Sample	Samtools: flagstat_mqc_generalstats_samtools_flagstat_flagstat_total_1	Samtools: flagstat_mqc_generalstats_samtools_flagstat_mapped_passed_1	Samtools: flagstat_mqc_generalstats_samtools_flagstat_mapped_passed_pct_1	Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate
ACR-139-TP1-hisat2_output	40.514601	31.644043999999997	78.11	
ACR-139-TP1_hisat2				74.96
ACR-139-TP2-hisat2_output	42.904337999999996	32.362061	75.43	
ACR-139-TP2_hisat2				72.67
ACR-139-TP3-hisat2_output	40.692395	32.856425	80.74	
ACR-139-TP3_hisat2				78.18
ACR-139-TP4-hisat2_output	46.419221	36.451170999999995	78.53	
ACR-139-TP4_hisat2				75.38
ACR-145-TP1-hisat2_output	55.888296	45.161238	80.81	
ACR-145-TP1_hisat2				75.15
ACR-145-TP2-hisat2_output	39.22077	25.300310999999997	64.51	
ACR-145-TP2_hisat2				60.66
ACR-145-TP3-hisat2_output	51.798755	39.742301999999995	76.72	
ACR-145-TP3_hisat2				73.84
ACR-145-TP4-hisat2_output	48.763251999999994	36.226167	74.29	
ACR-145-TP4_hisat2				70.68
ACR-150-TP1-hisat2_output	54.180265999999996	38.90488	71.81	
ACR-150-TP1_hisat2				66.72
ACR-150-TP2-hisat2_output	42.383162999999996	34.169086	80.62	
ACR-150-TP2_hisat2				77.57
ACR-150-TP3-hisat2_output	40.498238	32.629363999999995	80.57	
ACR-150-TP3_hisat2				77.67
ACR-150-TP4-hisat2_output	46.596213	37.880626	81.3	
ACR-150-TP4_hisat2				79.35
ACR-173-TP1-hisat2_output	46.990215	36.680081	78.06	
ACR-173-TP1_hisat2				71.84
ACR-173-TP2-hisat2_output	36.982057999999995	27.797302	75.16	
ACR-173-TP2_hisat2				71.35
ACR-173-TP3-hisat2_output	46.524235999999995	36.720695	78.93	
ACR-173-TP3_hisat2				76.39
ACR-173-TP4-hisat2_output	39.792121	30.116176	75.68	
ACR-173-TP4_hisat2				71.91
ACR-186-TP1-hisat2_output	36.091405	22.090135999999998	61.21	
ACR-186-TP1_hisat2				57.68
ACR-186-TP2-hisat2_output	38.990573	30.392414	77.95	
ACR-186-TP2_hisat2				74.98
ACR-186-TP3-hisat2_output	35.551004	27.270193	76.71	
ACR-186-TP3_hisat2				74.51
ACR-186-TP4-hisat2_output	41.898404	34.192248	81.61	
ACR-186-TP4_hisat2				79.03
ACR-225-TP1-hisat2_output	38.552065	30.632941	79.46	
ACR-225-TP1_hisat2				76.07
ACR-225-TP2-hisat2_output	44.658755	34.843641	78.02	
ACR-225-TP2_hisat2				74.74
ACR-225-TP3-hisat2_output	46.972696	37.224412	79.25	
ACR-225-TP3_hisat2				76.12
ACR-225-TP4-hisat2_output	36.448522	28.03238	76.91	
ACR-225-TP4_hisat2				73.59
ACR-229-TP1-hisat2_output	49.612812999999996	41.042398999999996	82.73	
ACR-229-TP1_hisat2				80.12
ACR-229-TP2-hisat2_output	41.803881	33.313398	79.69	
ACR-229-TP2_hisat2				77.46
ACR-229-TP3-hisat2_output	38.65566	31.201869	80.72	
ACR-229-TP3_hisat2				78.19
ACR-229-TP4-hisat2_output	52.002278	38.018518	73.11	
ACR-229-TP4_hisat2				68.96
ACR-237-TP1-hisat2_output	49.277546	39.059349999999995	79.26	
ACR-237-TP1_hisat2				76.89
ACR-237-TP2-hisat2_output	37.016338	26.888119999999997	72.64	
ACR-237-TP2_hisat2				69.57
ACR-237-TP3-hisat2_output	39.521107	32.434483	82.07	
ACR-237-TP3_hisat2				79.94
ACR-237-TP4-hisat2_output	54.813649	43.42297	79.22	
ACR-237-TP4_hisat2				76.01
ACR-244-TP1-hisat2_output	41.350463999999995	21.271891999999998	51.44	
ACR-244-TP1_hisat2				48.38
ACR-244-TP2-hisat2_output	48.088052	36.034495	74.93	
ACR-244-TP2_hisat2				72.21
ACR-244-TP3-hisat2_output	51.809329999999996	41.354431	79.82	
ACR-244-TP3_hisat2				76.54
ACR-244-TP4-hisat2_output	49.20214	36.699712999999996	74.59	
ACR-244-TP4_hisat2				71.53
ACR-265-TP1-hisat2_output	69.84222799999999	53.602337	76.75	
ACR-265-TP1_hisat2				72.29
ACR-265-TP2-hisat2_output	47.914939999999994	37.997824	79.3	
ACR-265-TP2_hisat2				76.74
ACR-265-TP3-hisat2_output	50.566296	39.720352	78.55	
ACR-265-TP3_hisat2				74.4
ACR-265-TP4-hisat2_output	53.756971	40.764652	75.83	
ACR-265-TP4_hisat2				72.78