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aih-tih-sc-64fc89-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-64fc89-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:13 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-64fc89-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-64fc89-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 20:55:56 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
75116372940	74298392736	2920	67389108280	4798911198	1911239244	199131094	0	0	0	8337256	234869637	1023528	0.034281	0.965719	0	0.907006	0.06459	0.025724	0.00268	0.971596	0.961016	0	0.536614	0.52114	0.71767	0.81674			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.270687
1	0.309451
2	0.367684
3	0.435879
4	0.504551
5	0.568829
6	0.625927
7	0.67516
8	0.730474
9	0.7829
10	0.830053
11	0.876531
12	0.927555
13	0.980202
14	1.016243
15	1.053522
16	1.077489
17	1.102618
18	1.112636
19	1.118953
20	1.129908
21	1.149727
22	1.168614
23	1.18071
24	1.182431
25	1.187163
26	1.183318
27	1.181934
28	1.182848
29	1.182894
30	1.181133
31	1.184534
32	1.178055
33	1.173008
34	1.16057
35	1.16437
36	1.159524
37	1.15101
38	1.148415
39	1.147106
40	1.136796
41	1.138383
42	1.143236
43	1.143788
44	1.144691
45	1.149998
46	1.146661
47	1.150408
48	1.14676
49	1.143558
50	1.14113
51	1.136668
52	1.129461
53	1.129051
54	1.135015
55	1.140833
56	1.143735
57	1.146026
58	1.141544
59	1.1378
60	1.132043
61	1.132836
62	1.130839
63	1.119327
64	1.108705
65	1.113282
66	1.112968
67	1.108717
68	1.108495
69	1.106058
70	1.095044
71	1.083907
72	1.079273
73	1.081522
74	1.073362
75	1.064587
76	1.053532
77	1.039523
78	1.032126
79	1.027008
80	1.012807
81	0.997757
82	0.98166
83	0.962142
84	0.943048
85	0.925122
86	0.906301
87	0.893023
88	0.874183
89	0.857637
90	0.837131
91	0.82087
92	0.795005
93	0.770226
94	0.740228
95	0.707606
96	0.677981
97	0.651233
98	0.615151
99	0.579036
100	0.541394