Depth of coverage of sequencing reads across platforms and regions.

For each sequencing platform (colored lines, with platforms as in S1 Table), the plot shows the depth of coverage of reads aligned to GRCh38 across the eight selected regions (Table 1). Depths are normalized by the average depth across each region for each dataset. Areas with apparent systematic lower depth in the TRA, TRB and TRG regions are highlighted with black triangles. Datasets generated with DNA from CD14+ monocyte and PMBC are denoted with solid and dashed lines, respectively. Decrease of sequencing depths is not identified in immunoglobulin regions, presumably due to the relatively low fraction (5–15%) of B cells in PBMC. Despite γδ T cells being rarer than α/β T cells, the coverage drop around T cell receptor γ genes can be explained by the fact that the γ locus is known to undergo rearrangement in most α/β T cells [65], and the drop around T cell receptor δ genes can be explained by the fact that any rearrangement at the α locus leads to the loss of the δ locus.[66]

(PNG)