Sample	Total input reads	Total input reads pct	Number of duplicate marked reads	Number of duplicate marked reads pct	Number of unique reads (excl. duplicate marked reads) pct	Reads with mate sequenced	Reads with mate sequenced pct	Reads without mate sequenced	Reads without mate sequenced pct	QC-failed reads	QC-failed reads pct	Mapped reads	Mapped reads pct	Mapped reads R1	Mapped reads R1 pct	Mapped reads R2	Mapped reads R2 pct	Mapped reads to pop-alt insertions (PAI)	Mapped reads to pop-alt insertions (PAI) pct	Mapped reads to non-ref decoys (NRD)	Mapped reads to non-ref decoys (NRD) pct	Mapped reads to ref-external sequences (PAI or NRD)	Mapped reads to ref-external sequences (PAI or NRD) pct	Mapped reads including ref-external or filtered or excluded	Mapped reads including ref-external or filtered or excluded pct	Unmapped reads	Unmapped reads pct	Unmapped reads minus ref-external mappings	Unmapped reads minus ref-external mappings pct	Unmapped reads minus filtered mappings	Unmapped reads minus filtered mappings pct	Unmapped reads minus excluded mappings	Unmapped reads minus excluded mappings pct	Unmapped reads minus ref-external or filtered or excluded	Unmapped reads minus ref-external or filtered or excluded pct	Singleton reads (itself mapped; mate unmapped)	Singleton reads (itself mapped; mate unmapped) pct	Paired reads (itself & mate mapped)	Paired reads (itself & mate mapped) pct	Properly paired reads	Properly paired reads pct	Not properly paired reads (discordant)	Not properly paired reads (discordant) pct	Paired reads mapped to different chromosomes	Paired reads mapped to different chromosomes pct	Paired reads mapped to different chromosomes (MAPQ>=10)	Paired reads mapped to different chromosomes (MAPQ>=10) pct	Reads mapping to multiple locations	Reads mapping to multiple locations pct	Reads with MAPQ [40:inf)	Reads with MAPQ [40:inf) pct	Reads with MAPQ [30:40)	Reads with MAPQ [30:40) pct	Reads with MAPQ [20:30)	Reads with MAPQ [20:30) pct	Reads with MAPQ [10:20)	Reads with MAPQ [10:20) pct	Reads with MAPQ [ 0:10)	Reads with MAPQ [ 0:10) pct	Reads with MAPQ NA (Unmapped reads)	Reads with MAPQ NA (Unmapped reads) pct	Reads with indel R1	Reads with indel R1 pct	Reads with indel R2	Reads with indel R2 pct	Total bases	Total bases R1	Total bases R2	Mapped bases	Mapped bases R1	Mapped bases R2	Soft-clipped bases	Soft-clipped bases pct	Soft-clipped bases R1	Soft-clipped bases R1 pct	Soft-clipped bases R2 pct	Hard-clipped bases	Hard-clipped bases pct	Hard-clipped bases R1	Hard-clipped bases R1 pct	Hard-clipped bases R2	Hard-clipped bases R2 pct	Mismatched bases R1	Mismatched bases R1 pct	Mismatched bases R2 pct	Mismatched bases R1 (excl. indels)	Mismatched bases R1 (excl. indels) pct	Mismatched bases R2 (excl. indels) pct	Q30 bases	Q30 bases pct	Q30 bases