Variants & FASTQ / FASTQ quality report
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The per-position quality plot shows the mean, median, quartiles (Q1/Q3) and 10th/90th percentiles (P10/P90) at each position. Illumina quality usually drops towards the end of the read; consider trimming stretches where the median stays below 20.
In the base content plot A/C/G/T should run roughly parallel; wobbles over the first few positions are common with random-primed libraries. A rise in N usually points to a problem in one cycle or tile.
Duplication is estimated from the first N reads (100,000 by default); a lower “distinct after de-duplication” means more duplicates. RNA-seq and amplicon data naturally carry more duplicates, so read it in light of the assay.
The adapter plot shows the share of reads in which an adapter fragment has appeared by each position; a rise towards the end means inserts shorter than the read length, so trim adapters before alignment. The FASTQ / FASTA conversion tool can trim and filter reads.
Metric definitions follow common sequencing QC practice (Andrews 2010, FastQC; Chen et al. 2018, Bioinformatics 34:i884, fastp); read and base counts and Q20/Q30 match fastp, and all other metrics match an independent Python reference implementation.
Runs in your browser; uncompressed FASTQ up to about 200 MB. Large files may take a few tens of seconds. Compressed .gz files cannot be read directly yet.
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