Fig. 2: Evaluation of LILAP sequencing data. | Nature Communications

Fig. 2: Evaluation of LILAP sequencing data.

From: Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes

Fig. 2

a The length distribution of CCS reads. The curves show the probability density (ISO1-1: n = 1723578, ISO1-2: n = 1722440). b Box plot showing the relationship between the QV of each CCS read and its subread passes. Bar chart indicating read count in each subreads pass. Reads with pass numbers higher than 30 were merged into the last bin. The left and right Y-axes represent QV and read count, respectively. Only reads with lengths between 3500 bp and 6000 bp were displayed (ISO1-1: n = 838596, ISO1-2: n = 744864). c The chromosomal distribution of relative read depth with 100-kb window size. Annoroad’s amplification-based sequencing data were denoted as aISO1-Anno, whereas PacBio’s data were labeled as aISO1-PB. Except for the aISO1-PB, all other datasets were derived from male flies. Consequently, the presence of a minority of reads mapped to chrY in aISO1-PB likely indicates mismapping. Notably, the dots positioned between chr2L (Left) and chr2R (Right), between chr3L and chr3R, and within chrX denote centromeres. d The relative read depth in regions with different GC content. Standard PacBio HiFi sequencing data, Tn5 tagmentation-based short-read (Illumina) data, and amplification-based PacBio HiFi sequencing data served as controls. The left and right Y-axes show the relative depth and the proportion of the corresponding GC bins, respectively. The relative depth was calculated as \(\frac{{depth\; of\; each\; window}}{{{{{{\rm{median}}}}}}\left({depth\; of\; all\; windows}\right)}\). e The relative data yield of two multiplexed HiFi sequencing libraries. Each contains a fly family. The relative data size was calculated as \((\frac{{the\; nucleotide\; number\; of\; CCS\; reads\; from\; each\; single\; fly}}{{the\; total\; nucleotide\; number\; of\; CCS\; reads\; from\; six\; flies}})\times 6\). SD stands for standard deviation. For Panels (a, b), boxes represent the first and third quartiles, with medians marked with the middle line, while whiskers represent the minimum and maximum values.

Back to article page