## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M4_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M4_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 18:41:33 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
407834790	407816130	20335755	238449761	90459317	28050532	30528019	0	9573443	136411	0.049865	0.584699	0.221814	0.068782	0.074857	0.806513	0.806476	0.985951	0.714926	0.0466	0.645909	0.092612			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.045096
1	0.055066
2	0.076915
3	0.124807
4	0.173826
5	0.262371
6	0.335986
7	0.425087
8	0.507301
9	0.572906
10	0.627602
11	0.665924
12	0.72569
13	0.770098
14	0.817019
15	0.848314
16	0.87365
17	0.889915
18	0.905129
19	0.952479
20	0.963929
21	0.986974
22	1.020785
23	1.051608
24	1.06046
25	1.068
26	1.067435
27	1.079271
28	1.093925
29	1.123055
30	1.160947
31	1.181806
32	1.177565
33	1.159445
34	1.173372
35	1.188474
36	1.185631
37	1.194059
38	1.182568
39	1.20999
40	1.24583
41	1.243906
42	1.243179
43	1.252937
44	1.244621
45	1.264201
46	1.280775
47	1.246909
48	1.225658
49	1.232182
50	1.215393
51	1.187999
52	1.182276
53	1.180279
54	1.211118
55	1.229058
56	1.289256
57	1.17205
58	1.18806
59	1.18944
60	1.229222
61	1.259015
62	1.222009
63	1.212198
64	1.225381
65	1.212418
66	1.195477
67	1.169356
68	1.149493
69	1.122818
70	1.128269
71	1.135785
72	1.164034
73	1.166203
74	1.16207
75	1.144495
76	1.138585
77	1.140824
78	1.135445
79	1.143491
80	1.127678
81	1.095591
82	1.086813
83	1.098851
84	1.084884
85	1.09948
86	1.10562
87	1.163916
88	1.144543
89	1.07491
90	1.035575
91	1.000232
92	0.960654
93	0.92327
94	0.891761
95	0.839707
96	0.84406
97	0.674791
98	0.524604
99	0.296743
100	0.100917