Sample	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-flagstat_total	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-mapped_passed	FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates	FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc	FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length	FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails	FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences	Cutadapt_mqc-generalstats-cutadapt-percent_trimmed	FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates	FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc	FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length	FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails	FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences	Bowtie2 (target)_mqc-generalstats-bowtie2_target-overall_alignment_rate	Bowtie2 (spike-in)_mqc-generalstats-bowtie2_spike_in-overall_alignment_rate	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-error_rate	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-non_primary_alignments	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-reads_mapped	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-reads_mapped_percent	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-reads_properly_paired_percent	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-reads_MQ0_percent	Samtools alignment scores_mqc-generalstats-samtools_alignment_scores-raw_total_sequences	Picard duplication stats_mqc-generalstats-picard_duplication_stats-PERCENT_DUPLICATION
JM4_R1	24036648	24036648	12.583051403640283	48.0	150.0	18.181818181818183	15116544.0	4.473766005422051	12.434457016502193	48.0	142.3871142393787	9.090909090909092	15101010.0	97.63	0.0	0.008199396	0.0	24036648.0	100.0	100.0	0.0	24036648.0	0.111439