## 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


## HISTOGRAM	java.lang.Integer
CYCLE	MEAN_QUALITY	MEAN_ORIGINAL_QUALITY
1	28.822222	31.290909
2	28.448485	31.567677
3	27.89697	35.622222
4	28.870707	36.127273
5	29.456566	36.39596
6	29.60404	40.369697
7	28.981818	40.515152
8	28.886869	40.327273
9	29.016162	40.684848
10	29.028283	40.709091
11	29.038384	40.862626
12	28.664646	40.779798
13	28.458586	40.735354
14	28.347475	40.628283
15	28.408081	40.634343
16	28.4	40.709091
17	28.294949	40.583838
18	28.321212	40.622222
19	28.250505	40.49697
20	28.373737	40.622222
21	28.315152	40.630303
22	28.351515	40.658586
23	28.353535	40.753535
24	28.244444	40.583838
25	28.121212	40.49899
26	28.062626	40.080808
27	27.929293	40.068687
28	27.927273	40.022222
29	27.925253	40.153535
30	28.183838	40.240404
31	28.042424	40.307071
32	28.30101	40.488889
33	28.290909	40.541414
34	28.123232	40.325253
35	28.20202	40.288889
36	28.173737	40.264646
37	28.080808	40.018182
38	28.181818	39.957576
39	27.919192	39.909091
40	28.268687	40.00202
41	28.044444	39.929293
42	28.143434	40.137374
43	28.147475	40.321212
44	28.276768	39.983838
45	28.307071	39.919192
46	28.406061	40.082828
47	28.167677	40.210101
48	28.379798	40.046465
49	28.311111	39.741414
50	28.557576	39.945455
51	28.383838	39.963636
52	28.626263	40.008081
53	28.713131	39.983838
54	28.70101	40.088889
55	28.818182	40.284848
56	28.620202	40.048485
57	28.549495	40.090909
58	28.555556	39.929293
59	28.323232	39.660606
60	28.50101	39.874747
61	28.585859	39.931313
62	28.361616	39.8
63	28.484848	39.937374
64	28.327273	39.711111
65	28.444444	39.432323
66	28.133333	39.064646
67	28.551515	39.79596
68	28.579798	39.656566
69	28.274747	39.325253
70	28.575758	39.680808
71	28.319192	39.305051
72	28.264646	39.127273
73	28.375758	39.214141
74	28.424242	39.452525
75	28.448485	39.40404
76	28.442424	38.751515
77	28.50101	39.155556
78	28.343434	39.319192
79	28.622222	39.527273
80	28.531313	39.628283
81	28.591919	39.816162
82	28.434343	39.545455
83	28.4	39.327273
84	28.523232	39.608081
85	28.561616	39.684848
86	28.557576	39.529293
87	28.547475	39.555556
88	28.622222	39.909091
89	28.676768	39.832323
90	28.658586	39.90303
91	28.567677	39.331313
92	28.250505	39.082828
93	28.349495	39.107071
94	28.478788	39.024242
95	28.359596	39.177778
96	28.4	39.135354
97	28.343434	38.991919
98	28.264646	38.753535
99	28.286869	38.892929
100	28.505051	39.228283
101	28.50303	39.133333
102	28.317172	38.89697
103	28.288889	38.723232
104	28.258586	38.581818
105	28.331313	39.088889
106	28.426263	38.860606
107	28.155556	38.513131
108	28.408081	38.416162
109	28.272727	38.012121
110	28.218182	37.985859
111	28.644444	38.288889
112	28.569697	38.264646
113	28.424242	38.127273
114	28.460606	37.989899
115	28.713131	38.29899
116	28.321212	37.684848
117	28.428283	37.642424
118	28.234343	37.59596
119	28.347475	37.789899
120	28.363636	37.517172
121	28.181818	37.137374
122	28.014141	36.977778
123	28.569697	37.309091
124	28.561616	37.387879
125	28.466667	37.474747
126	28.391919	37.117172
127	27.422222	35.923232
128	27.933333	36.450505
129	28.09899	36.616162
130	28.325253	36.866667
131	27.838384	36.072727
132	27.961616	35.90101
133	27.826263	35.678788
134	27.828283	35.838384
135	27.711111	35.533333
136	27.755556	35.674747
137	27.729293	35.278788
138	27.705051	35.311111
139	27.529293	34.581818
140	27.905051	34.951515
141	27.90303	35.230303
142	27.561616	34.557576
143	26.90101	34.066667
144	27.10101	33.628283
145	27.143434	33.717172
146	25.943434	32.923232
147	25.020202	32.852525
148	23.593939	32.468687
149	21.70101	31.886869
150	21.234343	30.852525
