Sample	total_passed	total_failed	secondary_passed	secondary_failed	supplementary_passed	supplementary_failed	duplicates_passed	duplicates_failed	mapped_passed	mapped_failed	mapped_passed_pct	mapped_failed_pct	paired in sequencing_passed	paired in sequencing_failed	read1_passed	read1_failed	read2_passed	read2_failed	properly paired_passed	properly paired_failed	properly paired_passed_pct	properly paired_failed_pct	with itself and mate mapped_passed	with itself and mate mapped_failed	singletons_passed	singletons_failed	singletons_passed_pct	singletons_failed_pct	with mate mapped to a different chr_passed	with mate mapped to a different chr_failed	with mate mapped to a different chr (mapQ >= 5)_passed	with mate mapped to a different chr (mapQ >= 5)_failed	flagstat_total
POR-216-TP1-hisat2_output	46189273	0	7623253	0	0	0	0	0	41186073	0	89.17	nan	38566020	0	19283010	0	19283010	0	28992700	0	75.18	nan	32473888	0	1088932	0	2.82	nan	522500	0	222334	0	46189273
POR-216-TP2-hisat2_output	45626628	0	8618956	0	0	0	0	0	42629999	0	93.43	nan	37007672	0	18503836	0	18503836	0	29482190	0	79.67	nan	33155618	0	855425	0	2.31	nan	572236	0	198010	0	45626628
POR-216-TP3-hisat2_output	40060641	0	8378815	0	0	0	0	0	37415006	0	93.4	nan	31681826	0	15840913	0	15840913	0	25445910	0	80.32	nan	28442002	0	594189	0	1.88	nan	479136	0	132760	0	40060641
POR-216-TP4-hisat2_output	54618779	0	12209691	0	0	0	0	0	51989797	0	95.19	nan	42409088	0	21204544	0	21204544	0	34112262	0	80.44	nan	39161396	0	618710	0	1.46	nan	747928	0	138390	0	54618779
POR-236-TP1-hisat2_output	51827320	0	9917518	0	0	0	0	0	48517961	0	93.61	nan	41909802	0	20954901	0	20954901	0	33612180	0	80.2	nan	37698132	0	902311	0	2.15	nan	655798	0	214580	0	51827320
POR-236-TP2-hisat2_output	50243233	0	11765947	0	0	0	0	0	48296620	0	96.13	nan	38477286	0	19238643	0	19238643	0	32107966	0	83.45	nan	35936100	0	594573	0	1.55	nan	655282	0	142826	0	50243233
POR-245-TP1-hisat2_output	46751278	0	8838472	0	0	0	0	0	43770227	0	93.62	nan	37912806	0	18956403	0	18956403	0	30205868	0	79.67	nan	34087122	0	844633	0	2.23	nan	597938	0	203302	0	46751278
POR-245-TP2-hisat2_output	42708679	0	9559937	0	0	0	0	0	41115709	0	96.27	nan	33148742	0	16574371	0	16574371	0	27613052	0	83.3	nan	31056508	0	499264	0	1.51	nan	586218	0	134422	0	42708679
POR-245-TP3-hisat2_output	48284229	0	11180891	0	0	0	0	0	45929777	0	95.12	nan	37103338	0	18551669	0	18551669	0	30629714	0	82.55	nan	34167520	0	581366	0	1.57	nan	605452	0	148336	0	48284229
POR-245-TP4-hisat2_output	40314391	0	6462777	0	0	0	0	0	35921569	0	89.1	nan	33851614	0	16925807	0	16925807	0	24701806	0	72.97	nan	28359600	0	1099192	0	3.25	nan	475618	0	188645	0	40314391
POR-260-TP1-hisat2_output	40366971	0	6286667	0	0	0	0	0	36769503	0	91.09	nan	34080304	0	17040152	0	17040152	0	26239634	0	76.99	nan	29452208	0	1030628	0	3.02	nan	494208	0	226193	0	40366971
POR-260-TP2-hisat2_output	43726243	0	9434569	0	0	0	0	0	41714362	0	95.4	nan	34291674	0	17145837	0	17145837	0	27622868	0	80.55	nan	31623226	0	656567	0	1.91	nan	655522	0	144926	0	43726243
POR-260-TP3-hisat2_output	42357666	0	8556632	0	0	0	0	0	40001728	0	94.44	nan	33801034	0	16900517	0	16900517	0	27279050	0	80.7	nan	30744008	0	701088	0	2.07	nan	547160	0	151303	0	42357666
POR-260-TP4-hisat2_output	47899467	0	9351319	0	0	0	0	0	45144153	0	94.25	nan	38548148	0	19274074	0	19274074	0	30783000	0	79.86	nan	34992304	0	800530	0	2.08	nan	630694	0	174910	0	47899467
POR-262-TP1-hisat2_output	49671103	0	9612519	0	0	0	0	0	45495966	0	91.59	nan	40058584	0	20029292	0	20029292	0	30696482	0	76.63	nan	35022726	0	860721	0	2.15	nan	624536	0	178722	0	49671103
POR-262-TP2-hisat2_output	50532535	0	9489071	0	0	0	0	0	47089608	0	93.19	nan	41043464	0	20521732	0	20521732	0	32685892	0	79.64	nan	36661108	0	939429	0	2.29	nan	570080	0	190154	0	50532535
POR-262-TP3-hisat2_output	53437949	0	11130627	0	0	0	0	0	50445184	0	94.4	nan	42307322	0	21153661	0	21153661	0	34247788	0	80.95	nan	38492434	0	822123	0	1.94	nan	698336	0	188281	0	53437949
