Sample	Samtools_mqc-generalstats-samtools-flagstat_total	Samtools_mqc-generalstats-samtools-mapped_passed	Samtools_mqc-generalstats-samtools-mapped_passed_pct	Bowtie 2 / HiSAT2_mqc-generalstats-bowtie_2_hisat2-overall_alignment_rate
1A1-hisat2_output	47427906	37003766	78.02	
1A10-hisat2_output	49115555	36504043	74.32	
1A10_hisat2				70.66
1A12-hisat2_output	39886398	32715359	82.02	
1A12_hisat2				79.85
1A1_hisat2				71.71
1A2-hisat2_output	49398866	36775191	74.45	
1A2_hisat2				71.41
1A8-hisat2_output	39181744	30539832	77.94	
1A8_hisat2				75.0
1A9-hisat2_output	48395176	36306271	75.02	
1A9_hisat2				72.27
1B1-hisat2_output	47796679	37568916	78.6	
1B10-hisat2_output	46895127	38146702	81.34	
1B10_hisat2				79.38
1B1_hisat2				75.36
1B2-hisat2_output	47386498	36979573	78.04	
1B2_hisat2				75.38
1B5-hisat2_output	49898482	41346567	82.86	
1B5_hisat2				80.23
1B9-hisat2_output	54026791	40895267	75.69	
1B9_hisat2				72.63
1C10-hisat2_output	40092973	30298551	75.57	
1C10_hisat2				71.73
1C4-hisat2_output	46910852	36785790	78.42	
1C4_hisat2				75.2
1D10-hisat2_output	48367129	38436443	79.47	
1D10_hisat2				76.84
1D3-hisat2_output	36624343	28188066	76.97	
1D3_hisat2				73.64
1D4-hisat2_output	55027544	43638346	79.3	
1D4_hisat2				76.08
1D6-hisat2_output	42024228	33520378	79.76	
1D6_hisat2				77.54
1D8-hisat2_output	37353634	27124095	72.61	
1D8_hisat2				69.5
1D9-hisat2_output	52367774	38285923	73.11	
1D9_hisat2				68.88
1E1-hisat2_output	51044626	40072931	78.51	
1E1_hisat2				74.28
1E3-hisat2_output	42707145	34414467	80.58	
1E3_hisat2				77.5
1E5-hisat2_output	41007791	33146490	80.83	
1E5_hisat2				78.22
1E9-hisat2_output	49589545	39272369	79.19	
1E9_hisat2				76.79
1F11-hisat2_output	37289343	28035246	75.18	
1F11_hisat2				71.33
1F4-hisat2_output	40816372	32895655	80.59	
1F4_hisat2				77.66
1F8-hisat2_output	52140562	39999608	76.71	
1F8_hisat2				73.79
1G5-hisat2_output	52310738	41782841	79.87	
1G5_hisat2				76.53
1H11-hisat2_output	39886398	32715359	82.02	
1H11_hisat2				79.85
1H12-hisat2_output	35950398	27494451	76.48	
1H12_hisat2				74.2
1H6-hisat2_output	52140562	39999608	76.71	
1H6_hisat2				73.79
1H7-hisat2_output	38984264	31491213	80.78	
1H7_hisat2				78.21
1H8-hisat2_output	42259740	34526462	81.7	
1H8_hisat2				79.07
2B2-hisat2_output	56512524	45332945	80.22	
2B2_hisat2				74.43
2B3-hisat2_output	43291883	32685040	75.5	
2B3_hisat2				72.67
2C1-hisat2_output	41491029	21401918	51.58	
2C1_hisat2				48.48
2C2-hisat2_output	40738653	31804249	78.07	
2C2_hisat2				74.95
2D2-hisat2_output	54877372	39104574	71.26	
2D2_hisat2				66.06
2E2-hisat2_output	36665245	22148458	60.41	
2E2_hisat2				56.86
2F1-hisat2_output	70432471	53982660	76.64	
2F1_hisat2				72.08
2G1-hisat2_output	39473080	25452736	64.48	
2G1_hisat2				60.61