## htsjdk.samtools.metrics.StringHeader
# CollectWgsMetrics INPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/mapped/NaomicfDNA2_S2_R1.dedup.bam OUTPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/alignment-metrics/NaomicfDNA2_S2_R1.dedup.wgs_metrics.txt MINIMUM_MAPPING_QUALITY=5 MINIMUM_BASE_QUALITY=10 INCLUDE_BQ_HISTOGRAM=true REFERENCE_SEQUENCE=/mnt/data/pipeline_genome_data/hg19/male.hg19.fa    COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Apr 03 03:13:35 PDT 2018

## METRICS CLASS	picard.analysis.CollectWgsMetrics$WgsMetrics
GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	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	HET_SNP_SENSITIVITY	HET_SNP_Q
2858674665	2.466798	3.08742	2	1	0.073636	0	0.005518	0.00001	0.009078	0.027871	0.116112	0.844126	0.138578	0.007506	0.001062	0.000523	0.000385	0.000313	0.000237	0.000195	0.000166	0.000146	0.000131	0.00012	0.00011	0.422694	2

## HISTOGRAM	java.lang.Integer
coverage	high_quality_coverage_count	unfiltered_baseq_count
0	445592528	0
1	623779127	0
2	617815527	0
3	470539230	0
4	304799234	0
5	178677664	0
6	98807802	0
7	53223456	0
8	28539456	0
9	15444304	0
10	8489315	0
11	4728723	0
12	2695793	0
13	1564352	0
14	943024	328580773
15	584553	0
16	377625	0
17	257780	0
18	183005	0
19	137840	0
20	108194	0
21	88636	58941820
22	75652	0
23	64886	0
24	56903	0
25	50465	0
26	44783	0
27	40592	142726863
28	36015	0
29	32570	0
30	30320	0
31	27242	0
32	25288	557726276
33	23155	0
34	21741	0
35	19990	0
36	19340	6027265783
37	17887	0
38	17257	0
39	15686	0
40	15086	0
41	14292	0
42	13555	0
43	12824	0
44	12117	0
45	11774	0
46	11162	0
47	10666	0
48	10345	0
49	9535	0
50	9912	0
51	9320	0
52	8851	0
53	8614	0
54	8231	0
55	8031	0
56	7654	0
57	7530	0
58	7346	0
59	6685	0
60	6624	0
61	6380	0
62	6361	0
63	6010	0
64	5597	0
65	5594	0
66	5519	0
67	5226	0
68	4942	0
69	4864	0
70	4806	0
71	4542	0
72	4436	0
73	4355	0
74	4275	0
75	4047	0
76	4056	0
77	3901	0
78	3869	0
79	3778	0
80	3546	0
81	3562	0
82	3413	0
83	3331	0
84	3468	0
85	3216	0
86	3322	0
87	3077	0
88	3006	0
89	3037	0
90	3047	0
91	2944	0
92	2864	0
93	2829	0
94	2845	0
95	2621	0
96	2585	0
97	2486	0
98	2392	0
99	2418	0
100	2391	0
101	2351	0
102	2230	0
103	2113	0
104	2147	0
105	2085	0
106	2087	0
107	2162	0
108	1980	0
109	2009	0
110	1974	0
111	1834	0
112	1812	0
113	1856	0
114	1760	0
115	1811	0
116	1731	0
117	1766	0
118	1720	0
119	1737	0
120	1584	0
121	1531	0
122	1509	0
123	1595	0
124	1500	0
125	1444	0
126	1439	0
127	1516	0
128	1550	0
129	1423	0
130	1451	0
131	1403	0
132	1363	0
133	1272	0
134	1249	0
135	1286	0
136	1348	0
137	1375	0
138	1259	0
139	1278	0
140	1303	0
141	1252	0
142	1142	0
143	1232	0
144	1200	0
145	1138	0
146	1176	0
147	1110	0
148	1166	0
149	1123	0
150	1087	0
151	1078	0
152	1061	0
153	1053	0
154	1059	0
155	1026	0
156	1067	0
157	1012	0
158	1027	0
159	981	0
160	989	0
161	984	0
162	1009	0
163	1006	0
164	953	0
165	966	0
166	895	0
167	961	0
168	949	0
169	939	0
170	925	0
171	979	0
172	878	0
173	965	0
174	858	0
175	851	0
176	871	0
177	822	0
178	886	0
179	836	0
180	827	0
181	862	0
182	833	0
183	803	0
184	844	0
185	864	0
186	806	0
187	785	0
188	821	0
189	823	0
190	776	0
191	772	0
192	755	0
193	806	0
194	799	0
195	734	0
196	821	0
197	791	0
198	738	0
199	771	0
200	724	0
201	703	0
202	717	0
203	795	0
204	772	0
205	686	0
206	666	0
207	710	0
208	711	0
209	656	0
210	678	0
211	699	0
212	676	0
213	655	0
214	693	0
215	654	0
216	640	0
217	644	0
218	672	0
219	665	0
220	612	0
221	671	0
222	587	0
223	612	0
224	684	0
225	650	0
226	609	0
227	595	0
228	556	0
229	581	0
230	524	0
231	547	0
232	545	0
233	558	0
234	496	0
235	501	0
236	488	0
237	496	0
238	486	0
239	500	0
240	505	0
241	557	0
242	619	0
243	528	0
244	550	0
245	541	0
246	516	0
247	487	0
248	509	0
249	489	0
250	159812	0