## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=LZ_M19_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LZ_M19_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
419854149	419830912	15710607	243869520	96577147	34955963	28727004	0	9943096	94904	0.037421	0.580876	0.230038	0.083262	0.068425	0.810914	0.810869	0.990546	0.770799	0.041779	0.53882	0.101331			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.043392
1	0.053829
2	0.080091
3	0.136089
4	0.189377
5	0.301485
6	0.382252
7	0.479743
8	0.550451
9	0.615918
10	0.695487
11	0.744962
12	0.78402
13	0.825602
14	0.866072
15	0.929234
16	0.952242
17	0.961448
18	0.995777
19	1.06686
20	1.037738
21	1.065887
22	1.091502
23	1.099044
24	1.115751
25	1.105671
26	1.120978
27	1.151468
28	1.179938
29	1.189276
30	1.229029
31	1.244926
32	1.23541
33	1.185012
34	1.199475
35	1.205566
36	1.188076
37	1.227772
38	1.219757
39	1.235256
40	1.25032
41	1.25508
42	1.256971
43	1.280996
44	1.261397
45	1.259608
46	1.276676
47	1.246358
48	1.228561
49	1.246659
50	1.228485
51	1.202534
52	1.204647
53	1.209838
54	1.24248
55	1.252052
56	1.292106
57	1.168897
58	1.197415
59	1.190719
60	1.213334
61	1.213923
62	1.186092
63	1.179627
64	1.184962
65	1.172752
66	1.181615
67	1.174233
68	1.135748
69	1.104665
70	1.114206
71	1.127082
72	1.131259
73	1.141728
74	1.154617
75	1.118469
76	1.115714
77	1.101239
78	1.067973
79	1.078377
80	1.053491
81	1.024709
82	1.034731
83	1.029179
84	1.026393
85	1.048539
86	1.045515
87	1.024303
88	0.987172
89	0.964748
90	0.938123
91	0.910361
92	0.871222
93	0.838909
94	0.789936
95	0.732859
96	0.75075
97	0.594818
98	0.469755
99	0.269387
100	0.102209