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
ACR-139-TP1-hisat2_output	40511050	31640631	78.1	
ACR-139-TP1_hisat2				74.96
ACR-139-TP2-hisat2_output	42903492	32361370	75.43	
ACR-139-TP2_hisat2				72.67
ACR-139-TP3-hisat2_output	40733234	32897352	80.76	
ACR-139-TP3_hisat2				78.18
ACR-139-TP4-hisat2_output	46418562	36450667	78.53	
ACR-139-TP4_hisat2				75.38
ACR-145-TP1-hisat2_output	55886001	45159089	80.81	
ACR-145-TP1_hisat2				75.15
ACR-145-TP2-hisat2_output	39221056	25300595	64.51	
ACR-145-TP2_hisat2				60.66
ACR-145-TP3-hisat2_output	51792426	39737439	76.72	
ACR-145-TP3_hisat2				73.85
ACR-145-TP4-hisat2_output	48758550	36221801	74.29	
ACR-145-TP4_hisat2				70.68
ACR-150-TP1-hisat2_output	54173749	38898453	71.8	
ACR-150-TP1_hisat2				66.72
ACR-150-TP2-hisat2_output	42384714	34171147	80.62	
ACR-150-TP2_hisat2				77.57
ACR-150-TP3-hisat2_output	40497948	32629229	80.57	
ACR-150-TP3_hisat2				77.67
ACR-150-TP4-hisat2_output	46596362	37880879	81.3	
ACR-150-TP4_hisat2				79.35
ACR-173-TP1-hisat2_output	46987081	36677108	78.06	
ACR-173-TP1_hisat2				71.84
ACR-173-TP2-hisat2_output	36981290	27796700	75.16	
ACR-173-TP2_hisat2				71.35
ACR-173-TP3-hisat2_output	46525312	36721543	78.93	
ACR-173-TP3_hisat2				76.39
ACR-173-TP4-hisat2_output	39785935	30109999	75.68	
ACR-173-TP4_hisat2				71.91
ACR-186-TP1-hisat2_output	36082259	22081067	61.2	
ACR-186-TP1_hisat2				57.68
ACR-186-TP2-hisat2_output	38827463	30232775	77.86	
ACR-186-TP2_hisat2				74.99
ACR-186-TP3-hisat2_output	35541264	27259468	76.7	
ACR-186-TP3_hisat2				74.51
ACR-186-TP4-hisat2_output	41893016	34186575	81.6	
ACR-186-TP4_hisat2				79.03
ACR-225-TP1-hisat2_output	38585242	30666331	79.48	
ACR-225-TP1_hisat2				76.07
ACR-225-TP2-hisat2_output	44657027	34840750	78.02	
ACR-225-TP2_hisat2				74.74
ACR-225-TP3-hisat2_output	46960476	37212061	79.24	
ACR-225-TP3_hisat2				76.12
ACR-225-TP4-hisat2_output	36448367	28032083	76.91	
ACR-225-TP4_hisat2				73.59
ACR-229-TP1-hisat2_output	49611408	41041241	82.73	
ACR-229-TP1_hisat2				80.12
ACR-229-TP2-hisat2_output	41804497	33314081	79.69	
ACR-229-TP2_hisat2				77.46
ACR-229-TP3-hisat2_output	38647851	31195451	80.72	
ACR-229-TP3_hisat2				78.19
ACR-229-TP4-hisat2_output	52021615	38038728	73.12	
ACR-229-TP4_hisat2				68.96
ACR-237-TP1-hisat2_output	49268825	39051178	79.26	
ACR-237-TP1_hisat2				76.89
ACR-237-TP2-hisat2_output	37015260	26887089	72.64	
ACR-237-TP2_hisat2				69.57
ACR-237-TP3-hisat2_output	39516201	32429673	82.07	
ACR-237-TP3_hisat2				79.94
ACR-237-TP4-hisat2_output	54803260	43412338	79.21	
ACR-237-TP4_hisat2				76.01
ACR-244-TP1-hisat2_output	41350474	21271909	51.44	
ACR-244-TP1_hisat2				48.38
ACR-244-TP2-hisat2_output	48085956	36030742	74.93	
ACR-244-TP2_hisat2				72.21
ACR-244-TP3-hisat2_output	51806578	41351806	79.82	
ACR-244-TP3_hisat2				76.54
ACR-244-TP4-hisat2_output	49058997	36556206	74.51	
ACR-244-TP4_hisat2				71.52
ACR-265-TP1-hisat2_output	69839168	53599313	76.75	
ACR-265-TP1_hisat2				72.29
ACR-265-TP2-hisat2_output	47908713	38010387	79.34	
ACR-265-TP2_hisat2				76.78
ACR-265-TP3-hisat2_output	50564759	39712538	78.54	
ACR-265-TP3_hisat2				74.39
ACR-265-TP4-hisat2_output	53683319	40687777	75.79	
ACR-265-TP4_hisat2				72.77