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
POR-216-TP1-hisat2_output	46189273	41186073	89.17	
POR-216-TP1_hisat2				87.03
POR-216-TP2-hisat2_output	45626628	42629999	93.43	
POR-216-TP2_hisat2				91.9
POR-216-TP3-hisat2_output	40060641	37415006	93.4	
POR-216-TP3_hisat2				91.65
POR-216-TP4-hisat2_output	54618779	51989797	95.19	
POR-216-TP4_hisat2				93.8
POR-236-TP1-hisat2_output	51827320	48517961	93.61	
POR-236-TP1_hisat2				92.1
POR-236-TP2-hisat2_output	50243233	48296620	96.13	
POR-236-TP2_hisat2				94.94
POR-245-TP1-hisat2_output	46751278	43770227	93.62	
POR-245-TP1_hisat2				92.14
POR-245-TP2-hisat2_output	42708679	41115709	96.27	
POR-245-TP2_hisat2				95.19
POR-245-TP3-hisat2_output	48284229	45929777	95.12	
POR-245-TP3_hisat2				93.65
POR-245-TP4-hisat2_output	40314391	35921569	89.1	
POR-245-TP4_hisat2				87.02
POR-260-TP1-hisat2_output	40366971	36769503	91.09	
POR-260-TP1_hisat2				89.44
POR-260-TP2-hisat2_output	43726243	41714362	95.4	
POR-260-TP2_hisat2				94.13
POR-260-TP3-hisat2_output	42357666	40001728	94.44	
POR-260-TP3_hisat2				93.03
POR-260-TP4-hisat2_output	47899467	45144153	94.25	
POR-260-TP4_hisat2				92.85
POR-262-TP1-hisat2_output	49671103	45495966	91.59	
POR-262-TP1_hisat2				89.58
POR-262-TP2-hisat2_output	50532535	47089608	93.19	
POR-262-TP2_hisat2				91.61
POR-262-TP3-hisat2_output	53437949	50445184	94.4	
POR-262-TP3_hisat2				92.93
POR-262-TP4-hisat2_output	43441240	41445719	95.41	
POR-262-TP4_hisat2				94.2
POR-69-TP1-hisat2_output	54980219	51807915	94.23	
POR-69-TP1_hisat2				92.72
POR-69-TP2-hisat2_output	49601152	47089265	94.94	
POR-69-TP2_hisat2				93.64
POR-69-TP3-hisat2_output	53736247	51667113	96.15	
POR-69-TP3_hisat2				95.02
POR-69-TP4-hisat2_output	43879067	42164487	96.09	
POR-69-TP4_hisat2				94.99
POR-72-TP1-hisat2_output	39251162	33977930	86.57	
POR-72-TP1_hisat2				83.64
POR-72-TP2-hisat2_output	40627916	31757535	78.17	
POR-72-TP2_hisat2				74.16
POR-72-TP3-hisat2_output	50099294	46172408	92.16	
POR-72-TP3_hisat2				90.36
POR-72-TP4-hisat2_output	54955132	51591528	93.88	
POR-72-TP4_hisat2				92.48
POR-73-TP1-hisat2_output	50816147	48053211	94.56	
POR-73-TP1_hisat2				93.1
POR-73-TP2-hisat2_output	55242486	52507836	95.05	
POR-73-TP2_hisat2				93.62
POR-73-TP3-hisat2_output	50383144	48620341	96.5	
POR-73-TP3_hisat2				95.38
POR-73-TP4-hisat2_output	46448048	44135369	95.02	
POR-73-TP4_hisat2				93.72
POR-74-TP1-hisat2_output	44501366	41026023	92.19	
POR-74-TP1_hisat2				90.35
POR-74-TP2-hisat2_output	44921522	43475817	96.78	
POR-74-TP2_hisat2				95.92
POR-74-TP3-hisat2_output	55045584	52027246	94.52	
POR-74-TP3_hisat2				93.05
POR-74-TP4-hisat2_output	50271201	48930447	97.33	
POR-74-TP4_hisat2				96.53
POR-83-TP1-hisat2_output	44361633	41877512	94.4	
POR-83-TP1_hisat2				93.04
POR-83-TP2-hisat2_output	47946786	44930219	93.71	
POR-83-TP2_hisat2				92.04
POR-83-TP3-hisat2_output	47923824	45932507	95.84	
POR-83-TP3_hisat2				94.65
POR-83-TP4-hisat2_output	59859965	56976910	95.18	
POR-83-TP4_hisat2				93.79