## htsjdk.samtools.metrics.StringHeader
# CollectWgsMetrics INPUT=in/sample.bam OUTPUT=picard/wgs.wgs_metrics REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 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 21:42:36 HST 2026

## METRICS CLASS	picard.analysis.WgsMetrics
GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	PCT_EXC_ADAPTER	PCT_EXC_MAPQ	PCT_EXC_DUPE	PCT_EXC_UNPAIRED	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_CAPPED	PCT_EXC_TOTAL	PCT_1X	PCT_5X	PCT_10X	PCT_15X	PCT_20X	PCT_25X	PCT_30X	PCT_40X	PCT_50X	PCT_60X	PCT_70X	PCT_80X	PCT_90X	PCT_100X	FOLD_80_BASE_PENALTY	FOLD_90_BASE_PENALTY	FOLD_95_BASE_PENALTY	HET_SNP_SENSITIVITY	HET_SNP_Q
6005	21.163197	30.601918	0	0	0	0	0.016403	0.003882	0.069148	0.046661	0	0.136093	0.415154	0.398168	0.380183	0.363364	0.34438	0.32806	0.307577	0.261449	0.226978	0.182182	0.125396	0.069609	0.022648	0.005995	?	?	?	0.402007	2

## HISTOGRAM	java.lang.Integer
coverage	high_quality_coverage_count
0	3512
1	29
2	24
3	20
4	29
5	29
6	11
7	25
8	22
9	21
10	22
11	7
12	19
13	23
14	30
15	29
16	12
17	22
18	26
19	25
20	26
21	22
22	27
23	15
24	8
25	26
26	22
27	30
28	24
29	21
30	23
31	20
32	30
33	31
34	38
35	30
36	28
37	26
38	26
39	25
40	17
41	19
42	22
43	23
44	24
45	25
46	20
47	22
48	18
49	17
50	15
51	17
52	23
53	28
54	30
55	29
56	34
57	30
58	29
59	34
60	32
61	24
62	33
63	33
64	29
65	43
66	32
67	48
68	26
69	41
70	40
71	35
72	27
73	36
74	31
75	32
76	26
77	38
78	41
79	29
80	20
81	28
82	40
83	30
84	31
85	34
86	30
87	24
88	20
89	25
90	15
91	18
92	13
93	12
94	12
95	3
96	7
97	7
98	3
99	10
100	4
101	10
102	4
103	1
104	4
105	5
106	1
107	4
108	2
109	1
110	0
111	0
112	0
113	0
114	0
115	0
116	0
117	0
118	0
119	0
120	0
121	0
122	0
123	0
124	0
125	0
126	0
127	0
128	0
129	0
130	0
131	0
132	0
133	0
134	0
135	0
136	0
137	0
138	0
139	0
140	0
141	0
142	0
143	0
144	0
145	0
146	0
147	0
148	0
149	0
150	0
151	0
152	0
153	0
154	0
155	0
156	0
157	0
158	0
159	0
160	0
161	0
162	0
163	0
164	0
165	0
166	0
167	0
168	0
169	0
170	0
171	0
172	0
173	0
174	0
175	0
176	0
177	0
178	0
179	0
180	0
181	0
182	0
183	0
184	0
185	0
186	0
187	0
188	0
189	0
190	0
191	0
192	0
193	0
194	0
195	0
196	0
197	0
198	0
199	0
200	0
201	0
202	0
203	0
204	0
205	0
206	0
207	0
208	0
209	0
210	0
211	0
212	0
213	0
214	0
215	0
216	0
217	0
218	0
219	0
220	0
221	0
222	0
223	0
224	0
225	0
226	0
227	0
228	0
229	0
230	0
231	0
232	0
233	0
234	0
235	0
236	0
237	0
238	0
239	0
240	0
241	0
242	0
243	0
244	0
245	0
246	0
247	0
248	0
249	0
250	0

