## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=in/sample.bam OUTPUT=picard/cmm METRIC_ACCUMULATION_LEVEL=[ALL_READS, LIBRARY, SAMPLE, READ_GROUP] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectGcBiasMetrics, CollectInsertSizeMetrics, CollectQualityYieldMetrics, CollectSequencingArtifactMetrics, MeanQualityByCycle, QualityScoreDistribution] REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false DO_NOT_CREATE_PLOTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 24 21:42:13 HST 2026

## METRICS CLASS	picard.analysis.BaseDistributionByCycleMetrics
READ_END	CYCLE	PCT_A	PCT_C	PCT_G	PCT_T	PCT_N
1	1	31.515152	18.181818	21.616162	28.080808	0.606061
1	2	30.707071	18.787879	24.646465	25.858586	0
1	3	30.909091	20.20202	24.242424	24.646465	0
1	4	33.333333	17.979798	23.636364	25.050505	0
1	5	31.111111	15.555556	22.626263	30.707071	0
1	6	32.727273	20.40404	24.646465	22.222222	0
1	7	30.10101	16.565657	24.040404	29.292929	0
1	8	30.909091	19.59596	20.40404	29.090909	0
1	9	31.717172	18.181818	20.20202	29.89899	0
1	10	30.707071	17.171717	24.646465	27.474747	0
1	11	30.707071	15.555556	28.686869	25.050505	0
1	12	34.747475	17.373737	22.626263	25.252525	0
1	13	34.949495	17.979798	23.838384	23.232323	0
1	14	32.121212	17.777778	25.858586	24.242424	0
1	15	32.929293	18.787879	23.838384	24.444444	0
1	16	31.515152	17.979798	25.050505	25.454545	0
1	17	30.30303	18.585859	25.050505	26.060606	0
1	18	29.090909	20.606061	24.646465	25.656566	0
1	19	30.707071	21.010101	22.828283	25.454545	0
1	20	30.505051	17.373737	26.262626	25.858586	0
1	21	28.080808	16.969697	27.272727	27.676768	0
1	22	29.89899	15.959596	27.878788	26.262626	0
1	23	26.666667	18.989899	27.878788	26.464646	0
1	24	32.121212	14.141414	27.878788	25.858586	0
1	25	30.505051	17.979798	25.050505	26.464646	0
1	26	35.353535	17.575758	24.242424	22.828283	0
1	27	28.686869	21.414141	22.626263	27.272727	0
1	28	29.090909	18.383838	24.848485	27.676768	0
1	29	29.090909	19.59596	24.646465	26.666667	0
1	30	28.080808	19.191919	26.060606	26.666667	0
1	31	31.111111	21.212121	25.050505	22.626263	0
1	32	31.515152	18.585859	22.222222	27.676768	0
1	33	29.69697	20.20202	23.636364	26.464646	0
1	34	31.111111	18.989899	24.242424	25.656566	0
1	35	29.090909	22.626263	21.010101	27.272727	0
1	36	28.888889	22.020202	22.626263	26.464646	0
1	37	28.888889	17.171717	23.434343	30.505051	0
1	38	29.292929	20.40404	19.393939	30.707071	0.20202
1	39	31.111111	21.616162	24.646465	22.626263	0
1	40	30.707071	18.585859	24.040404	26.666667	0
1	41	31.515152	18.181818	22.626263	27.676768	0
1	42	28.686869	17.373737	26.868687	27.070707	0
1	43	30.505051	18.989899	23.232323	27.272727	0
1	44	34.141414	17.979798	23.030303	24.848485	0
1	45	29.090909	17.777778	27.272727	25.858586	0
1	46	34.747475	19.79798	20.20202	25.252525	0
1	47	29.090909	19.191919	25.050505	26.666667	0
1	48	34.141414	14.747475	24.848485	26.262626	0
1	49	30.707071	19.393939	25.050505	24.848485	0
1	50	31.111111	18.585859	24.646465	25.656566	0
1	51	26.262626	20.40404	24.242424	29.090909	0
