Illumina BasicQC Report

The number of read-pairs per sample at the start of the analysis is shown.

This plot shows the mean base quality score for each position in a fastq file. The higher the score the better the base call. Green indicates very good quality, yellow indicates reasonable quality, and red indicates poor quality. The quality of calls degrade as the sequencing run progresses, so it is common to see base calls turning yellow towards the end of a read. It is common to see base calls turning red in short insert libraries (16s/18s, small RNA, amplicon). R2 read quality is typically slightly lower overall than R1 read quality. This metric is calculated by FastQC.

This plot shows the mean base quality score for each position in a fastq file. The higher the score the better the base call. Green indicates very good quality, yellow indicates reasonable quality, and red indicates poor quality. The quality of calls degrade as the sequencing run progresses, so it is common to see base calls turning yellow towards the end of a read. It is common to see base calls turning red in short insert libraries (16s/18s, small RNA, amplicon). R2 read quality is typically slightly lower overall than R1 read quality. This metric is calculated by FastQC.

This plot shows the cumulative proportion of each sample in which sequencing adapter sequences have been seen at each position. Once an adapter sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages only increase as the read length goes on. It is common to see significant adapter sequence content at the ends of reads in short insert libraries (16s/18s, small RNA, amplicon). This metric is calculated by FastQC.

This plot shows the percentage of R1 reads that remain after deduplication (removing duplicated sequences), which is a measure of library diversity. Sequence data from genomic DNA libraries typically have high library diversity, and data from targeted sequencing libraries typically have low diversity. This metric is calculated by FastQC.

The first 10,000 R1 reads from each sample are aligned to a selection of common reference genomes and sequence contaminants, and the number of reads aligning to each reference is shown. Reads aligning to multiple references are assigned to the reference with the most alignments. This plot provides a simple method to verify the sequence content of each library.