R1	Q30 bases R1 pct	Q30 bases R2	Q30 bases R2 pct	Q30 bases (excl. dups & clipped bases)	Total alignments	Secondary alignments	Secondary alignments pct	Supplementary (chimeric) alignments	Supplementary (chimeric) alignments pct	Estimated read length	Bases in reference genome	Bases in target bed [% of genome]	Bases in target bed [% of genome] pct	Input bases divided by reference genome size	Input bases divided by target bed size	Insert length: mean	Insert length: median	Insert length: standard deviation	DRAGEN mapping rate [mil. reads/second]	Q30 bases (excl. dups & clipped bases) pct	Mapped bases R1 pct	Mapped bases R2 pct
Alp13-1-100 | Alp13-1-100	127526	100.0	0	0.0	100.0	127526	100.0	0	0.0	0	0.0	125850	98.69	63351	99.35	62499	98.02	12	0.01	6	0.0	18	0.01	125868	98.7	1676	1.31	1658	1.3	1676	1.31	1676	1.31	1658	1.3	862	0.68	124988	98.01	121438	95.23	3550	2.78	108	0.09	76	0.06	35	0.03	125766	98.62	11	0.01	10	0.01	9	0.01	54	0.04	1676	1.31	1846	2.91	2688	4.3	19049236	9528179	9521057	18884414	9509595	9374819	119622	0.63	49462	0.52	0.75	0	0.0	0	0.0	0	0.0	21778	0.23	0.26	19795	0.21	0.22	18387350	96.53	9313875	97.75	9073475	95.3	18296722	126033	0	0.0	183	0.15	149.38	3217346917	45372	0.0	0.01	419.85	229.39	217.0	47.87	0.06	96.04963684632811	49.92113594476965	49.21362200562795
Alp13-1-20 | Alp13-1-20	136886	100.0	0	0.0	100.0	136886	100.0	0	0.0	0	0.0	133432	97.48	67099	98.04	66333	96.92	5	0.0	12	0.01	17	0.01	133449	97.49	3454	2.52	3437	2.51	3454	2.52	3454	2.52	3437	2.51	794	0.58	132638	96.9	127472	93.12	5166	3.77	128	0.1	97	0.07	65	0.05	133298	97.38	18	0.01	18	0.01	11	0.01	87	0.06	3454	2.52	1910	2.85	2883	4.35	20199121	10101347	10097774	19974187	10047006	9927181	145283	0.73	61197	0.61	0.85	0	0.0	0	0.0	0	0.0	21626	0.22	0.28	19587	0.19	0.25	19366099	95.88	9845854	97.47	9520245	94.28	19253295	133604	0	0.0	172	0.13	147.56	3217346917	45372	0.0	0.01	445.19	226.78	217.0	106.74	0.07	95.3174893105497	49.739817886134745	49.14659900299622
Alp22-1-100 | Alp22-1-100	137870	100.0	0	0.0	100.0	137870	100.0	0	0.0	0	0.0	136613	99.09	68746	99.73	67867	98.45	5	0.0	28	0.02	33	0.02	136646	99.11	1257	0.91	1224	0.89	1257	0.91	1257	0.91	1224	0.89	905	0.66	135708	98.43	130842	94.9	4866	3.53	100	0.07	85	0.06	72	0.05	136384	98.92	21	0.02	60	0.04	42	0.03	106	0.08	1257	0.91	1993	2.9	2162	3.19	20648414	10327940	10320474	20481746	10310700	10171046	139109	0.68	74305	0.72	0.64	0	0.0	0	0.0	0	0.0	16004	0.16	0.33	13688	0.13	0.31	19824038	96.01	10095265	97.75	9728773	94.27	19712153	136796	0	0.0	183	0.13	149.77	3217346917	45372	0.0	0.01	455.09	225.69	222.0	137.53	0.07	95.46570017435721	49.934585774965576	49.25824327234044
