## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M80_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M80_metrics    MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] END_BIAS_BASES=100 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: Fri Feb 23 11:57:46 EST 2024

## 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
2110605600	1961631784	8191402	1408289843	357821863	68530723	118797953	0	12314739	21691	9631	6058198	105435	0.001587	0.998413	0.004176	0.717918	0.18241	0.034936	0.060561	0.900328	0.83678	0.998242	0.544352	0.360196	0.136701	2.263141			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.109719
1	0.196093
2	0.343427
3	0.495232
4	0.614097
5	0.729937
6	0.823851
7	0.891322
8	0.943233
9	0.983077
10	1.00602
11	1.03341
12	1.063501
13	1.087581
14	1.108116
15	1.127166
16	1.141652
17	1.155016
18	1.171792
19	1.189685
20	1.203713
21	1.21095
22	1.219291
23	1.222364
24	1.224397
25	1.226458
26	1.229288
27	1.238549
28	1.250774
29	1.268712
30	1.272568
31	1.272808
32	1.270261
33	1.267798
34	1.266963
35	1.269035
36	1.26796
37	1.26492
38	1.266539
39	1.270051
40	1.27533
41	1.271622
42	1.277835
43	1.280875
44	1.275959
45	1.26692
46	1.25952
47	1.251402
48	1.241836
49	1.239078
50	1.233865
51	1.228189
52	1.227269
53	1.228845
54	1.22351
55	1.216269
56	1.216146
57	1.222213
58	1.226033
59	1.221003
60	1.218444
61	1.209179
62	1.186879
63	1.171298
64	1.159588
65	1.143547
66	1.126723
67	1.122489
68	1.112013
69	1.097998
70	1.083263
71	1.07005
72	1.061677
73	1.050822
74	1.03098
75	1.007949
76	0.988477
77	0.96705
78	0.954847
79	0.943244
80	0.917807
81	0.892236
82	0.867553
83	0.842094
84	0.819571
85	0.793334
86	0.766247
87	0.736849
88	0.705564
89	0.660478
90	0.608926
91	0.55442
92	0.49511
93	0.433815
94	0.365989
95	0.293426
96	0.226572
97	0.16315
98	0.109687
99	0.066539
100	0.03717

