## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M18_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M18_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 14:05:42 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
405215085	405188512	34535028	225804257	86063089	34493598	24306120	0	9092517	97126	0.085232	0.557282	0.212403	0.08513	0.059987	0.769685	0.769634	0.989431	0.775194	0.045123	0.555581	0.09666			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.043093
1	0.053191
2	0.077456
3	0.131621
4	0.180707
5	0.286026
6	0.350663
7	0.440815
8	0.52643
9	0.589018
10	0.662452
11	0.713095
12	0.749314
13	0.798116
14	0.843104
15	0.888523
16	0.919736
17	0.93902
18	0.972544
19	1.038204
20	1.0255
21	1.062511
22	1.093495
23	1.108503
24	1.121934
25	1.126878
26	1.118665
27	1.137639
28	1.166292
29	1.178468
30	1.237298
31	1.244934
32	1.234172
33	1.185239
34	1.200101
35	1.196416
36	1.183692
37	1.210793
38	1.211254
39	1.239534
40	1.252151
41	1.251762
42	1.270313
43	1.296016
44	1.293245
45	1.282944
46	1.294825
47	1.257425
48	1.245744
49	1.262159
50	1.246184
51	1.223024
52	1.205826
53	1.196852
54	1.237112
55	1.252596
56	1.283076
57	1.163349
58	1.173614
59	1.173334
60	1.190428
61	1.224386
62	1.211991
63	1.212523
64	1.210592
65	1.191748
66	1.185556
67	1.166077
68	1.140237
69	1.105307
70	1.100696
71	1.112901
72	1.135575
73	1.153145
74	1.171008
75	1.140443
76	1.138581
77	1.120132
78	1.081702
79	1.08605
80	1.081741
81	1.069684
82	1.060135
83	1.025274
84	1.036483
85	1.080035
86	1.067163
87	1.049024
88	0.989233
89	0.981996
90	0.946226
91	0.907141
92	0.869792
93	0.830467
94	0.787799
95	0.738946
96	0.727335
97	0.599677
98	0.480387
99	0.28156
100	0.099377