## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M3_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed May 09 18:41:34 EDT 2018

## METRICS CLASS	picard.analysis.RnaSeqMetrics
PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
420744357	420724510	24172038	238099456	94729535	32698107	31033087	0	9696049	128273	0.057453	0.565927	0.225158	0.077719	0.073761	0.791085	0.791048	0.986943	0.703797	0.042997	0.643617	0.091166			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.04451
1	0.054384
2	0.078633
3	0.128275
4	0.177282
5	0.265057
6	0.350176
7	0.451586
8	0.528748
9	0.60471
10	0.6697
11	0.70899
12	0.751988
13	0.790131
14	0.834299
15	0.884838
16	0.915687
17	0.932545
18	0.944066
19	1.005124
20	1.000938
21	1.034738
22	1.064393
23	1.094459
24	1.097929
25	1.103411
26	1.095917
27	1.106584
28	1.126372
29	1.160392
30	1.184495
31	1.201531
32	1.181138
33	1.173656
34	1.18897
35	1.195891
36	1.177735
37	1.183247
38	1.170251
39	1.190261
40	1.221046
41	1.240955
42	1.244713
43	1.253306
44	1.244571
45	1.253788
46	1.266774
47	1.240053
48	1.229595
49	1.238133
50	1.230053
51	1.200933
52	1.18889
53	1.197953
54	1.218634
55	1.219514
56	1.264353
57	1.156323
58	1.176525
59	1.176303
60	1.208221
61	1.234181
62	1.191768
63	1.188919
64	1.2024
65	1.183695
66	1.177
67	1.15543
68	1.135214
69	1.12065
70	1.113168
71	1.111911
72	1.1318
73	1.142141
74	1.133028
75	1.123179
76	1.126255
77	1.11709
78	1.110689
79	1.113517
80	1.109927
81	1.084259
82	1.061537
83	1.06678
84	1.075847
85	1.076272
86	1.077568
87	1.135927
88	1.12114
89	1.039172
90	0.996114
91	0.967217
92	0.949162
93	0.919054
94	0.880557
95	0.832241
96	0.826371
97	0.661069
98	0.523241
99	0.29839
100	0.103406