## htsjdk.samtools.metrics.StringHeader
# picard.analysis.directed.CollectTargetedPcrMetrics AMPLICON_INTERVALS=fullintervals.txt TARGET_INTERVALS=[noprimerintervals.txt] INPUT=/data_all/1/56GSID_10k_mate1_RG.bam OUTPUT=56gsid_10k_mate1_rgbam.targetPCRmetrics.txt PER_TARGET_COVERAGE=56gsid_10k_mate1_rgbam.perTargetCov.txt REFERENCE_SEQUENCE=/data_all/3/hs_b37_chr2_small.fasta    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false COVERAGE_CAP=200 SAMPLE_SIZE=10000 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
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Mar 29 07:55:12 UTC 2017

## METRICS CLASS	picard.analysis.directed.TargetedPcrMetrics
CUSTOM_AMPLICON_SET	GENOME_SIZE	AMPLICON_TERRITORY	TARGET_TERRITORY	TOTAL_READS	PF_READS	PF_BASES	PF_UNIQUE_READS	PCT_PF_READS	PCT_PF_UQ_READS	PF_UQ_READS_ALIGNED	PF_SELECTED_PAIRS	PF_SELECTED_UNIQUE_PAIRS	PCT_PF_UQ_READS_ALIGNED	PF_BASES_ALIGNED	PF_UQ_BASES_ALIGNED	ON_AMPLICON_BASES	NEAR_AMPLICON_BASES	OFF_AMPLICON_BASES	ON_TARGET_BASES	ON_TARGET_FROM_PAIR_BASES	PCT_AMPLIFIED_BASES	PCT_OFF_AMPLICON	ON_AMPLICON_VS_SELECTED	MEAN_AMPLICON_COVERAGE	MEAN_TARGET_COVERAGE	MEDIAN_TARGET_COVERAGE	FOLD_ENRICHMENT	ZERO_CVG_TARGETS_PCT	PCT_EXC_DUPE	PCT_EXC_MAPQ	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_OFF_TARGET	FOLD_80_BASE_PENALTY	PCT_TARGET_BASES_1X	PCT_TARGET_BASES_2X	PCT_TARGET_BASES_10X	PCT_TARGET_BASES_20X	PCT_TARGET_BASES_30X	AT_DROPOUT	GC_DROPOUT	HET_SNP_SENSITIVITY	HET_SNP_Q	SAMPLE	LIBRARY	READ_GROUP
fullintervals	3001	325	325	20000	20000	2853790	20000	1	1	157	78	78	0.00785	22389	22389	19212	3085	92	19212	19212	0.995891	0.004109	0.861641	59.113846	59.113846	33	7.923563	0	0	0	0	0	0.1419	3.111255	1	1	1	0.793846	0.590769	0	0	0.999525	33			

## HISTOGRAM	java.lang.Integer
coverage	count	baseq_count
0	0	0
1	0	0
2	0	0
3	0	0
4	0	0
5	0	0
6	0	0
7	0	0
8	0	0
9	0	0
10	0	0
11	0	0
12	0	0
13	1	0
14	34	1490
15	0	0
16	2	0
17	23	0
18	0	0
19	7	0
20	0	0
21	0	141
22	0	0
23	0	0
24	0	0
25	0	0
26	43	0
27	20	0
28	0	438
29	3	0
30	14	0
31	0	0
32	1	1041
33	54	0
34	0	0
35	0	0
36	1	0
37	0	16102
38	2	0
39	2	0
40	0	0
41	0	0
42	0	0
43	0	0
44	0	0
45	0	0
46	0	0
47	0	0
48	0	0
49	0	0
50	0	0
51	0	0
52	0	0
53	0	0
54	0	0
55	0	0
56	0	0
57	0	0
58	0	0
59	0	0
60	0	0
61	0	0
62	0	0
63	0	0
64	0	0
65	0	0
66	0	0
67	0	0
68	0	0
69	0	0
70	0	0
71	0	0
72	0	0
73	0	0
74	0	0
75	0	0
76	0	0
77	0	0
78	0	0
79	0	0
80	0	0
81	0	0
82	0	0
83	0	0
84	0	0
85	0	0
86	0	0
87	0	0
88	0	0
89	0	0
90	0	0
91	0	0
92	0	0
93	0	0
94	0	0
95	0	0
96	0	0
97	0	0
98	0	0
99	0	0
100	0	0
101	0	0
102	0	0
103	0	0
104	0	0
105	0	0
106	0	0
107	0	0
108	43	0
109	6	0
110	0	0
111	1	0
112	0	0
113	0	0
114	0	0
115	0	0
116	0	0
117	1	0
118	0	0
119	3	0
120	2	0
121	2	0
122	1	0
123	0	0
124	19	0
125	0	0
126	0	0
127	1	0
128	3	0
129	36	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

