## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M1_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
474754170	474734849	18645891	281070492	110266546	31425847	33331437	0	11378236	173105	0.039276	0.592058	0.23227	0.066197	0.070211	0.824328	0.824294	0.985014	0.723759	0.043832	0.618274	0.089719			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.043945
1	0.053939
2	0.078204
3	0.125183
4	0.16841
5	0.257581
6	0.338306
7	0.439238
8	0.520494
9	0.589229
10	0.644832
11	0.688172
12	0.737186
13	0.776333
14	0.823946
15	0.866625
16	0.894501
17	0.914401
18	0.920458
19	0.963162
20	0.974358
21	1.013507
22	1.043492
23	1.072733
24	1.083566
25	1.091916
26	1.086038
27	1.090222
28	1.115676
29	1.154184
30	1.178011
31	1.185928
32	1.15131
33	1.143055
34	1.168602
35	1.179006
36	1.178672
37	1.197655
38	1.175812
39	1.206664
40	1.241733
41	1.239738
42	1.246129
43	1.246654
44	1.228886
45	1.253759
46	1.279423
47	1.247536
48	1.230795
49	1.237802
50	1.233796
51	1.215577
52	1.196935
53	1.201142
54	1.220213
55	1.23068
56	1.277413
57	1.163754
58	1.1821
59	1.175883
60	1.206379
61	1.243388
62	1.205078
63	1.188351
64	1.203991
65	1.190331
66	1.186958
67	1.160204
68	1.148136
69	1.129829
70	1.120432
71	1.132052
72	1.144679
73	1.152412
74	1.147935
75	1.132721
76	1.137097
77	1.135156
78	1.142376
79	1.140695
80	1.128718
81	1.105321
82	1.078969
83	1.083328
84	1.088762
85	1.093783
86	1.103656
87	1.165729
88	1.13479
89	1.05132
90	1.014565
91	0.9785
92	0.948605
93	0.925503
94	0.888501
95	0.823417
96	0.809991
97	0.665202
98	0.525952
99	0.295326
100	0.098801