Inspect a FASTQ file, review its quality, and take the report with you.
Raw FASTQ analysis or imported FastQC results
Start with a QC guide, then set cutoffs for this analysis. For quality, higher is better; for N content, lower is better. Values between pass and review are flagged for review. Changing a value affects the next run; the report always shows the cutoffs actually used.
These cutoffs guide review for the selected workflow; they are not diagnostic acceptance criteria. Read count is not a coverage estimate.
Mean Phred score at each base position
Applied guide appears with the report.
Percentage of A, C, G, T and N across all reads
GC content is descriptive. Interpretation depends on your organism and library preparation.
Read counts grouped by sequence length
Variable lengths may be expected for trimmed or long-read data.
A quick check before your next step
All reads in an accepted file are analyzed. This prototype supports four-line, single-end FASTQ with A/C/G/T/N bases and Phred+33 scores. Limits: 50 MB input, 100 MB decompressed, 200,000 reads, 100,000 bases per read. Files above a limit are rejected rather than sampled. The selected guide provides starting thresholds; any edits apply only when a new analysis runs. Reports retain the thresholds that were applied.
Mean quality is the arithmetic mean of all base scores. Q30 is the share of bases with a score of at least 30. Current QC guides use Phred+33 and the selected encoding is retained in the report. N content flags depend on the selected QC guide. Duplicate fraction is estimated from bounded sequence hashes; it is descriptive for generic short reads, context-dependent for amplicons, and not evaluated for the exploratory long-read guide. The parser accepts only four-line single-end records; multiline FASTQ and paired-end validation are not supported. For long reads, charts group adjacent positions into at most 600 points; checks still use every position. These are simplified prototype rules, not FastQC-equivalent checks. Adapter detection and classification are not included.
FastQC ZIP imports preserve the statuses and modules found in the archive; they do not rerun FastQC in the browser. This web prototype is independent of the Kmeggie+ CLI. It is not a validated diagnostic tool. Reports stay local to this tab unless exported; validated JSON exports can be reopened locally.