## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M71_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M71_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
2356436700	2189567019	10861395	1550752028	416857904	61803902	149291790	0	13727042	25193	11353	6738767	127173	0.001682	0.998318	0.004961	0.708246	0.190384	0.028227	0.068183	0.89863	0.834994	0.998168	0.522901	0.368968	0.150094	2.201829			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.107851
1	0.192027
2	0.333094
3	0.482434
4	0.596379
5	0.710392
6	0.801639
7	0.871735
8	0.924232
9	0.962759
10	0.995348
11	1.027958
12	1.05952
13	1.086022
14	1.107375
15	1.132205
16	1.149645
17	1.163839
18	1.18121
19	1.197576
20	1.212358
21	1.21936
22	1.226463
23	1.232189
24	1.235826
25	1.234204
26	1.233466
27	1.240135
28	1.253091
29	1.270589
30	1.279223
31	1.281197
32	1.279312
33	1.273816
34	1.278814
35	1.284236
36	1.282018
37	1.280536
38	1.283201
39	1.286621
40	1.279983
41	1.267079
42	1.267567
43	1.26382
44	1.259551
45	1.250948
46	1.246113
47	1.244476
48	1.235805
49	1.230846
50	1.221872
51	1.213223
52	1.206554
53	1.206326
54	1.204375
55	1.199858
56	1.201153
57	1.203361
58	1.208731
59	1.207899
60	1.206237
61	1.197988
62	1.175787
63	1.163069
64	1.1533
65	1.140865
66	1.128764
67	1.122596
68	1.113893
69	1.099224
70	1.082772
71	1.070996
72	1.061845
73	1.051806
74	1.034999
75	1.016712
76	0.999369
77	0.980019
78	0.969813
79	0.954723
80	0.929621
81	0.901792
82	0.87555
83	0.848886
84	0.828281
85	0.80389
86	0.776735
87	0.74576
88	0.712392
89	0.667737
90	0.616303
91	0.562704
92	0.506054
93	0.445452
94	0.378313
95	0.309855
96	0.243798
97	0.177647
98	0.116446
99	0.06759
100	0.036542

