Defective Genome Deletion Union
Measure the union of annotated viral genome deletions without double counting overlaps; deletion fraction does not establish interference.
Description
Merge overlapping genome deletion intervals and count the distinct bases removed.
A deletion interval identifies a stretch removed from a reference genome. When annotations overlap, adding their lengths counts some bases more than once. Taking the union counts each removed base once and makes the retained-length calculation meaningful.
Coordinates use zero-based, half-open intervals: start is included and end is excluded, so [100, 200) spans 100 bases. This convention is also used by BED records; convert one-based inclusive annotations before entering them.1
The tool reports deleted bases, the deleted fraction of the supplied genome, and retained bases. The word defective in its name does not mean the calculator establishes whether the resulting genome can replicate or interfere with another virus.
When to use Defective Genome Deletion Union
Use it to summarize deletion annotations on one reference genome, including duplicate, overlapping, or adjacent calls that should not be counted twice.
How to use Defective Genome Deletion Union and interpret its calculation
- Enter a positive integer genomeLengthBp.
- Enter aligned deletionStartsBp and deletionEndsBp lists in the same coordinate system. Each start must be smaller than its end, and each end must fit within the genome.
- Run the tool and read the three length summaries. Use an empty pair of lists to represent no annotated deletions.
The implementation pairs starts and ends, sorts intervals by start, and merges intervals whose next start is at or before the current end. Thus both overlaps and touching intervals merge. It sums end minus start over the merged intervals.
deleted = length(union of deletion intervals); deleted fraction = deleted / genome length; retained = genome length − deleted All lengths are in bases, and the fraction is dimensionless.
{
"input": {
"genomeLengthBp": 1000,
"deletionStartsBp": [
100,
150
],
"deletionEndsBp": [
200,
250
]
},
"output": {
"deletedBases": 150,
"deletedGenomeFraction": 0.15,
"retainedGenomeBases": 850
}
}| Boundary case | Behavior |
|---|---|
| No deletions | Deleted bases and fraction are zero; all bases remain. |
| Repeated interval | It contributes its length once. |
| Touching intervals [0, 10) and [10, 20) | The union contains 20 bases. |
| Start equals end, negative coordinate, or end beyond genome | The input is rejected. |
Limitations and assumptions
Coordinates must be nonnegative safe integers, with a positive safe-integer genome length. Lists must align; their original order need not be sorted.
The union describes the supplied intervals on one coordinate axis. Combining calls from different viral variants would create a synthetic union rather than the deletion content of any one observed genome.
It does not inspect sequence, validate breakpoints, detect insertions, or assess retained genes, packaging signals, infectivity, or defective-interfering activity.
Alternative or Complementary methods
Inspect biologically important intervals separately after computing total deletion length. If the task is to assign reported breakpoint positions to annotations, a point-overlap calculation is more suitable.
References
-
Genome Browser FAQ: BED format — UCSC Genome Browser
Similar or alternative tools
- Retained Packaging Signal Interval
Check a supplied packaging-signal interval against retained genomic coordinates.
- Breakpoint Region Overlap
Assign breakpoint points to caller-defined genomic regions.