1	52	34.545455	18.383838	22.020202	25.050505	0
1	53	35.353535	15.757576	26.060606	22.828283	0
1	54	32.323232	17.777778	23.232323	26.666667	0
1	55	36.565657	15.151515	23.434343	24.848485	0
1	56	31.919192	18.383838	27.070707	22.626263	0
1	57	28.888889	15.353535	26.060606	29.69697	0
1	58	32.727273	17.979798	24.040404	25.252525	0
1	59	31.111111	22.020202	18.787879	28.080808	0
1	60	31.515152	17.171717	25.454545	25.858586	0
1	61	27.474747	18.181818	28.686869	25.656566	0
1	62	30.909091	17.373737	25.454545	26.262626	0
1	63	32.525253	18.585859	24.242424	24.646465	0
1	64	30.505051	20.606061	23.838384	25.050505	0
1	65	31.515152	17.777778	23.232323	27.474747	0
1	66	27.878788	18.585859	25.252525	28.282828	0
1	67	30.10101	22.222222	24.848485	22.828283	0
1	68	30.707071	18.787879	24.444444	26.060606	0
1	69	33.535354	15.555556	28.282828	22.626263	0
1	70	31.515152	17.373737	26.060606	25.050505	0
1	71	32.525253	16.161616	26.666667	24.646465	0
1	72	32.929293	18.181818	24.040404	24.848485	0
1	73	31.111111	17.373737	24.040404	27.474747	0
1	74	32.323232	19.59596	24.242424	23.838384	0
1	75	28.686869	19.393939	23.636364	28.282828	0
1	76	27.474747	18.989899	26.666667	26.868687	0
1	77	31.919192	19.59596	25.656566	22.828283	0
1	78	33.333333	18.585859	25.454545	22.626263	0
1	79	34.545455	16.767677	23.030303	25.656566	0
1	80	33.737374	16.363636	22.020202	27.878788	0
1	81	27.676768	22.828283	28.686869	20.808081	0
1	82	35.151515	19.59596	22.222222	23.030303	0
1	83	35.555556	16.767677	19.79798	27.878788	0
1	84	32.121212	17.373737	25.252525	25.252525	0
1	85	31.717172	15.757576	29.090909	23.434343	0
1	86	32.929293	17.171717	26.060606	23.838384	0
1	87	34.747475	15.151515	21.616162	28.484848	0
1	88	30.10101	18.181818	27.676768	24.040404	0
1	89	30.909091	17.777778	25.454545	25.858586	0
1	90	34.747475	18.181818	22.424242	24.646465	0
1	91	34.343434	18.585859	22.626263	24.444444	0
1	92	32.929293	22.626263	22.626263	21.818182	0
1	93	35.555556	16.565657	21.616162	26.262626	0
1	94	32.525253	17.979798	23.030303	26.464646	0
1	95	31.919192	20.20202	25.252525	22.626263	0
1	96	34.747475	17.777778	24.444444	23.030303	0
1	97	32.727273	17.373737	22.020202	27.878788	0
1	98	32.323232	16.161616	25.050505	26.464646	0
1	99	33.737374	18.989899	25.656566	21.616162	0
1	100	36.161616	16.565657	24.040404	23.232323	0
1	101	32.727273	17.777778	22.222222	27.272727	0
1	102	32.929293	16.767677	24.848485	25.454545	0
1	103	31.717172	20.808081	23.030303	24.444444	0
1	104	33.131313	18.585859	23.636364	24.646465	0
1	105	29.89899	19.79798	24.444444	25.858586	0
1	106	29.090909	15.757576	26.060606	29.090909	0
1	107	30.707071	18.181818	28.282828	22.626263	0.20202
1	108	34.141414	17.171717	24.040404	24.646465	0
1	109	32.525253	15.959596	25.656566	25.858586	0
1	110	27.878788	22.626263	26.060606	23.434343	0
1	111	31.515152	15.959596	26.262626	26.262626	0
1	112	35.353535	15.353535	23.838384	25.252525	0.20202
1	113	33.333333	17.373737	27.272727	22.020202	0
1	114	32.525253	18.181818	26.060606	23.232323	0
