Library coverage analysis.

Analysis of coverage in the pilot and final gDNA fragments, and the pilot and final plasmid libraries. Genomic coverage (reported as bp covered, forward, reverse, and unstranded) was calculated using fragments of the appropriate orientation, inferred from mapped reads and the coverage function in the GenomicRanges R/Bioconductor package. The total number of covered bp are indicated, and the corresponding percentage of the HM1:IMSS reference genome that this represents. Forward fragments are in the same orientation as genes that are in the forward orientation in the reference genome. Reverse fragments are in the same orientation as genes that are in the reverse orientation in the reference genome. Stranded fragments are in the same orientation as genes, and are the combined total of both forward and reverse fragments. Unstranded fragments are the total number of fragments, both in the same orientation as genes in the reference genome and in the opposite orientation as genes. Genes that are targeted are those with at least one unique fragment with greater than or equal to 27nt that overlaps the gene. Genes that are missed are those that do not fit the criteria for targeted genes. Genes that are targeted by multiple fragments are those with two or more unique fragments. Counts were calculated using the countOverlaps function in the GenomicRanges package and annotation from AmoebaDB. The number of unique fragments is the total number of unique fragments in each sample.