## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M34_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M34_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 14:06:05 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
583877580	583842088	41191095	345132993	121111786	41320884	35103114	0	13598913	138810	0.070552	0.591141	0.207439	0.070774	0.060124	0.79858	0.798532	0.989896	0.781708	0.043778	0.517385	0.113469			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.046256
1	0.055969
2	0.084024
3	0.137352
4	0.184125
5	0.292293
6	0.371301
7	0.476164
8	0.557506
9	0.622208
10	0.697141
11	0.747481
12	0.793111
13	0.850092
14	0.906814
15	0.949431
16	0.973423
17	0.984167
18	0.98876
19	1.045651
20	1.055752
21	1.093827
22	1.126722
23	1.156621
24	1.166793
25	1.157052
26	1.141983
27	1.160436
28	1.200577
29	1.221168
30	1.269722
31	1.264001
32	1.228892
33	1.193275
34	1.214894
35	1.207375
36	1.202939
37	1.230925
38	1.204752
39	1.234815
40	1.269492
41	1.26378
42	1.280926
43	1.310654
44	1.292577
45	1.296979
46	1.298104
47	1.261961
48	1.246325
49	1.254929
50	1.238701
51	1.217927
52	1.201332
53	1.201204
54	1.234538
55	1.23759
56	1.277803
57	1.174366
58	1.178593
59	1.16707
60	1.184813
61	1.200767
62	1.166086
63	1.175548
64	1.185276
65	1.175266
66	1.166159
67	1.144568
68	1.122319
69	1.088323
70	1.090015
71	1.105121
72	1.114103
73	1.130716
74	1.127065
75	1.110421
76	1.117905
77	1.09487
78	1.064534
79	1.073582
80	1.062805
81	1.035744
82	1.032001
83	1.01302
84	1.008812
85	1.033064
86	1.01625
87	1.011185
88	0.955
89	0.936734
90	0.90873
91	0.882819
92	0.835159
93	0.804859
94	0.763261
95	0.708115
96	0.704892
97	0.576587
98	0.455055
99	0.263543
100	0.088865