1	115	33.131313	19.79798	21.414141	25.656566	0
1	116	34.747475	17.373737	22.020202	25.858586	0
1	117	29.292929	16.565657	26.060606	28.080808	0
1	118	30.505051	19.59596	26.262626	23.636364	0
1	119	29.494949	20.606061	24.646465	25.252525	0
1	120	32.929293	17.171717	24.040404	25.858586	0
1	121	30.30303	19.191919	22.020202	28.484848	0
1	122	24.646465	21.818182	25.454545	28.080808	0
1	123	30.707071	18.787879	22.626263	27.878788	0
1	124	31.919192	20.606061	23.030303	24.444444	0
1	125	30.707071	19.79798	23.838384	25.656566	0
1	126	29.494949	19.393939	26.060606	25.050505	0
1	127	33.333333	17.777778	25.050505	22.828283	1.010101
1	128	35.555556	16.969697	21.818182	25.656566	0
1	129	30.10101	19.191919	25.252525	25.454545	0
1	130	34.545455	17.979798	22.424242	25.050505	0
1	131	31.515152	21.212121	22.828283	24.444444	0
1	132	30.10101	19.79798	22.626263	27.474747	0
1	133	30.707071	18.787879	24.848485	25.656566	0
1	134	30.30303	19.191919	22.424242	28.080808	0
1	135	28.888889	19.59596	28.282828	23.232323	0
1	136	30.707071	23.434343	21.616162	24.242424	0
1	137	31.515152	22.626263	22.020202	23.838384	0
1	138	30.30303	19.393939	23.636364	26.666667	0
1	139	29.494949	18.383838	29.494949	22.626263	0
1	140	32.525253	17.171717	25.656566	24.646465	0
1	141	30.30303	17.373737	23.434343	28.888889	0
1	142	27.070707	22.626263	24.848485	25.252525	0.20202
1	143	30.909091	18.787879	23.232323	27.070707	0
1	144	28.888889	18.989899	25.656566	26.464646	0
1	145	31.919192	20.20202	22.020202	25.858586	0
1	146	31.919192	17.979798	24.444444	25.656566	0
1	147	28.888889	21.414141	24.242424	25.454545	0
1	148	30.10101	18.181818	23.838384	27.878788	0
1	149	33.737374	17.373737	22.222222	26.666667	0
1	150	33.131313	19.191919	25.252525	22.424242	0
1	151	35.353535	17.777778	24.040404	22.828283	0
2	152	34.764826	17.791411	21.676892	24.744376	1.022495
2	153	33.537832	19.427403	21.881391	24.948875	0.204499
2	154	32.310838	17.791411	23.721881	26.175869	0
2	155	31.90184	18.200409	24.335378	25.357873	0.204499
2	156	34.560327	15.541922	21.676892	28.220859	0
2	157	31.083845	17.382413	24.335378	27.198364	0
2	158	30.470348	16.359918	27.402863	25.766871	0
2	159	32.719836	17.791411	22.699387	26.789366	0
2	160	34.969325	18.404908	22.699387	23.312883	0.613497
2	161	31.697342	19.222904	22.290389	26.584867	0.204499
2	162	32.924335	18.609407	23.517382	24.948875	0
2	163	30.265849	17.791411	26.789366	25.153374	0
2	164	37.627812	17.177914	22.903885	22.290389	0
2	165	35.582822	16.973415	22.290389	25.153374	0
2	166	30.674847	18.200409	24.130879	26.993865	0
2	167	32.924335	17.382413	26.175869	23.517382	0
2	168	31.697342	18.200409	23.312883	25.562372	1.226994
2	169	34.151329	20.0409	21.063395	24.744376	0
2	170	32.719836	19.631902	21.881391	25.766871	0
2	171	31.697342	19.018405	24.130879	25.153374	0
2	172	35.173824	17.382413	17.99591	29.447853	0
2	173	32.924335	17.586912	24.539877	24.948875	0
2	174	31.492843	17.586912	25.357873	25.562372	0
2	175	30.06135	20.245399	23.517382	26.175869	0
2	176	33.128834	20.449898	20.245399	23.108384	3.067485
