## htsjdk.samtools.metrics.StringHeader
# CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=picard/nonzero.wgs_metrics.pdf INPUT=in/sample.bam OUTPUT=picard/nonzero.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 21:42:51 HST 2026

## METRICS CLASS	picard.analysis.CollectWgsMetricsWithNonZeroCoverage$WgsMetricsWithNonZeroCoverage
CATEGORY	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
WHOLE_GENOME	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
NON_ZERO_REGIONS	2493	50.976735	27.126692	55	22	0	0	0.016403	0.003882	0.069148	0.046661	0	0.136093	1	0.959085	0.915764	0.875251	0.829523	0.790213	0.740874	0.629763	0.546731	0.438829	0.302046	0.167669	0.054553	0.01444	2.317124	4.248061	10.195347	0.968331	15

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