151	22.020202	27.252525
152	26.390593	30.660532
153	26.705521	31.261759
154	26.271984	34.071575
155	27.867076	34.93047
156	28.437628	35.263804
157	28.754601	39.202454
158	28.282209	39.537832
159	27.850716	39.132924
160	27.676892	39.083845
161	28.034765	39.697342
162	27.789366	39.398773
163	27.728016	39.425358
164	27.533742	39.316973
165	27.609407	39.392638
166	27.691207	39.286299
167	27.603272	39.456033
168	27.329243	38.807771
169	27.406953	38.90593
170	27.484663	39.134969
171	27.680982	39.513292
172	27.627812	39.429448
173	27.98773	39.791411
174	27.838446	39.588957
175	27.693252	39.535787
176	26.721881	37.899796
177	27.672802	39.179959
178	27.537832	39.112474
179	27.631902	39.267894
180	27.666667	39.298569
181	27.660532	39.265849
182	27.570552	39.124744
183	27.762781	39.271984
184	27.539877	38.858896
185	27.734151	39.071575
186	27.619632	38.717791
187	27.903885	38.879346
188	27.777096	38.691207
189	27.803681	38.535787
190	27.783231	38.629857
191	27.584867	38.316973
192	27.605317	38.572597
193	27.599182	38.316973
194	27.660532	38.312883
195	27.766871	38.437628
196	27.531697	37.973415
197	27.685072	38.249489
198	27.633947	38.269939
199	27.701431	38.267894
200	27.404908	37.693252
201	27.269939	37.738241
202	27.302658	37.781186
203	27.597137	37.985685
204	27.803681	38.474438
205	27.703476	38.147239
206	27.597137	38.357873
207	27.625767	38.087935
208	27.364008	37.766871
209	27.042945	37.361963
210	27.294479	37.689162
211	27.470348	37.873211
212	27.398773	37.811861
213	27.595092	37.98364
214	27.284254	37.314928
215	27.288344	37.638037
216	27.280164	37.613497
217	27.382413	37.568507
218	26.924335	36.907975
219	26.822086	36.838446
220	27.171779	37.0818
221	27.09407	37.09407
222	26.912065	36.795501
223	26.93047	36.668712
224	27.03272	36.95092
225	27.341513	37.304703
226	26.99591	36.255624
227	26.836401	35.237219
228	27.521472	36.359918
229	27.582822	36.91002
230	27.503067	37.161554
231	27.607362	37.390593
232	27.603272	37.314928
233	27.644172	37.505112
234	27.650307	37.341513
235	27.728016	37.466258
236	27.124744	36.541922
237	26.842536	36.278119
238	26.813906	36.07362
239	26.948875	35.985685
240	27.159509	36.408998
241	26.815951	36
242	26.883436	35.631902
243	27.224949	36.312883
244	27.261759	36.206544
245	27.312883	35.9591
246	27.042945	35.662577
247	26.830266	35.556237
248	27	35.529652
249	26.728016	35.278119
250	26.578732	34.740286
251	26.787321	35.120654
252	26.498978	34.871166
253	26.768916	34.940695
254	26.903885	34.869121
255	26.654397	34.717791
256	26.93047	35.063395
257	26.746421	34.750511
258	26.386503	34.265849
259	26.464213	34.151329
260	26.552147	34.106339
261	26.644172	34.116564
262	26.633947	34.05726
263	26.523517	33.490798
264	26.464213	33.550102
265	26.353783	33.226994
266	25.91002	32.9182
267	26.210634	33.247444
268	25.932515	32.578732
269	25.719836	32.672802
270	25.944785	32.458078
271	26.157464	32.642127
272	25.400818	31.541922
273	25.161554	31.323108
274	25.09816	31.147239
275	25.104294	31.224949
276	25.190184	31.302658
277	25.388548	31.705521
278	24.701431	30.079755
279	24.865031	30.269939
280	24.564417	29.721881
281	24.562372	29.740286
282	24.744376	29.977505
283	24.515337	29.278119
284	24.323108	29.762781
285	23.631902	28.809816
286	24.087935	28.948875
287	23.828221	27.973415
288	23.756646	28.239264
289	23.533742	28.110429
290	23.05726	27.237219
291	23.126789	27.619632
292	23.05317	27.153374
293	22.406953	26.327198
294	22.525562	26.705521
295	22.092025	26.278119
296	21.535787	25.359918
297	21	25.396728
298	19.95092	24.756646
299	18.259714	24.104294
300	16.116564	23.331288
301	15.546012	22.114519
302	15.703476	18.803681

