Frequency-Weighted Squared Error (FWSE) is also given for each method. Raw: Sequence generated by simulation (SimSeq); Seg: this study; GATK1: dbsnp 142 is used as known database of SNPs, no misalignment issue (mapped by crossmap); GATK2: SNPs in the entire dataset of 13 mtDNA genome sequences, no misalignment issue; GATK3: the actual genetic variants (both SNPs and indels) for just the particular mtDNA genome sequence are used, no misalignment issue; GATK4: dbsnp142 is used, with potential misalignment issues (mapped by BWA)

Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us