## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M15_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M15_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: Sun May 13 14:05:43 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
491109597	491079891	34276803	274851537	107016726	41163739	33785303	0	11155419	106705	0.069799	0.559688	0.217921	0.083823	0.068798	0.777609	0.777562	0.990525	0.77631	0.041693	0.541395	0.095092			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.044799
1	0.055326
2	0.081634
3	0.133316
4	0.181957
5	0.288477
6	0.366931
7	0.480072
8	0.559262
9	0.618624
10	0.687516
11	0.735667
12	0.782162
13	0.827535
14	0.871102
15	0.920079
16	0.94557
17	0.95755
18	0.961318
19	1.028596
20	1.035923
21	1.090245
22	1.12496
23	1.136064
24	1.13491
25	1.123051
26	1.11571
27	1.145434
28	1.174422
29	1.181255
30	1.219436
31	1.234733
32	1.221374
33	1.192354
34	1.203773
35	1.216909
36	1.20301
37	1.232931
38	1.219715
39	1.218152
40	1.239608
41	1.248593
42	1.25969
43	1.282731
44	1.267469
45	1.275167
46	1.281487
47	1.248455
48	1.233446
49	1.249261
50	1.25148
51	1.229922
52	1.203332
53	1.210265
54	1.245512
55	1.242391
56	1.279245
57	1.172388
58	1.184206
59	1.174274
60	1.191631
61	1.222833
62	1.189844
63	1.186253
64	1.184972
65	1.180012
66	1.190947
67	1.173791
68	1.140858
69	1.099149
70	1.096706
71	1.110244
72	1.140204
73	1.152488
74	1.148866
75	1.12146
76	1.135895
77	1.1108
78	1.068159
79	1.078918
80	1.061348
81	1.033533
82	1.03293
83	1.025028
84	1.038916
85	1.061401
86	1.043425
87	1.032346
88	0.993301
89	0.97111
90	0.933134
91	0.901061
92	0.864026
93	0.832663
94	0.787303
95	0.723371
96	0.717171
97	0.594429
98	0.464377
99	0.272181
100	0.097236