## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=M2WTF_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/M2WTF_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 10:56:55 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
1473012600	1472905727	114412040	713707036	294962688	123062698	226761265	0	0	0	43574	12985432	32615	0.003344	0.996656	0.077678	0.484557	0.200259	0.083551	0.153955	0.684816	0.684767	0	0.886312	0.027223	0.735434	0.044624			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.029335
1	0.043252
2	0.078592
3	0.134943
4	0.174881
5	0.258058
6	0.354129
7	0.436496
8	0.494382
9	0.556842
10	0.60316
11	0.634909
12	0.700252
13	0.73969
14	0.764925
15	0.778908
16	0.797544
17	0.826761
18	0.854839
19	0.871397
20	0.903383
21	0.941963
22	0.950887
23	0.961698
24	0.969874
25	0.9895
26	1.008867
27	1.047416
28	1.068718
29	1.047307
30	1.05847
31	1.054249
32	1.073841
33	1.081764
34	1.127056
35	1.142759
36	1.153925
37	1.164545
38	1.139235
39	1.125605
40	1.149282
41	1.176509
42	1.191911
43	1.204899
44	1.207185
45	1.185567
46	1.17619
47	1.145194
48	1.140183
49	1.156697
50	1.154367
51	1.134444
52	1.130572
53	1.1371
54	1.163772
55	1.175169
56	1.178137
57	1.192943
58	1.218817
59	1.247726
60	1.239431
61	1.207815
62	1.176849
63	1.182099
64	1.188823
65	1.213776
66	1.196207
67	1.16384
68	1.16442
69	1.146105
70	1.137079
71	1.157097
72	1.156555
73	1.16859
74	1.126882
75	1.114965
76	1.118649
77	1.136858
78	1.137527
79	1.12725
80	1.12282
81	1.125944
82	1.139638
83	1.13134
84	1.15141
85	1.179723
86	1.164373
87	1.171895
88	1.208693
89	1.245106
90	1.221163
91	1.214338
92	1.219937
93	1.186639
94	1.140538
95	1.103928
96	1.077961
97	0.99286
98	0.799541
99	0.501475
100	0.193784