metric	value	note
Analysis mode	denovo / no-reference	reference-guided or de novo RNA-seq analysis mode
Samples	24	RNA-seq samples included in the run
Route	de novo salmon (assembled transcriptome)	no-reference route: assembly plus Salmon quantification against assembled transcripts
DE source	de novo transcript counts	count-like matrix built from assembled transcript quantification
Avg Salmon reads	457133.12	mean estimated_num_reads across samples; in de novo mode these reads are quantified against the assembled transcriptome
Avg mapped %	N/A (de novo)	not applicable without reference genome alignment
featureCounts assigned	N/A (de novo)	not applicable without reference genome feature counting
QC assigned tags	N/A (de novo)	not applicable without reference genome alignment QC
Tested genes	9592	genes retained for DESeq2 testing
Significant genes	713	padj and log2FC filtered DE genes
Up / down genes	221 / 492	direction split among significant genes
ORA terms	1427	over-representation result rows
GSEA terms	4369	preranked enrichment result rows
De novo filtered transcripts	9609	assembled transcriptome after length filtering
De novo N50	1308	filtered de novo transcript N50
De novo BUSCO	skipped	BUSCO completeness step status when available
De novo matrix semantics	transcript-level only; no tx2gene/cluster aggregation	transcript-level only unless explicit tx2gene or cluster mapping was supplied
De novo transcript rows	9609	transcript-level expression feature rows
Pseudo-gene rows	0	gene or cluster rows from optional mapping
Annotated transcripts	8285	transcripts with homology annotation evidence
GO gene sets	5705	annotation-derived GMT gene sets available for enrichment
Collected plots	14	PNG/PDF plot groups in this report
Linked HTML reports	26	copied QC/report HTML bundles linked from this report