## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M5_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M5_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 18:41:32 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
388058979	388040046	18633978	212834148	91352528	30600234	34626901	0	8871502	110547	0.048021	0.548485	0.23542	0.078858	0.089235	0.783905	0.783867	0.987692	0.707001	0.039523	0.651944	0.080501			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.045547
1	0.053821
2	0.078231
3	0.126122
4	0.170787
5	0.259374
6	0.335815
7	0.437895
8	0.519307
9	0.579436
10	0.631009
11	0.673806
12	0.720495
13	0.771131
14	0.829313
15	0.862873
16	0.883151
17	0.897298
18	0.948063
19	1.002423
20	0.982009
21	1.007332
22	1.042628
23	1.068472
24	1.084221
25	1.088361
26	1.073149
27	1.086556
28	1.111485
29	1.140085
30	1.175327
31	1.178083
32	1.163209
33	1.148744
34	1.16189
35	1.183465
36	1.175199
37	1.180986
38	1.162214
39	1.198813
40	1.223941
41	1.228881
42	1.229922
43	1.251082
44	1.233859
45	1.2408
46	1.264877
47	1.225626
48	1.230681
49	1.248197
50	1.241364
51	1.212382
52	1.182508
53	1.195235
54	1.22498
55	1.230458
56	1.286234
57	1.176717
58	1.189309
59	1.187703
60	1.218318
61	1.253521
62	1.198398
63	1.181823
64	1.196681
65	1.18031
66	1.180405
67	1.176854
68	1.155185
69	1.11904
70	1.115302
71	1.116242
72	1.130342
73	1.13776
74	1.131856
75	1.111885
76	1.115205
77	1.115584
78	1.108753
79	1.123252
80	1.121962
81	1.091968
82	1.077717
83	1.089098
84	1.099914
85	1.113695
86	1.112232
87	1.166611
88	1.13585
89	1.054789
90	1.028166
91	0.997282
92	0.967883
93	0.952058
94	0.91569
95	0.865299
96	0.858137
97	0.705807
98	0.55629
99	0.310517
100	0.110464