## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=WTM_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WTM_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 10:53:18 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
1460295150	1460094175	317928645	652705115	197689421	49641027	242129967	0	0	0	15675	10978909	17498	0.001426	0.998574	0.217745	0.447029	0.135395	0.033999	0.165832	0.582424	0.582344	0	0.715823	0.037309	0.713992	0.067432			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.034165
1	0.042862
2	0.072566
3	0.126661
4	0.176794
5	0.261627
6	0.364682
7	0.452613
8	0.529732
9	0.585255
10	0.62517
11	0.652524
12	0.724282
13	0.770416
14	0.808807
15	0.836068
16	0.849529
17	0.878611
18	0.906685
19	0.936447
20	0.971374
21	0.991411
22	1.005085
23	1.027944
24	1.037072
25	1.060831
26	1.081091
27	1.117956
28	1.130608
29	1.12725
30	1.1443
31	1.150967
32	1.163251
33	1.173302
34	1.192838
35	1.204738
36	1.206918
37	1.211383
38	1.198743
39	1.200184
40	1.212892
41	1.213714
42	1.223856
43	1.227988
44	1.216127
45	1.194715
46	1.193963
47	1.184573
48	1.180017
49	1.189847
50	1.194004
51	1.174082
52	1.176628
53	1.20304
54	1.220965
55	1.216504
56	1.201293
57	1.186666
58	1.209695
59	1.235667
60	1.240188
61	1.218985
62	1.18165
63	1.187875
64	1.186873
65	1.189658
66	1.162632
67	1.152609
68	1.149667
69	1.145293
70	1.147563
71	1.160374
72	1.155785
73	1.143979
74	1.132645
75	1.117983
76	1.112846
77	1.127341
78	1.123699
79	1.117173
80	1.105675
81	1.085287
82	1.074142
83	1.074933
84	1.07925
85	1.103101
86	1.106139
87	1.100213
88	1.111589
89	1.113034
90	1.086861
91	1.076723
92	1.062668
93	1.022058
94	0.979827
95	0.943812
96	0.896575
97	0.794813
98	0.607886
99	0.355623
100	0.118722