Table 1.
Quality metric comparison between suggested commercial sequencing quality and results from both HTMGS sequencing chips.
Fig 1.
Summary of quality control metrics for the reads generated by the HTMGS protocol by MultiQC.
A) Phred quality scores remained consistent per base in read when considering size selection methods; B) sequence GC content followed a normal distribution. The green line represents ‘excellent’ quality reads whereas orange lines represent ‘medium’ read quality scores; C) read length distribution for all samples was between 150–250bp due to the size selection method. The orange lines represent ‘medium’ read quality scores.
Fig 2.
Median coverage density plot for all 315 HTMGS runs showing consistent median coverage between all sequencing chips.
Fig 3.
Evidence of correct variant calling in the HTMGS method via examination of mtDNA variant distribution and concordance.
The solar plot summarises the variants detected via the HTMGS protocol. Each dot represents a detected variant. The inner ring of the plot represents the mitochondrial genome and is coloured based on genomic region as summarised in the plot legend. The X-axis represents the mitochondrial base pair location with the Y-axis representing the variant frequency in the NI population from 0 (not present in the NI sample) to 1 (total concordance of the variant in the NI sample). The location of the data points in relation to the inner ring represents the allele count with those on the centre ring correlating to 1/315 in the NI pedigree whereas variants toward the outer ring varying and those touching the outer ring representing total concordance of the variant in the NI sample (315/315).
Table 2.
Commercial kit verses HTMGS method cost comparisons for each major step used to complete Ion Torrent PGM whole mitochondrial sequencing.