2	177	31.90184	18.609407	23.721881	25.766871	0
2	178	33.742331	16.564417	25.766871	23.92638	0
2	179	31.083845	20.858896	22.903885	25.153374	0
2	180	31.492843	18.200409	26.175869	24.130879	0
2	181	31.90184	18.609407	24.130879	25.357873	0
2	182	29.856851	19.631902	23.92638	26.584867	0
2	183	34.969325	19.836401	23.108384	22.08589	0
2	184	32.310838	17.791411	25.97137	23.92638	0
2	185	24.539877	16.973415	27.811861	30.674847	0
2	186	34.151329	17.791411	26.380368	21.676892	0
2	187	29.243354	19.427403	24.948875	26.380368	0
2	188	30.06135	17.99591	25.357873	26.584867	0
2	189	28.220859	20.449898	24.130879	26.993865	0.204499
2	190	33.537832	17.586912	24.744376	24.130879	0
2	191	31.083845	17.382413	23.108384	28.425358	0
2	192	30.674847	18.200409	25.766871	25.357873	0
2	193	30.470348	16.155419	25.97137	27.402863	0
2	194	29.652352	16.359918	26.789366	27.198364	0
2	195	31.288344	16.564417	26.175869	25.97137	0
2	196	33.94683	17.177914	22.699387	26.175869	0
2	197	30.879346	20.0409	23.517382	25.562372	0
2	198	31.288344	18.609407	24.130879	25.97137	0
2	199	33.537832	20.0409	22.494888	23.92638	0
2	200	33.537832	19.222904	22.699387	24.539877	0
2	201	30.879346	17.382413	28.834356	22.903885	0
2	202	35.582822	17.177914	21.472393	25.766871	0
2	203	31.90184	17.382413	25.562372	25.153374	0
2	204	34.764826	15.746421	24.744376	24.744376	0
2	205	32.106339	19.018405	26.175869	22.699387	0
2	206	29.038855	20.449898	25.766871	24.744376	0
2	207	29.652352	17.791411	23.92638	28.629857	0
2	208	30.674847	17.99591	24.744376	26.584867	0
2	209	28.629857	18.813906	24.539877	27.198364	0.817996
2	210	28.834356	21.063395	25.153374	24.948875	0
2	211	31.288344	19.631902	23.721881	25.357873	0
2	212	31.288344	17.586912	25.153374	25.97137	0
2	213	27.811861	17.177914	28.425358	26.584867	0
2	214	31.083845	16.359918	28.220859	24.335378	0
2	215	31.288344	20.858896	23.721881	24.130879	0
2	216	33.128834	18.200409	24.744376	23.92638	0
2	217	31.697342	17.791411	25.97137	24.539877	0
2	218	30.06135	20.245399	25.97137	23.721881	0
2	219	31.697342	18.404908	27.198364	22.699387	0
2	220	32.310838	17.99591	25.97137	23.721881	0
2	221	30.674847	19.427403	28.220859	21.676892	0
2	222	32.310838	19.631902	25.357873	22.699387	0
2	223	34.764826	19.427403	22.494888	23.312883	0
2	224	29.652352	19.018405	27.607362	23.721881	0
2	225	31.288344	20.0409	27.607362	21.063395	0
2	226	31.083845	15.95092	24.744376	28.220859	0
2	227	33.333333	21.063395	24.130879	21.472393	0
2	228	33.333333	20.654397	22.08589	23.92638	0
2	229	32.515337	18.404908	23.312883	25.766871	0
2	230	29.447853	17.791411	26.380368	26.380368	0
2	231	30.265849	16.973415	26.993865	25.766871	0
2	232	31.697342	18.813906	26.789366	22.699387	0
2	233	33.128834	19.018405	24.744376	23.108384	0
2	234	32.515337	17.99591	26.380368	23.108384	0
2	235	31.492843	19.222904	25.153374	24.130879	0
2	236	30.674847	17.99591	24.948875	26.380368	0
2	237	34.151329	16.564417	26.175869	23.108384	0
2	238	29.652352	19.836401	26.175869	24.335378	0
2	239	35.99182	18.609407	22.290389	22.903885	0.204499
