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
POC-201-TP1-hisat2_output	41174050	29364379	71.32	
POC-201-TP1_hisat2				70.02
POC-201-TP2-hisat2_output	45517777	30854809	67.79	
POC-201-TP2_hisat2				65.49
POC-201-TP3-hisat2_output	32673502	14602360	44.69	
POC-201-TP3_hisat2				42.92
POC-219-TP1-hisat2_output	42562141	28919178	67.95	
POC-219-TP1_hisat2				66.52
POC-219-TP2-hisat2_output	38781495	24912143	64.24	
POC-219-TP2_hisat2				62.61
POC-219-TP3-hisat2_output	42307122	7823100	18.49	
POC-219-TP3_hisat2				17.69
POC-219-TP4-hisat2_output	39567889	22463089	56.77	
POC-219-TP4_hisat2				55.18
POC-222-TP1-hisat2_output	40164884	29343758	73.06	
POC-222-TP1_hisat2				71.71
POC-222-TP2-hisat2_output	45803207	30439060	66.46	
POC-222-TP2_hisat2				64.83
POC-222-TP3-hisat2_output	47218626	34523236	73.11	
POC-222-TP3_hisat2				71.75
POC-222-TP4-hisat2_output	34657515	23720144	68.44	
POC-222-TP4_hisat2				66.98
POC-255-TP1-hisat2_output	39199349	26876099	68.56	
POC-255-TP1_hisat2				67.25
POC-255-TP2-hisat2_output	41599630	27848509	66.94	
POC-255-TP2_hisat2				65.45
POC-255-TP3-hisat2_output	49689338	25437574	51.19	
POC-255-TP3_hisat2				49.28
POC-255-TP4-hisat2_output	42689542	30134353	70.59	
POC-255-TP4_hisat2				69.28
POC-259-TP1-hisat2_output	37038914	22827935	61.63	
POC-259-TP1_hisat2				59.9
POC-259-TP2-hisat2_output	43378839	27622208	63.68	
POC-259-TP2_hisat2				61.76
POC-259-TP3-hisat2_output	45070221	29223144	64.84	
POC-259-TP3_hisat2				63.58
POC-259-TP4-hisat2_output	39615382	28040543	70.78	
POC-259-TP4_hisat2				69.44
POC-40-TP1-hisat2_output	37469293	26166083	69.83	
POC-40-TP1_hisat2				68.35
POC-40-TP2-hisat2_output	43906135	30856671	70.28	
POC-40-TP2_hisat2				68.93
POC-40-TP3-hisat2_output	42459845	29904585	70.43	
POC-40-TP3_hisat2				68.81
POC-40-TP4-hisat2_output	39703973	28402790	71.54	
POC-40-TP4_hisat2				70.3
POC-42-TP1-hisat2_output	37406504	25828128	69.05	
POC-42-TP1_hisat2				67.56
POC-42-TP2-hisat2_output	45277636	31528090	69.63	
POC-42-TP2_hisat2				68.47
POC-42-TP3-hisat2_output	40734857	29021273	71.24	
POC-42-TP3_hisat2				69.95
POC-42-TP4-hisat2_output	32984694	18514322	56.13	
POC-42-TP4_hisat2				54.41
POC-52-TP1-hisat2_output	32269399	5907282	18.31	
POC-52-TP1_hisat2				17.29
POC-52-TP2-hisat2_output	43665618	29884124	68.44	
POC-52-TP2_hisat2				67.04
POC-52-TP3-hisat2_output	37292275	25062839	67.21	
POC-52-TP3_hisat2				65.84
POC-52-TP4-hisat2_output	36648945	26474241	72.24	
POC-52-TP4_hisat2				70.91
POC-53-TP1-hisat2_output	40782859	27296768	66.93	
POC-53-TP1_hisat2				65.39
POC-53-TP2-hisat2_output	39570322	26243359	66.32	
POC-53-TP2_hisat2				64.79
POC-53-TP3-hisat2_output	43106868	30009073	69.62	
POC-53-TP3_hisat2				68.19
POC-53-TP4-hisat2_output	40361251	23200989	57.48	
POC-53-TP4_hisat2				56.2
POC-57-TP1-hisat2_output	38309566	26847438	70.08	
POC-57-TP1_hisat2				68.54
POC-57-TP2-hisat2_output	39048221	23000517	58.9	
POC-57-TP2_hisat2				57.11
POC-57-TP3-hisat2_output	45458318	32840537	72.24	
POC-57-TP3_hisat2				70.8
POC-57-TP4-hisat2_output	42924069	31955524	74.45	
POC-57-TP4_hisat2				73.34