## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M33_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M33_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 14:06:06 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
516226326	516196923	38442756	296813449	109329932	40177573	31447081	0	11865874	105424	0.074473	0.575	0.211799	0.077834	0.060921	0.786799	0.786754	0.991194	0.768976	0.03927	0.529813	0.097755			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.045521
1	0.055722
2	0.080437
3	0.132325
4	0.187801
5	0.29322
6	0.381223
7	0.485425
8	0.563856
9	0.626573
10	0.710066
11	0.757574
12	0.787563
13	0.832586
14	0.880539
15	0.924921
16	0.948883
17	0.960231
18	1.001241
19	1.07385
20	1.054065
21	1.084558
22	1.11153
23	1.125081
24	1.142504
25	1.135577
26	1.137351
27	1.165215
28	1.201129
29	1.222109
30	1.267889
31	1.261504
32	1.246131
33	1.216443
34	1.211499
35	1.206117
36	1.203515
37	1.237646
38	1.211074
39	1.22384
40	1.259726
41	1.259901
42	1.279236
43	1.309632
44	1.291435
45	1.291146
46	1.303958
47	1.255235
48	1.238532
49	1.253912
50	1.239684
51	1.208699
52	1.194544
53	1.206493
54	1.23689
55	1.24635
56	1.285587
57	1.184389
58	1.194581
59	1.185398
60	1.202884
61	1.201853
62	1.162248
63	1.164072
64	1.171252
65	1.164995
66	1.159209
67	1.151548
68	1.131854
69	1.096994
70	1.075233
71	1.086165
72	1.100643
73	1.103852
74	1.108753
75	1.107557
76	1.114246
77	1.095226
78	1.071052
79	1.076671
80	1.058512
81	1.032947
82	1.035576
83	1.019312
84	1.011988
85	1.038421
86	1.025537
87	1.015904
88	0.956146
89	0.954913
90	0.920312
91	0.894158
92	0.856233
93	0.828519
94	0.784266
95	0.723036
96	0.719089
97	0.579248
98	0.454907
99	0.265205
100	0.096032