Alp22-1-20 | Alp22-1-20	124804	100.0	0	0.0	100.0	124804	100.0	0	0.0	0	0.0	123613	99.05	62205	99.68	61408	98.41	4	0.0	26	0.02	30	0.02	123643	99.07	1191	0.95	1161	0.93	1191	0.95	1191	0.95	1161	0.93	815	0.65	122798	98.39	121942	97.71	856	0.69	114	0.09	92	0.07	79	0.06	123410	98.88	20	0.02	42	0.03	44	0.04	97	0.08	1191	0.95	1816	2.92	1946	3.17	18673778	9339487	9334291	18523173	9324295	9198878	133794	0.72	68301	0.73	0.71	0	0.0	0	0.0	0	0.0	13306	0.14	0.47	11302	0.12	0.44	17711726	94.85	9125091	97.7	8586635	91.99	17608679	123787	0	0.0	174	0.14	149.62	3217346917	45372	0.0	0.01	411.57	223.13	222.0	112.21	0.07	94.29628541155411	49.93255783591301	49.260936913783596
Alp32-1-100 | Alp32-1-100	118542	100.0	0	0.0	100.0	118542	100.0	0	0.0	0	0.0	117550	99.16	59087	99.69	58463	98.64	9	0.01	9	0.01	18	0.02	117568	99.18	992	0.84	974	0.82	992	0.84	992	0.84	974	0.82	632	0.53	116918	98.63	116056	97.9	862	0.73	118	0.1	94	0.08	82	0.07	117377	99.02	6	0.01	40	0.03	23	0.02	104	0.09	992	0.84	2777	4.7	5046	8.63	17734911	8861551	8873360	17614871	8848463	8766408	331730	1.88	49183	0.56	3.22	0	0.0	0	0.0	0	0.0	28587	0.32	0.91	12149	0.14	0.76	16499135	93.03	8646098	97.57	7853037	88.5	16374711	117597	0	0.0	47	0.04	149.61	3217346917	45372	0.0	0.01	390.88	238.15	244.0	106.66	0.07	92.3303815846609	49.89290896356909	49.4302339605764
Alp32-1-20 | Alp32-1-20	132436	100.0	0	0.0	100.0	132436	100.0	0	0.0	0	0.0	131500	99.29	66092	99.81	65408	98.78	3	0.0	20	0.02	23	0.02	131523	99.31	936	0.71	913	0.69	936	0.71	936	0.71	913	0.69	690	0.52	130810	98.77	129992	98.15	818	0.62	128	0.1	103	0.08	87	0.07	131317	99.16	6	0.0	47	0.04	22	0.02	108	0.08	936	0.71	3182	4.81	5123	7.83	19850478	9919811	9930667	19721115	9906391	9814724	321951	1.63	55944	0.56	2.71	0	0.0	0	0.0	0	0.0	33057	0.33	0.88	13997	0.14	0.74	18481573	93.1	9680433	97.59	8801140	88.63	18350774	131538	0	0.0	38	0.03	149.89	3217346917	45372	0.0	0.01	437.51	237.03	244.0	48.54	0.07	92.44499804992101	49.90505014539197	49.443262776845984
Alp42-1-100 | Alp42-1-100	125326	100.0	0	0.0	100.0	125326	100.0	0	0.0	0	0.0	123217	98.32	62136	99.16	61081	97.48	11	0.01	8	0.01	19	0.02	123236	98.33	2109	1.68	2090	1.67	2109	1.68	2109	1.68	2090	1.67	1063	0.85	122154	97.47	115358	92.05	6796	5.42	148	0.12	122	0.1	57	0.05	123098	98.22	6	0.0	14	0.01	15	0.01	84	0.07	2109	1.68	1731	2.79	1461	2.39	18681019	9352566	9328453	18451180	9316477	9134703	112402	0.61	54508	0.59	0.63	0	0.0	0	0.0	0	0.0	11316	0.12	0.24	9436	0.1	0.22	17876030	95.69	9094563	97.24	8781467	94.14	17783981	123253	0	0.0	36	0.03	149.06	3217346917	45372	0.0	0.01	411.73	239.58	235.0	87.01	0.06	95.19813132249371	49.87135337745762	48.89831223874886
Alp42-1-20 | Alp42-1-20	135068	100.0	0	0.0	100.0	135068	100.0	0	0.0	0	0.0	132629	98.19	66806	98.92	65823	97.47	3	0.0	4	0.0	7	0.01	132636	98.2	2439	1.81	2432	1.8	2439	1.81	2439	1.81	2432	1.8	1003	0.74	131626	97.45	124400	92.1	7226	5.35	134	0.1	108	0.08	67	0.05	132494	98.09	15	0.01	9	0.01	18	0.01	93	0.07	2439	1.81	1846	2.76	1621	2.46	20092736	10057545	10035191	19860710	10016111	9844599	124858	0.63	59693	0.6	0.66	0	0.0	0	0.0	0	0.0	11636	0.12	0.32	9622	0.1	0.31	19071801	94.92	9772588	97.17	9299213	92.67	18970809	132674	0	0.0	45	0.03	148.76	3217346917	45372	0.0	0.01	442.84	239.72	235.0	153.24	0.06	94.41625570554453	49.84941324068559	48.99581122252341
