RNA Output

LowQ

Splice variant score < passing quality score threshold value of 1.

PASS

Splice variant score ≥ passing quality score threshold value of 1.

LowUniqueAlignments

All splice junction supporting reads map to a unique genomic interval near at least one of the two splice sites.

DOUBLE_BROKEN_EXON

Confidence filter

If both breakpoints are distant from annotated exon boundaries, the number of supporting reads do not satisfy a high threshold requirement (≥ 10 supporting reads).

LOW_MAPQ

Confidence filter

All fusion supporting read alignments at either of the breakpoints have MAPQ < 20.

LOW_UNIQUE_ALIGNMENTS

Confidence filter

All fusion supporting read alignments map to a unique genomic interval at either of the breakpoints.

LOW_SCORE

Confidence filter

The fusion candidate has probabilistic score as determined by the features of the candidate.

MIN_SUPPORT

Confidence filter

The fusion candidate has very few fusion supporting reads (< 5 supporting read pairs).

READ_THROUGH

Confidence filter

The breakpoints are cis neighbors (< 200 kbp) on the reference genome.

ANCHOR_SUPPORT

Information only

Read alignments of fusion supporting reads are not long enough (12 bp) at either of the two breakpoints.

HOMOLOGOUS

Information only

The candidate is likely a false candidate generated because the two genes involved have high gene homology.

LOW_ALT_TO_REF

Information only

The number of fusion supporting reads is < 1% of the number of reads supporting the reference transcript at either of the two breakpoints.

LOW_GENE_COVERAGE

Information only

Each breakpoint in an enriched gene has fewer than 125 bp with nonzero read coverage.

NO_COMPLETE_SPLIT_READS

Confidence filter

For every fusion-supporting split read, the total number of aligned bases across two breakpoints is less 60% of the read length.

UNENRICHED_GENE

Confidence filter

Neither of the two parent genes is in the enrichment panel.

Gene A

The gene associated with the A side of the fusion. A semicolon delimited list is used for multiple genes.

Gene B

The gene associated with the B side of the fusion. A semicolon delimited list is used for multiple genes.

Gene A Breakpoint

[Information only] The chromosome and offset of the Gene A side of the fusion.

Gene A Location

Location of the breakpoint within Gene A: - IntactExon—Matches exon boundary - BrokenExon—Inside an exon - Intronic—Within an intron - Intergenic—No gene overlap (currently excluded) If multiple genes are in Gene A, then semicolon separated list of locations. This column is used internally to identify genes to report when a breakpoint occurs in a region overlapping multiple genes. Occasionally, additional values are listed for genes that were excluded from the GeneA list.

Gene A Sense

Boolean indicating whether left/right breakpoint order suggests fusion transcript is in the same sense of Gene A. If multiple genes are in Gene A, then semicolon separated list of bools.

Gene A Strand

Strand of Gene A, + for forward, - for reverse.

Gene B Breakpoint

[Information only] The chromosome and offset of the Gene B side of the fusion.

Gene B Location

Location of the breakpoint within Gene B: - IntactExon—Matches exon boundary - BrokenExon—Inside an exon - Intronic—Within an intron - Intergenic—No gene overlap (currently excluded) If multiple genes in Gene B, then semicolon separated list of locations. This column is used internally to identify genes to report when a breakpoint occurs in a region overlapping multiple genes. Occasionally, additional values are listed for genes that were excluded from the GeneB list.

Gene B Sense

Boolean indicating whether left/right breakpoint order suggests fusion transcript is in the same sense of Gene B. If multiple genes are in Gene B, then semicolon separated list of bools.

Gene B Strand

Strand of Gene B, + for forward, - for reverse.

Score

The quality of fusion as determined by DRAGEN server.

Filter

The filter associated with the fusion as determined by the respective caller. Results from different callers are not equivalent.

Ref A Dedup

Gene A uniquely mapping reads paired across or split by the junction. Does not support fusion. Duplicate reads are not included.

Ref B Dedup

Gene B uniquely mapping reads paired across or split by the junction. Does not support fusion. Duplicate reads are not included.

Alt Split Dedup

Uniquely mapping reads split by the junction. Supports fusion. Duplicate reads are not included.

Alt Pair Dedup

Uniquely mapping reads paired across junction. Supports fusion. Duplicate reads are not included.

KeepFusion

The determination whether the fusion should be kept or dropped from the list of fusions.

Fusion Directionality Known

Whether fusion directionality is known and indicated by gene order.