Fig. 2

Reach of short read and long read technologies. The callable and mappable regions for NA12878 spanning various repetitive or duplicated sequences on GRCh38 are shown. Feature locations are determined based on BED tracks downloaded from the UCSC Genome Browser [48]. Other than the Gencode regions [49, 50], all features are subsets of the Repeat Masker [51] track. Four coverage statistics for long reads (shades of red) and three for short reads (shades of blue) are shown. The labels “PacBio Mappable” and “Nanopore Mappable” describe areas where at least one primary read with GQ ≥ 30 has mapped, and “Long Read Mappable” describes where this is true for at least one of the long read technologies. “Long Read Callable” describes areas where both read technologies have coverage of at least 20 and less than twice the median coverage. “GIAB High Confidence,” “GATK Callable,” and “Short Read Mappable” are the regions associated with the evaluation callsets. For the feature-specific plots, the numbers on the right detail coverage over the feature and coverage over the whole genome (parenthesized)