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aih-tih-sc-28eb14-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-28eb14-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 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-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-28eb14-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 20:36:04 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
76935444556	76197742292	5954	69107125513	4951995614	1919850276	218764935	0	0	0	6706507	241200178	1138003	0.027053	0.972947	0	0.906945	0.064989	0.025196	0.002871	0.971933	0.962614	0	0.517716	0.516089	0.758521	0.789688			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.274107
1	0.303761
2	0.346286
3	0.400301
4	0.459575
5	0.518048
6	0.576423
7	0.635863
8	0.686975
9	0.734468
10	0.776724
11	0.817402
12	0.864447
13	0.90677
14	0.946337
15	0.980166
16	1.015154
17	1.038192
18	1.059445
19	1.083697
20	1.105542
21	1.129686
22	1.146227
23	1.159192
24	1.163523
25	1.164842
26	1.169544
27	1.173199
28	1.17817
29	1.17929
30	1.176928
31	1.176111
32	1.179452
33	1.18178
34	1.181251
35	1.183714
36	1.18327
37	1.182133
38	1.185284
39	1.186636
40	1.179481
41	1.175364
42	1.175206
43	1.183679
44	1.178611
45	1.175739
46	1.174712
47	1.176843
48	1.173989
49	1.171985
50	1.160601
51	1.163184
52	1.16686
53	1.165028
54	1.166793
55	1.16573
56	1.156727
57	1.147553
58	1.148333
59	1.141374
60	1.135379
61	1.131047
62	1.131119
63	1.126258
64	1.127241
65	1.129692
66	1.120376
67	1.116116
68	1.111409
69	1.10435
70	1.102146
71	1.089022
72	1.080809
73	1.071921
74	1.068307
75	1.062175
76	1.051691
77	1.043246
78	1.032764
79	1.024485
80	1.011102
81	0.998494
82	0.984717
83	0.971052
84	0.959754
85	0.950637
86	0.933509
87	0.923518
88	0.906888
89	0.88813
90	0.869799
91	0.848125
92	0.820745
93	0.787452
94	0.758225
95	0.728113
96	0.696125
97	0.661872
98	0.622677
99	0.586366
100	0.545318