## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=Ezh12M_1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/Ezh12M_1_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 10:57:16 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
1378263225	1377962624	476931706	417542642	150621736	88584212	244282328	0	0	0	17702	7360181	13840	0.002399	0.997601	0.346114	0.303014	0.109308	0.064286	0.177278	0.412322	0.412232	0	0.676866	0.03817	0.814808	0.056376			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.034869
1	0.042308
2	0.070252
3	0.123578
4	0.174258
5	0.259976
6	0.361649
7	0.453415
8	0.52424
9	0.575115
10	0.609926
11	0.639256
12	0.699598
13	0.73898
14	0.775679
15	0.802853
16	0.81814
17	0.841506
18	0.860262
19	0.886378
20	0.913905
21	0.941746
22	0.969588
23	0.981777
24	0.989196
25	1.00298
26	1.015609
27	1.045535
28	1.064747
29	1.06459
30	1.079962
31	1.093397
32	1.100977
33	1.104195
34	1.109924
35	1.130054
36	1.138376
37	1.148494
38	1.145003
39	1.158709
40	1.175833
41	1.176329
42	1.188138
43	1.199962
44	1.190445
45	1.18144
46	1.171124
47	1.157482
48	1.149478
49	1.163829
50	1.168843
51	1.145975
52	1.138963
53	1.17098
54	1.18922
55	1.196226
56	1.191444
57	1.186754
58	1.204084
59	1.221725
60	1.250924
61	1.230624
62	1.184936
63	1.194538
64	1.197848
65	1.201416
66	1.172802
67	1.168348
68	1.168555
69	1.16236
70	1.172129
71	1.182523
72	1.183296
73	1.167145
74	1.156326
75	1.144572
76	1.156912
77	1.186992
78	1.182862
79	1.166595
80	1.157154
81	1.147164
82	1.1406
83	1.145838
84	1.157197
85	1.178038
86	1.176043
87	1.167334
88	1.172324
89	1.180459
90	1.172841
91	1.170431
92	1.163764
93	1.121828
94	1.078877
95	1.039391
96	0.994254
97	0.886096
98	0.674283
99	0.400422
100	0.135841