Sample	FastQC_mqc-generalstats-fastqc-percent_duplicates	FastQC_mqc-generalstats-fastqc-percent_fails	FastQC_mqc-generalstats-fastqc-percent_gc	FastQC_mqc-generalstats-fastqc-avg_sequence_length	FastQC_mqc-generalstats-fastqc-total_sequences	Picard_mqc-generalstats-picard-PERCENT_DUPLICATION	QualiMap_mqc-generalstats-qualimap-total_reads	QualiMap_mqc-generalstats-qualimap-mapped_reads	QualiMap_mqc-generalstats-qualimap-percentage_aligned	QualiMap_mqc-generalstats-qualimap-general_error_rate	QualiMap_mqc-generalstats-qualimap-median_coverage	QualiMap_mqc-generalstats-qualimap-10_x_pc	QualiMap_mqc-generalstats-qualimap-5_x_pc	QualiMap_mqc-generalstats-qualimap-avg_gc	QualiMap_mqc-generalstats-qualimap-median_insert_size	QualiMap_mqc-generalstats-qualimap-mean_coverage	QualiMap_mqc-generalstats-qualimap-50_x_pc	QualiMap_mqc-generalstats-qualimap-30_x_pc	QualiMap_mqc-generalstats-qualimap-1_x_pc	Prokka_mqc-generalstats-prokka-CDS	Prokka_mqc-generalstats-prokka-bases	Prokka_mqc-generalstats-prokka-organism	Prokka_mqc-generalstats-prokka-contigs
ea1 | 1EA_L7_R1_001.fastq.gz	51.805386238501875	18.181818181818183	44.0	100.0	31289121.0																		
ea1 | 1EA_L7_R2_001.fastq.gz	46.8481602169596	9.090909090909092	44.0	100.0	31289121.0																		
ea1 | 2EA_L7_R1_001.fastq.gz	50.015946224441	18.181818181818183	44.0	100.0	27654135.0																		
ea1 | 2EA_L7_R2_001.fastq.gz	45.37919211626318	9.090909090909092	44.0	100.0	27654135.0																		
ea1 | 3EA_L7_R1_001.fastq.gz	44.70502704806746	9.090909090909092	44.0	100.0	19072239.0																		
ea1 | 3EA_L7_R2_001.fastq.gz	39.69479562551955	9.090909090909092	44.0	100.0	19072239.0																		
ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.070136																	
ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | asm_pair-smds.bam							53792017.0	52615191.0	97.81226645582002	0.45999999999999996													
ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats											13	59.53011586872276	76.6339409932194	45.03105658273829	354	2.76020860405249	23.32028619425975	34.90457685999996	96.71205887419704				
ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.065609																	
ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | asm_pair-smds.bam							47944215.0	46926157.0	97.87657801884961	0.44999999999999996													
ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats											12	55.59673223640758	73.33098998905409	45.11010927877621	345	2.449835226122598	19.67405018177029	32.327720850849474	96.09894990713607				
ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.057264																	
ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | asm_pair-smds.bam							33590705.0	32901005.0	97.94675342479415	0.45999999999999996													
ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats											8	45.99366835884384	64.21251415905992	44.86609831169762	352	1.6898591532433198	13.75535671962545	23.319238828449063	93.38867847222053				
ea1 | prokka | strain																				100621	112759075	Genus species	37502
ea2 | 4EA_L7_R1_001.fastq.gz	51.24217875178133	18.181818181818183	45.0	100.0	28444516.0																		
ea2 | 4EA_L7_R2_001.fastq.gz	47.11551146322527	9.090909090909092	45.0	100.0	28444516.0																		
ea2 | 5EA_L7_R1_001.fastq.gz	50.293954388405965	18.181818181818183	44.0	100.0	29103408.0																		
ea2 | 5EA_L7_R2_001.fastq.gz	46.37061869288858	9.090909090909092	44.0	100.0	29103408.0																		
ea2 | 6EA_L7_R1_001.fastq.gz	50.30088327209562	18.181818181818183	45.0	100.0	26487448.0																		
ea2 | 6EA_L7_R2_001.fastq.gz	45.99468824957525	9.090909090909092	45.0	100.0	26487448.0																		
ea2 | map | 4EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.069261																	
ea2 | map | 5EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.064131																	
ea2 | map | 6EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.065679																	
ea2 | prokka | strain																				100403	112274132	Genus species	35847
ea2 | prokka_old | strain																				100403	112274132	Genus species	35847
tsb1 | 1TSB_L7_R1_001.fastq.gz	58.50160426690012	27.27272727272727	48.0	100.0	29868150.0																		
tsb1 | 1TSB_L7_R2_001.fastq.gz	54.57911364016695	27.27272727272727	48.0	100.0	29868150.0																		
tsb1 | 2TSB_L7_R1_001.fastq.gz	52.50068184201548	27.27272727272727	48.0	100.0	20760296.0																		
tsb1 | 2TSB_L7_R2_001.fastq.gz	48.53500254326604	18.181818181818183	48.0	100.0	20760296.0																		
tsb1 | 3TSB_L7_R1_001.fastq.gz	49.17412467065774	18.181818181818183	47.0	100.0	24858276.0																		
tsb1 | 3TSB_L7_R2_001.fastq.gz	44.69991518455074	18.181818181818183	47.0	100.0	24858276.0																		
tsb1 | map | 1TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.083127																	
tsb1 | map | 2TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.070083																	
tsb1 | map | 3TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.063952																	
tsb1 | prokka | strain																				105038	115478339	Genus species	41324
tsb2 | 4TSB_L7_R1_001.fastq.gz	47.66328226914005	18.181818181818183	48.0	100.0	24477758.0																		
tsb2 | 4TSB_L7_R2_001.fastq.gz	42.33588065888622	18.181818181818183	48.0	100.0	24477758.0																		
tsb2 | 5TSB_L7_R1_001.fastq.gz	50.01753396502978	27.27272727272727	47.0	100.0	28122371.0																		
tsb2 | 5TSB_L7_R2_001.fastq.gz	45.79606915906146	18.181818181818183	47.0	100.0	28122371.0																		
tsb2 | 6TSB_L7_R1_001.fastq.gz	56.35656283802987	27.27272727272727	48.0	100.0	27290878.0																		
tsb2 | 6TSB_L7_R2_001.fastq.gz	51.61051609447181	27.27272727272727	48.0	100.0	27290878.0																		
tsb2 | map | 4TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.061994																	
tsb2 | map | 5TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.064606																	
tsb2 | map | 6TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam						0.077756																	
tsb2 | prokka | strain																				98344	108531306	Genus species	32969
