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aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:00 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-ecc0bc-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ecc0bc-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 21:12:57 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
55325525526	54607181650	8730	49136816555	3560247216	1699927182	210181967	0	0	0	8590919	193425434	833466	0.042526	0.957474	0	0.899823	0.065197	0.03113	0.003849	0.965021	0.952491	0	0.589605	0.488249	0.727551	0.771071			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.322329
1	0.353183
2	0.404819
3	0.464967
4	0.50815
5	0.5509
6	0.611968
7	0.666913
8	0.716715
9	0.756349
10	0.790288
11	0.838707
12	0.881234
13	0.918334
14	0.952634
15	0.975669
16	0.992144
17	1.005494
18	1.012942
19	1.025458
20	1.038152
21	1.04838
22	1.066509
23	1.086447
24	1.096105
25	1.102609
26	1.109594
27	1.119488
28	1.133543
29	1.13585
30	1.138007
31	1.142032
32	1.140641
33	1.152093
34	1.146404
35	1.156668
36	1.161619
37	1.161252
38	1.163183
39	1.165138
40	1.163033
41	1.159143
42	1.169029
43	1.181252
44	1.18782
45	1.202305
46	1.201605
47	1.197221
48	1.191987
49	1.188407
50	1.181267
51	1.175844
52	1.170218
53	1.166517
54	1.165619
55	1.167194
56	1.159585
57	1.149434
58	1.141323
59	1.138102
60	1.141054
61	1.145654
62	1.151412
63	1.140013
64	1.136802
65	1.136368
66	1.125378
67	1.121841
68	1.123247
69	1.120013
70	1.10731
71	1.094921
72	1.090797
73	1.087388
74	1.084106
75	1.07372
76	1.066036
77	1.055168
78	1.04227
79	1.034371
80	1.024555
81	1.013316
82	0.999902
83	0.988381
84	0.977017
85	0.966142
86	0.94717
87	0.936177
88	0.920368
89	0.905534
90	0.887068
91	0.866129
92	0.836026
93	0.803076
94	0.771154
95	0.742231
96	0.71023
97	0.675701
98	0.634011
99	0.589284
100	0.544919