Alp52-1-100 | Alp52-1-100	120162	100.0	0	0.0	100.0	120162	100.0	0	0.0	0	0.0	119177	99.18	59968	99.81	59209	98.55	18	0.01	29	0.02	47	0.04	119224	99.22	985	0.82	938	0.78	985	0.82	985	0.82	938	0.78	765	0.64	118412	98.54	114670	95.43	3742	3.11	96	0.08	72	0.06	80	0.07	119036	99.06	7	0.01	22	0.02	16	0.01	96	0.08	985	0.82	2516	4.2	2404	4.06	18031718	9019542	9012176	17894771	9008074	8886697	125778	0.7	39125	0.43	0.98	0	0.0	0	0.0	0	0.0	20069	0.22	0.4	17416	0.19	0.38	17353970	96.24	8811842	97.7	8542128	94.78	17272247	119217	0	0.0	40	0.03	150.06	3217346917	45372	0.0	0.01	397.42	224.12	214.0	39.25	0.07	95.78813843472929	49.95682607724899	49.283695541378805
Alp52-1-20 | Alp52-1-20	134678	100.0	0	0.0	100.0	134678	100.0	0	0.0	0	0.0	133605	99.2	67176	99.76	66429	98.65	22	0.02	35	0.03	57	0.04	133662	99.25	1073	0.8	1016	0.75	1073	0.8	1073	0.8	1016	0.75	763	0.57	132842	98.64	129548	96.19	3294	2.45	102	0.08	80	0.06	88	0.07	133417	99.06	16	0.01	28	0.02	22	0.02	122	0.09	1073	0.8	2522	3.75	2621	3.95	20197797	10103002	10094795	20052750	10086890	9965860	142883	0.71	46050	0.46	0.97	0	0.0	0	0.0	0	0.0	22088	0.22	0.45	19355	0.19	0.42	19327438	95.69	9864173	97.64	9463265	93.74	19234610	133650	0	0.0	45	0.03	149.97	3217346917	45372	0.0	0.01	445.16	222.85	214.0	42.07	0.07	95.23122744525058	49.94054549612515	49.34132172929553
Alp62-1-100 | Alp62-1-100	154422	100.0	0	0.0	100.0	154422	100.0	0	0.0	0	0.0	152512	98.76	76909	99.61	75603	97.92	42	0.03	32	0.02	74	0.05	152586	98.81	1910	1.24	1836	1.19	1910	1.24	1910	1.24	1836	1.19	1332	0.86	151180	97.9	145202	94.03	5978	3.87	248	0.16	191	0.13	540	0.35	151733	98.26	58	0.04	66	0.04	40	0.03	615	0.4	1910	1.24	5095	6.62	2939	3.89	23087419	11555418	11532001	22829101	11524172	11304929	223685	0.98	83511	0.72	1.24	0	0.0	0	0.0	0	0.0	25187	0.22	0.27	19518	0.17	0.24	22218828	96.24	11286306	97.67	10932522	94.8	22044000	152831	0	0.0	319	0.21	149.51	3217346917	45372	0.0	0.01	508.85	229.88	223.0	125.17	0.08	95.48057320742522	49.91537598897477	48.965754898804406
Alp62-1-20 | Alp62-1-20	159672	100.0	0	0.0	100.0	159672	100.0	0	0.0	0	0.0	157833	98.85	79499	99.58	78334	98.12	44	0.03	31	0.02	75	0.05	157908	98.9	1839	1.15	1764	1.1	1839	1.15	1839	1.15	1764	1.1	1193	0.75	156640	98.1	146726	91.89	9914	6.21	216	0.14	154	0.1	526	0.33	157031	98.35	64	0.04	61	0.04	58	0.04	619	0.39	1839	1.15	4539	5.71	2813	3.59	23874811	11948726	11926085	23630774	11914450	11716324	230241	0.97	85252	0.72	1.24	0	0.0	0	0.0	0	0.0	25088	0.21	0.31	20066	0.17	0.28	22867564	95.78	11664888	97.62	11202676	93.93	22687282	158181	0	0.0	348	0.22	149.52	3217346917	45372	0.0	0.01	526.2	228.0	220.0	105.35	0.08	95.0260171693087	49.90385054775931	49.073996858027485
