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aih-tih-sc-966ec5-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-966ec5-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:46 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-966ec5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-966ec5-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 20:40:02 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
69561081395	68696493431	5004	61743265089	5050728777	1601688303	300806258	0	0	0	14431397	231623686	1099205	0.058651	0.941349	0	0.898783	0.073522	0.023315	0.004379	0.972306	0.960221	0	0.567736	0.510244	0.707958	0.847748			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.265952
1	0.306718
2	0.355329
3	0.412293
4	0.477955
5	0.547743
6	0.606546
7	0.660061
8	0.718372
9	0.766229
10	0.815473
11	0.870925
12	0.921705
13	0.961216
14	0.999364
15	1.026471
16	1.050816
17	1.072028
18	1.0826
19	1.102747
20	1.117711
21	1.129585
22	1.144387
23	1.156677
24	1.164934
25	1.167432
26	1.169139
27	1.165832
28	1.169101
29	1.165253
30	1.165234
31	1.168651
32	1.158337
33	1.160378
34	1.155523
35	1.149562
36	1.144001
37	1.141551
38	1.144345
39	1.144385
40	1.13869
41	1.142734
42	1.145387
43	1.142587
44	1.137385
45	1.147029
46	1.145821
47	1.144657
48	1.145299
49	1.153344
50	1.164798
51	1.160086
52	1.156977
53	1.155051
54	1.162712
55	1.165832
56	1.162623
57	1.159318
58	1.1512
59	1.143269
60	1.134573
61	1.13145
62	1.136961
63	1.134893
64	1.142611
65	1.145681
66	1.13594
67	1.13007
68	1.123973
69	1.114612
70	1.108373
71	1.101376
72	1.099197
73	1.091607
74	1.087144
75	1.078393
76	1.066653
77	1.052673
78	1.038639
79	1.035203
80	1.021963
81	1.007081
82	0.992044
83	0.969168
84	0.957102
85	0.941667
86	0.92103
87	0.908033
88	0.889571
89	0.872396
90	0.854065
91	0.835525
92	0.812609
93	0.784745
94	0.752667
95	0.715959
96	0.676383
97	0.640071
98	0.601246
99	0.561495
100	0.521413