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aih-tih-sc-184b05-R1_A23YTGFLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-184b05-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:04 PM

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## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-184b05-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-184b05-R1_A23YTGFLT4_1_rna_metrics.txt --TMP_DIR ./tmp --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Jun 03 20:45:59 GMT 2026

## 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
76005487780	75029922347	4840	67389831478	5327724630	2043832285	268529114	0	0	0	9607984	238559248	1198580	0.038716	0.961284	0	0.898173	0.071008	0.02724	0.003579	0.969181	0.956741	0	0.553963	0.569851	0.671907	0.928366			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.288842
1	0.339492
2	0.401422
3	0.477284
4	0.556317
5	0.627297
6	0.694387
7	0.759028
8	0.817826
9	0.865644
10	0.910708
11	0.951383
12	0.982483
13	1.018239
14	1.049209
15	1.072638
16	1.095187
17	1.108501
18	1.124839
19	1.138512
20	1.157598
21	1.167503
22	1.174084
23	1.183761
24	1.184419
25	1.181655
26	1.179102
27	1.171941
28	1.170737
29	1.173729
30	1.175703
31	1.174632
32	1.170261
33	1.172295
34	1.16428
35	1.166566
36	1.15864
37	1.149588
38	1.154128
39	1.152352
40	1.148241
41	1.143754
42	1.1494
43	1.153214
44	1.151351
45	1.161243
46	1.158685
47	1.16084
48	1.153709
49	1.14735
50	1.136313
51	1.13049
52	1.122339
53	1.122625
54	1.123998
55	1.127422
56	1.125407
57	1.122498
58	1.116371
59	1.108837
60	1.104128
61	1.108179
62	1.109547
63	1.101766
64	1.103993
65	1.105938
66	1.106568
67	1.103202
68	1.103143
69	1.093403
70	1.080456
71	1.068935
72	1.067267
73	1.064075
74	1.056775
75	1.048387
76	1.040086
77	1.022264
78	1.00819
79	0.995775
80	0.979625
81	0.965465
82	0.951014
83	0.935835
84	0.922201
85	0.904599
86	0.883092
87	0.871747
88	0.852838
89	0.837934
90	0.817473
91	0.801803
92	0.773182
93	0.740574
94	0.707716
95	0.67765
96	0.648126
97	0.62119
98	0.586949
99	0.553521
100	0.516654