## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M11_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M11_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 18:42:29 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
364826979	364810676	16833003	210911129	83923009	27364887	25784150	0	8576751	125255	0.046142	0.578139	0.230045	0.075011	0.070678	0.808184	0.808148	0.985606	0.711088	0.047931	0.635987	0.091089			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.045562
1	0.056018
2	0.077491
3	0.126083
4	0.172003
5	0.263279
6	0.344428
7	0.430821
8	0.512688
9	0.581702
10	0.641228
11	0.685593
12	0.739752
13	0.782047
14	0.825692
15	0.860323
16	0.890776
17	0.913395
18	0.952289
19	1.010214
20	0.990472
21	1.023889
22	1.037902
23	1.061391
24	1.072627
25	1.083592
26	1.082827
27	1.089973
28	1.118779
29	1.153012
30	1.19039
31	1.181088
32	1.151464
33	1.132625
34	1.158227
35	1.172693
36	1.175531
37	1.193224
38	1.178701
39	1.207256
40	1.234453
41	1.239499
42	1.240112
43	1.267847
44	1.268083
45	1.270157
46	1.286906
47	1.245642
48	1.239911
49	1.256393
50	1.237752
51	1.202002
52	1.184794
53	1.187468
54	1.218355
55	1.231336
56	1.290415
57	1.177539
58	1.192961
59	1.196731
60	1.225435
61	1.255931
62	1.209725
63	1.207526
64	1.209677
65	1.193437
66	1.177293
67	1.152233
68	1.138848
69	1.121006
70	1.11025
71	1.121729
72	1.142634
73	1.150824
74	1.141985
75	1.113798
76	1.12036
77	1.110694
78	1.107692
79	1.122494
80	1.109097
81	1.095715
82	1.086612
83	1.080187
84	1.083362
85	1.101241
86	1.11195
87	1.1705
88	1.132394
89	1.040731
90	0.998708
91	0.977159
92	0.948559
93	0.91343
94	0.876518
95	0.819321
96	0.815667
97	0.669397
98	0.534956
99	0.304532
100	0.103237