HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph
Fig 6
Correlation between mean coverage depth and reported confidence scores on simulated paired-end FASTQ data.
Distribution of posterior probabilities for precise haplogroup assignment for reads generated from four different simulated paired-end FASTQ samples (without added NuMT reads). As coverage depth increases, HaploCart posterior probabilities tend to increase, which is the desired behavior. In contrast, HaploGrep2 quality scores obey this behavior only for three of the four samples; the quality score for samples assigned to haplogroup H2a2a1 are always precisely 0.5. HaploCart is therefore less biased towards the haplogroup of the sample. Regression curves are polynomials of the third degree.