AlpP2-NG011977-1-100 | AlpP2-NG011977-1-100	129634	100.0	0	0.0	100.0	129634	100.0	0	0.0	0	0.0	125160	96.55	63099	97.35	62061	95.75	2	0.0	22	0.02	24	0.02	125184	96.57	4474	3.45	4450	3.43	4474	3.45	4474	3.45	4450	3.43	1066	0.82	124094	95.73	62258	48.03	61836	47.7	112	0.09	86	0.07	47	0.04	125081	96.49	6	0.0	5	0.0	4	0.0	64	0.05	4474	3.45	2294	3.64	2806	4.52	19164264	9584550	9579714	18865577	9512930	9352647	48838	0.26	25218	0.27	0.25	0	0.0	0	0.0	0	0.0	9534	0.1	0.21	7129	0.07	0.18	18336268	95.68	9321883	97.26	9014385	94.1	18304809	125165	0	0.0	5	0.0	147.83	3217346917	45372	0.0	0.01	422.38	256.51	273.0	103.54	0.06	95.51532477323418	49.638900820819416	48.80253684670593
AlpP2-NG011977-1-20 | AlpP2-NG011977-1-20	133116	100.0	0	0.0	100.0	133116	100.0	0	0.0	0	0.0	125412	94.21	63217	94.98	62195	93.44	4	0.0	66	0.05	70	0.05	125482	94.27	7704	5.79	7634	5.73	7704	5.79	7704	5.79	7634	5.73	1074	0.81	124338	93.41	124046	93.19	292	0.22	134	0.11	105	0.08	73	0.05	125304	94.13	4	0.0	13	0.01	7	0.01	84	0.06	7704	5.79	2221	3.51	2754	4.43	19332887	9668555	9664332	18903274	9530538	9372736	57041	0.3	33495	0.35	0.25	0	0.0	0	0.0	0	0.0	9540	0.1	0.24	7199	0.08	0.21	18327685	94.8	9350816	96.71	8976869	92.89	18287586	125421	0	0.0	9	0.01	145.23	3217346917	45372	0.0	0.01	426.1	241.88	245.0	82.96	0.07	94.59314586590197	49.29702428819866	48.480788203024204
AlpP3-1-100 | AlpP3-1-100	148190	100.0	0	0.0	100.0	148190	100.0	0	0.0	0	0.0	144613	97.59	72819	98.28	71794	96.89	8	0.01	8	0.01	16	0.01	144629	97.6	3577	2.41	3561	2.4	3577	2.41	3577	2.41	3561	2.4	1049	0.71	143564	96.88	142456	96.13	1108	0.75	172	0.12	114	0.08	101	0.07	144407	97.45	8	0.01	20	0.01	34	0.02	144	0.1	3577	2.41	2107	2.89	2929	4.08	21813954	10902454	10911500	21552257	10849019	10703238	103958	0.48	42143	0.39	0.58	0	0.0	0	0.0	0	0.0	21528	0.2	0.36	19003	0.18	0.33	21026581	96.39	10637923	97.57	10388658	95.21	20957549	144863	0	0.0	250	0.17	147.2	3217346917	45372	0.0	0.01	480.78	226.28	222.0	91.47	0.08	96.07404966564063	49.734307682137775	49.066015267108384
AlpP3-1-20 | AlpP3-1-20	135936	100.0	0	0.0	100.0	135936	100.0	0	0.0	0	0.0	128991	94.89	64881	95.46	64110	94.32	4	0.0	8	0.01	12	0.01	129003	94.9	6945	5.11	6933	5.1	6945	5.11	6945	5.11	6933	5.1	849	0.62	128142	94.27	126416	93.0	1726	1.27	174	0.14	116	0.09	132	0.1	128716	94.69	23	0.02	38	0.03	36	0.03	178	0.13	6945	5.11	1833	2.83	2549	3.98	19405531	9697906	9707625	19031170	9569668	9461502	120274	0.63	53271	0.56	0.71	0	0.0	0	0.0	0	0.0	20202	0.21	0.42	18081	0.19	0.39	18494285	95.3	9395309	96.88	9098976	93.73	18405839	129138	0	0.0	147	0.11	142.75	3217346917	45372	0.0	0.01	427.7	222.29	222.0	65.05	0.07	94.84841718580131	49.314125957182	48.756728171983546
