## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=M2Ezh12F_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/M2Ezh12F_2_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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Mar 09 11:02:18 EDT 2020

## 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	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_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
1391526000	1391430866	165152880	667215117	234530351	124115233	200417285	0	0	0	35606	11627448	24154	0.003053	0.996947	0.118693	0.479517	0.168553	0.0892	0.144037	0.648071	0.648026	0	0.821133	0.034854	0.694203	0.057088			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.033657
1	0.046817
2	0.079487
3	0.139851
4	0.199308
5	0.28971
6	0.38796
7	0.465005
8	0.533661
9	0.590146
10	0.638873
11	0.670034
12	0.74018
13	0.773068
14	0.803832
15	0.823663
16	0.828848
17	0.842629
18	0.86306
19	0.89076
20	0.92779
21	0.947947
22	0.964859
23	0.983669
24	0.998679
25	1.007675
26	1.031832
27	1.062445
28	1.07499
29	1.055911
30	1.092217
31	1.099955
32	1.1188
33	1.119972
34	1.132977
35	1.126545
36	1.134148
37	1.147636
38	1.137349
39	1.147827
40	1.170182
41	1.189104
42	1.199183
43	1.201574
44	1.195977
45	1.173405
46	1.158692
47	1.134719
48	1.143814
49	1.15394
50	1.15343
51	1.132036
52	1.122392
53	1.141038
54	1.17613
55	1.182345
56	1.171127
57	1.172411
58	1.197053
59	1.224189
60	1.235826
61	1.215644
62	1.18107
63	1.191365
64	1.199873
65	1.211579
66	1.184634
67	1.163787
68	1.173716
69	1.149958
70	1.155789
71	1.175444
72	1.162449
73	1.157248
74	1.125062
75	1.115177
76	1.116275
77	1.131556
78	1.149038
79	1.146373
80	1.143192
81	1.13591
82	1.1276
83	1.103718
84	1.116122
85	1.148058
86	1.14485
87	1.144557
88	1.166194
89	1.191997
90	1.165315
91	1.16478
92	1.172188
93	1.131167
94	1.105227
95	1.064987
96	1.010808
97	0.906194
98	0.708314
99	0.444635
100	0.179288