Reports

Reports

insilicoPCR produces report files that summarize primer hits, predicted amplicons, and consolidated results across samples.

Report types

• runtime and quality logs (QAlog.txt)
• detailed per-sample BLAST hit tables (detailed_report/<sample>/<sample>.tsv)
• consolidated TSV report (consolidated_report/report.tsv)
• synthetic gel images rendered from the consolidated report

If a report.tsv already exists in the output folder, a new run writes report(1).tsv, report(2).tsv, and so on instead of overwriting it.

Consolidated report

The consolidated report is the primary summary table: one row per predicted amplicon that passed the amplicon calling rules.

Standard PCR mode columns

Column	Meaning
Sample	Sample name (from the input file name)
Gene	Assay name (primer ID without the -F/-R/-P suffix)
GenomeLocation	1-based start-end of the product on the contig
AmpliconSize	Product length in bp, primers included
Contig	Contig/sequence ID the product sits on
Contig Description	Free text from the contig FASTA header
ForwardPrimers / ReversePrimers	Primer IDs that formed the pair (degenerate variants keep their _n suffix)
ForwardMismatches / ReverseMismatches	Mismatches + indels + unaligned 3' bases for each primer
Forward3PrimeMismatches / Reverse3PrimeMismatches	Number of imperfections within the 3'-end window (default last 5 bases)
Strand	+ when the forward primer matched the plus strand; - when the assay matched the reverse strand

qPCR/probe columns

When at least one assay in the primer file defines a -P probe, the report appends:

Column	Meaning
Probe	Probe ID
ProbeLocation	1-based start-end of the probe on the contig
ProbeSize	Length of the probe match
ProbeMismatches	Mismatches + indels in the probe alignment

For an assay that defines a probe, a row is only written when the probe lies entirely within the amplicon. Probe-less assays in the same run keep these columns empty.

Detailed per-sample reports

The detailed_report folder keeps the raw BLAST tabular output per sample (with a header line), useful for auditing why a primer hit was or was not accepted. Columns follow BLAST -outfmt "6 qseqid sseqid positive mismatch gaps evalue bitscore slen length qstart qend qseq sstart send sseq".

Mode behavior

The probe requirement is decided per assay (since version 0.8.0): assays with a -P probe require probe support inside the amplicon, while probe-less assays are reported on their primer pair alone — both can live in the same primer FASTA file. See Standard PCR vs qPCR.

Synthetic gel

The synthetic gel visualizer reads consolidated result data and displays predicted amplicons as gel-like bands. See Synthetic Gel Visualizer.