Display example MultiQC plots

docs/output.md

@@ -59,10 +59,9 @@ Genomes are aligned witn [`lastal`](https://gitlab.com/mcfrith/last/-/blob/main/
 
 </details>
 
-Dot plots representing the pairwise genome alignments, produced with the [`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst) tool. In the one-to-one alignment example below, the `hg38` human genome (_target_) is represented on the horizontal axis and a monkey genopme (_Macaca mulatta_ accession number `GCA\_003339765.3`) on the vertical axis (_query_). Regions containing unknown (`N`) sequences are on pink background. Forward (+/+) alignments are plotted in red and reverse (+/– or –/+) in blue. _Target_ (human) contigs are displayed in their original order.  _Query_ contigs (monkey) are reordered and possibly reverse-complemented to diagonalise the plot as much as possible. The names of reverse-complemented contigs are printed in blue.
+Dot plots representing the pairwise genome alignments, produced with the [`last-dotplot`](https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst) tool. In the one-to-one alignment example below, the `hg38` human genome (_target_) is represented on the horizontal axis and a monkey genopme (_Macaca mulatta_ accession number `GCA\_003339765.3`) on the vertical axis (_query_). Regions containing unknown (`N`) sequences are on pink background. Forward (+/+) alignments are plotted in red and reverse (+/– or –/+) in blue. _Target_ (human) contigs are displayed in their original order. _Query_ contigs (monkey) are reordered and possibly reverse-complemented to diagonalise the plot as much as possible. The names of reverse-complemented contigs are printed in blue.
 
- ![Example of a dot-plot produced by the pipeline after aligning human and macaque genomes](images/Homo_sapiens_GCA_000001405.29_GRCh38.p14___Macaca_mulatta_GCA_003339765.3.o2o_plt.png
- "Human–Monkey comparison") 
+![Example of a dot-plot produced by the pipeline after aligning human and macaque genomes](images/Homo_sapiens_GCA_000001405.29_GRCh38.p14___Macaca_mulatta_GCA_003339765.3.o2o_plt.png "Human–Monkey comparison") 
 
 ### `N` regions
 
@@ -94,6 +93,32 @@ The poly-N regions longer than 9 bases in each genome sequence often indicate co
 
 Results generated by MultiQC collate pipeline QC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
+The example MultiQC plots below were generated on this pipeline's full test dataset, which aligns the `hg38` human genome to other primate genomes.
+
+#### Base content
+
+The pipeline reports the base content of every query genome, like in the example below:
+
+![Example of a base content report for primate genomes](images/mqc_base_content_summary-pct.png "Primate genome base content") 
+
+#### Contig length statistics
+
+Contig length statistics can be displayed by MultiQC as violin plots.
+
+![Example of a contig length report for primate genomes](images/mqc_contigs_length_statistics.png "Contig length statistics")
+
+#### TRaining parameters
+
+Alignment parameters computed by `last-train` can be displayed by MultiQC as violin plots.
+
+![Example of alignment parameters for primate genomes aligned to the human genome](images/mqc_train-stats.png "Alignment parameters") 
+
+#### Alignment
+
+Alignment statistics can be displayed by MultiQC as violin plots.
+
+![Example of alignment statistics for primate genomes aligned to the human genome](images/mqc_last_o2o-stats.png "Alignment statistics") 
+
 ### Pipeline information
 
 <details markdown="1">