## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M72_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M72_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 11:57:45 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
1800335100	1625114760	10227575	1142817392	294048271	83389456	94632066	0	10351696	21814	9726	5060518	116757	0.001918	0.998082	0.006293	0.703223	0.18094	0.051313	0.058231	0.884163	0.79811	0.997897	0.643966	0.389709	0.097041	2.85014			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.122349
1	0.215713
2	0.368067
3	0.532959
4	0.655574
5	0.775471
6	0.86298
7	0.930902
8	0.988117
9	1.029443
10	1.058616
11	1.088154
12	1.112858
13	1.126387
14	1.141901
15	1.160275
16	1.177216
17	1.191813
18	1.207493
19	1.222563
20	1.23612
21	1.243868
22	1.246196
23	1.241573
24	1.239148
25	1.238872
26	1.237342
27	1.245078
28	1.256998
29	1.270668
30	1.269441
31	1.262429
32	1.25493
33	1.251606
34	1.264789
35	1.273082
36	1.269148
37	1.265979
38	1.270396
39	1.277219
40	1.27379
41	1.266592
42	1.27651
43	1.276341
44	1.270679
45	1.265852
46	1.260436
47	1.253311
48	1.242735
49	1.231179
50	1.210289
51	1.195949
52	1.186377
53	1.187678
54	1.186994
55	1.188624
56	1.191053
57	1.19749
58	1.204929
59	1.200662
60	1.196606
61	1.188772
62	1.170937
63	1.16413
64	1.152629
65	1.136244
66	1.120613
67	1.114494
68	1.105008
69	1.091997
70	1.07592
71	1.060709
72	1.043284
73	1.026195
74	1.011885
75	0.997906
76	0.986373
77	0.968457
78	0.958966
79	0.94743
80	0.919864
81	0.89033
82	0.862528
83	0.833066
84	0.805503
85	0.775277
86	0.74466
87	0.720488
88	0.692965
89	0.646603
90	0.592629
91	0.530686
92	0.468939
93	0.404203
94	0.334196
95	0.261246
96	0.196598
97	0.13784
98	0.0865
99	0.049351
100	0.024925