2	240	34.151329	18.200409	22.494888	25.153374	0
2	241	35.787321	14.110429	25.562372	24.539877	0
2	242	32.106339	17.382413	22.08589	28.425358	0
2	243	34.355828	17.99591	22.494888	25.153374	0
2	244	31.492843	16.359918	27.607362	24.335378	0.204499
2	245	34.764826	16.768916	22.08589	26.380368	0
2	246	33.537832	15.95092	26.175869	24.335378	0
2	247	31.697342	21.881391	26.584867	19.836401	0
2	248	33.94683	16.564417	22.699387	26.789366	0
2	249	31.288344	15.337423	28.834356	24.539877	0
2	250	34.560327	19.222904	24.744376	21.472393	0
2	251	34.560327	19.018405	24.130879	22.290389	0
2	252	26.789366	22.494888	25.766871	24.948875	0
2	253	33.128834	18.813906	25.766871	22.290389	0
2	254	33.537832	19.427403	19.222904	27.811861	0
2	255	31.492843	20.0409	23.108384	25.357873	0
2	256	32.719836	20.654397	22.290389	24.335378	0
2	257	33.333333	20.654397	25.562372	20.449898	0
2	258	32.310838	19.222904	25.766871	22.699387	0
2	259	30.674847	15.132924	27.607362	26.584867	0
2	260	32.924335	14.723926	27.811861	24.539877	0
2	261	35.99182	19.018405	24.130879	20.858896	0
2	262	31.90184	19.222904	24.335378	24.539877	0
2	263	34.969325	17.99591	22.699387	24.335378	0
2	264	32.106339	18.813906	22.699387	26.380368	0
2	265	28.220859	17.586912	28.834356	25.357873	0
2	266	33.537832	20.449898	24.539877	21.472393	0
2	267	32.924335	18.404908	25.357873	23.312883	0
2	268	29.038855	20.0409	24.335378	26.584867	0
2	269	31.90184	18.813906	25.97137	23.312883	0
2	270	29.038855	17.382413	24.948875	28.629857	0
2	271	33.537832	17.586912	23.92638	24.948875	0
2	272	31.492843	18.404908	27.811861	22.290389	0
2	273	31.492843	19.222904	25.97137	23.312883	0
2	274	33.128834	19.018405	24.130879	23.721881	0
2	275	32.924335	20.449898	25.97137	20.654397	0
2	276	30.674847	20.654397	24.744376	23.92638	0
2	277	28.834356	19.222904	26.175869	25.766871	0
2	278	32.719836	14.519427	21.472393	31.288344	0
2	279	31.697342	20.654397	24.744376	22.903885	0
2	280	29.038855	19.222904	25.357873	26.380368	0
2	281	33.94683	17.382413	22.903885	25.766871	0
2	282	30.470348	15.95092	26.584867	26.993865	0
2	283	33.128834	20.449898	23.517382	22.903885	0
2	284	28.834356	23.312883	23.108384	24.744376	0
2	285	30.879346	23.108384	22.699387	23.312883	0
2	286	35.99182	18.609407	21.472393	23.92638	0
2	287	28.834356	18.404908	25.766871	26.993865	0
2	288	31.083845	16.359918	25.562372	26.993865	0
2	289	32.515337	20.245399	23.517382	23.721881	0
2	290	33.537832	20.245399	22.494888	23.721881	0
2	291	27.607362	23.108384	25.357873	23.92638	0
2	292	32.515337	19.427403	24.948875	23.108384	0
2	293	30.470348	20.245399	22.699387	26.584867	0
2	294	32.719836	19.836401	24.539877	22.903885	0
2	295	32.924335	17.382413	24.744376	24.948875	0
2	296	32.515337	14.519427	28.01636	24.948875	0
2	297	31.288344	21.267894	23.92638	23.517382	0
2	298	32.515337	17.586912	25.357873	24.539877	0
2	299	32.924335	17.791411	27.198364	22.08589	0
2	300	33.333333	18.200409	23.517382	24.948875	0
2	301	34.969325	18.609407	23.721881	22.699387	0
2	302	30.265849	21.472393	24.335378	23.92638	0


