276    ◾    Bioinformatics

We can view the visualization file on the Internet browser using “q2-tools view” as follows:

qiime tools view viz/demux-yoga-qc.qzv

The report displayed on the Internet browser will have two tabs: Overview and Interactive

Quality Plot. The Overview report tab shows Demultiplexed sequence count summary,

forward and reverse reads frequency histogram, and Per-sample sequence counts. The

summary count section shows minimum, median, mean, maximum, and total number

of reads across the samples for forward reads and reverse reads (this is only in paired

end). Figure 7.7 shows that the summary statistics for forward reads and reverse reads are

the same. The minimum number of reads in a sample is 7702 and the maximum num-

ber of reads is 95075. The median and mean of reads across all samples are 25588.0 and

30018.709302, respectively. The total number of forward reads in all samples is 2581609

and is the same for reverse reads. The histogram shows the distribution of the number

of reads versus number of samples. The histograms can be downloaded as pdf files. The

Per-sample sequence counts table, below the histogram, lists sample ID and number of

forward reads and reverse reads in each sample. The Interactive Quality Plot section shows

plots for the per base Phred quality score across reads for both forward and reverse reads

(Figure 7.8). These plots are similar to the QC plots discussed in Chapter 1. They will help

us to determine if the sequences need trimming or filtering. If you hover the mouse over a

specific position on the plot, the table below the plot will update itself to display the seven-

number summary statistics for that base position. This table corresponds to what is visu-

ally represented by the box plot at that position.

FIGURE 7.7  Sequence count summary and histograms of reads of yoga data.