## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G221_M78_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G221_M78_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 11:57:48 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
2243794200	2114133883	11758461	1459528899	423840084	93305306	125701133	0	12890005	89607	42578	6351749	99231	0.006659	0.993341	0.005562	0.690367	0.200479	0.044134	0.059458	0.890847	0.839368	0.993096	0.514296	0.331398	0.182276	1.696268			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.102786
1	0.172797
2	0.291676
3	0.417817
4	0.519186
5	0.620946
6	0.708202
7	0.771777
8	0.825058
9	0.869942
10	0.905167
11	0.937541
12	0.967484
13	0.988422
14	1.006311
15	1.028996
16	1.048288
17	1.061079
18	1.079621
19	1.102804
20	1.121167
21	1.133551
22	1.14431
23	1.15434
24	1.16299
25	1.170433
26	1.1755
27	1.184843
28	1.19828
29	1.214221
30	1.217566
31	1.221131
32	1.220904
33	1.221518
34	1.218757
35	1.216935
36	1.215982
37	1.215116
38	1.219145
39	1.224558
40	1.228768
41	1.232401
42	1.242356
43	1.247634
44	1.248615
45	1.244547
46	1.242697
47	1.242958
48	1.238018
49	1.23442
50	1.231957
51	1.233023
52	1.234557
53	1.241295
54	1.239951
55	1.237193
56	1.240708
57	1.246591
58	1.250064
59	1.253409
60	1.253713
61	1.24087
62	1.221565
63	1.209519
64	1.198737
65	1.185643
66	1.179017
67	1.17943
68	1.172169
69	1.163006
70	1.154005
71	1.144046
72	1.135648
73	1.12379
74	1.110099
75	1.096711
76	1.085127
77	1.068254
78	1.057197
79	1.045861
80	1.022341
81	0.997978
82	0.974152
83	0.949689
84	0.926512
85	0.898903
86	0.872448
87	0.839611
88	0.804773
89	0.755254
90	0.700543
91	0.642191
92	0.574916
93	0.509548
94	0.439116
95	0.361723
96	0.28675
97	0.211257
98	0.141676
99	0.081462
100	0.038872

