Output Report (-o)

The output report is saved to the user-provided output directory in a file named based on the input BAM files (/path/to/output/XXXXX_deletion.tab from some input XXXXX.bam). Below is a sample report based on the results from running DeletionID on a whole genome sequencing dataset of the APE3 deleted knockout from the Yeast Knockout Collection (ERS838258 sample downloaded from ENA and generated by Puddu et al, 2019).

LEU2 No Data Detected
URA3 No Data Detected
APE3 -3.3992739779627357

The first column of the report lists out the intervals (ORFs) with significantly depleted reads, sorted by the DeletionID score values in the second column which sort the more negative scores (more read depleted intervals) first. This sample is from an APE3 knockout in a LEU2 and URA3 knockout background so we expect all three gene intervals to show up in the report. LEU2 and URA3 show No Data Detected which indicates no reads mapped to this interval. APE3 shows a very strong depletion with a large negative score (-3.3992...) confirming the knockout as likely.