Hi @James Fellows Yates I am continueing our discussing on extracting overrepresented read counts from the multiqc output here. So I am trying to identify how many overrepresented reads there are per sample. And I use the multiqc report for that. I ran MAG version 5.0.0. and I see in my multiqc output folder, the folder: multiqc_report_data in that folder in have the multiqc_data.json file and I have many yaml files, like

fastqc_overrepresented_sequences_plot.yaml

. I have no txt files in that folder. The content of that yaml file looks like this for one sample:

TEI135_run0_raw_1:
  Sum of remaining overrepresented sequences: '0.8894559198826477'
  Top overrepresented sequence: '0.5302254727651685'
TEI135_run0_raw_2:
  Sum of remaining overrepresented sequences: '1.1311732716864724'
  Top overrepresented sequence: '0.495179754975124'

that is not very helpfull, since it does not give me actual read counts per sample.