POR-262-TP4-hisat2_output	43441240	0	9059332	0	0	0	0	0	41445719	0	95.41	nan	34381908	0	17190954	0	17190954	0	27733586	0	80.66	nan	31795426	0	590961	0	1.72	nan	616504	0	143494	0	43441240
POR-69-TP1-hisat2_output	54980219	0	11375975	0	0	0	0	0	51807915	0	94.23	nan	43604244	0	21802122	0	21802122	0	35368592	0	81.11	nan	39512628	0	919312	0	2.11	nan	669628	0	202965	0	54980219
POR-69-TP2-hisat2_output	49601152	0	10129774	0	0	0	0	0	47089265	0	94.94	nan	39471378	0	19735689	0	19735689	0	32681464	0	82.8	nan	36172802	0	786689	0	1.99	nan	590868	0	183077	0	49601152
POR-69-TP3-hisat2_output	53736247	0	12155285	0	0	0	0	0	51667113	0	96.15	nan	41580962	0	20790481	0	20790481	0	33877198	0	81.47	nan	38879736	0	632092	0	1.52	nan	816232	0	161049	0	53736247
POR-69-TP4-hisat2_output	43879067	0	9688445	0	0	0	0	0	42164487	0	96.09	nan	34190622	0	17095311	0	17095311	0	27979484	0	81.83	nan	31919122	0	556920	0	1.63	nan	637664	0	138071	0	43879067
POR-72-TP1-hisat2_output	39251162	0	7022742	0	0	0	0	0	33977930	0	86.57	nan	32228420	0	16114210	0	16114210	0	23099022	0	71.67	nan	26136356	0	818832	0	2.54	nan	412374	0	143964	0	39251162
POR-72-TP2-hisat2_output	40627916	0	6302412	0	0	0	0	0	31757535	0	78.17	nan	34325504	0	17162752	0	17162752	0	21916490	0	63.85	nan	24729278	0	725845	0	2.11	nan	393858	0	146971	0	40627916
POR-72-TP3-hisat2_output	50099294	0	9377956	0	0	0	0	0	46172408	0	92.16	nan	40721338	0	20360669	0	20360669	0	31482670	0	77.31	nan	35922820	0	871632	0	2.14	nan	637292	0	190145	0	50099294
POR-72-TP4-hisat2_output	54955132	0	10242576	0	0	0	0	0	51591528	0	93.88	nan	44712556	0	22356278	0	22356278	0	35185210	0	78.69	nan	40348526	0	1000426	0	2.24	nan	754596	0	228015	0	54955132
POR-73-TP1-hisat2_output	50816147	0	10771637	0	0	0	0	0	48053211	0	94.56	nan	40044510	0	20022255	0	20022255	0	33348960	0	83.28	nan	36537460	0	744114	0	1.86	nan	539666	0	159420	0	50816147
POR-73-TP2-hisat2_output	55242486	0	12396162	0	0	0	0	0	52507836	0	95.05	nan	42846324	0	21423162	0	21423162	0	34491490	0	80.5	nan	39354968	0	756706	0	1.77	nan	791218	0	162398	0	55242486
POR-73-TP3-hisat2_output	50383144	0	12260484	0	0	0	0	0	48620341	0	96.5	nan	38122660	0	19061330	0	19061330	0	31317166	0	82.15	nan	35820352	0	539505	0	1.42	nan	794036	0	141413	0	50383144
POR-73-TP4-hisat2_output	46448048	0	9612516	0	0	0	0	0	44135369	0	95.02	nan	36835532	0	18417766	0	18417766	0	30412312	0	82.56	nan	33819996	0	702857	0	1.91	nan	593748	0	164193	0	46448048
POR-74-TP1-hisat2_output	44501366	0	8479604	0	0	0	0	0	41026023	0	92.19	nan	36021762	0	18010881	0	18010881	0	28371952	0	78.76	nan	31691486	0	854933	0	2.37	nan	486150	0	165585	0	44501366
POR-74-TP2-hisat2_output	44921522	0	9481544	0	0	0	0	0	43475817	0	96.78	nan	35439978	0	17719989	0	17719989	0	29360990	0	82.85	nan	33525756	0	468517	0	1.32	nan	623084	0	126548	0	44921522
POR-74-TP3-hisat2_output	55045584	0	11641094	0	0	0	0	0	52027246	0	94.52	nan	43404490	0	21702245	0	21702245	0	34494336	0	79.47	nan	39643874	0	742278	0	1.71	nan	783018	0	180849	0	55045584
POR-74-TP4-hisat2_output	50271201	0	11590091	0	0	0	0	0	48930447	0	97.33	nan	38681110	0	19340555	0	19340555	0	31883000	0	82.43	nan	36853986	0	486370	0	1.26	nan	831704	0	148417	0	50271201
POR-83-TP1-hisat2_output	44361633	0	8686093	0	0	0	0	0	41877512	0	94.4	nan	35675540	0	17837770	0	17837770	0	27913750	0	78.24	nan	32402396	0	789023	0	2.21	nan	670040	0	170380	0	44361633
POR-83-TP2-hisat2_output	47946786	0	10046204	0	0	0	0	0	44930219	0	93.71	nan	37900582	0	18950291	0	18950291	0	30390282	0	80.18	nan	34128468	0	755547	0	1.99	nan	608922	0	166509	0	47946786
POR-83-TP3-hisat2_output	47923824	0	10697940	0	0	0	0	0	45932507	0	95.84	nan	37225884	0	18612942	0	18612942	0	30595536	0	82.19	nan	34635558	0	599009	0	1.61	nan	685858	0	142236	0	47923824
POR-83-TP4-hisat2_output	59859965	0	13444849	0	0	0	0	0	56976910	0	95.18	nan	46415116	0	23207558	0	23207558	0	37695266	0	81.21	nan	42729050	0	803011	0	1.73	nan	803062	0	183437	0	59859965