The following examples include rows from each section. Quantiles are listed second and can be any whole integer 0–100. Locations are listed first and can be either specific positions or ranges. ![]() Phred-scale quality value for bases at a given location and a given quantile of the distribution. Locations are listed second and can be either specific positions or ranges. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is. Sequences are listed first in the metric description in quotes. Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Number of times an adapter or other kmer sequence is found, starting at a given position in the input reads. ![]() Total number of reads with each GC content percentile between 0% and 100%.Īverage Phred-scale read mean quality for reads with each GC content percentile between 0% and 100%. Lengths can be either specific sizes or ranges, depending on the settings specified using -fastqc-granularity. Total number of reads with each observed length. The nucleotide is listed second and can be A, C, G, T, N. Locations are given first and can be either specific positions or ranges. Number of bases of each specific nucleotide at given locations in the read. N or ambiguous bases are assumed to have the system default value, usually QV2. The nucleotide is listed second and can be A, C, G, or T. Each average Phred-scale quality value is rounded to the nearest integer.Īverage Phred-scale quality value of bases with a specific nucleotide and at a given location in the read. The following metric types compose the sections. ![]() Each section is categorized into separate rows by length, position, or other relevant categorical variables. The reported metrics are organized into eight sections by metric type. The FastQC metrics are output to a CSV file format in the run output directory called
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