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aih-tih-sc-9b89b4-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-9b89b4-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:59 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-9b89b4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-9b89b4-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 20:42:02 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
72685728775	71907131528	3852	65672331781	4440348459	1533557321	260890115	0	0	0	10362829	240229515	1059271	0.041353	0.958647	0	0.913294	0.061751	0.021327	0.003628	0.975045	0.9646	0	0.549983	0.49032	0.727763	0.803507			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.304122
1	0.33665
2	0.387776
3	0.445431
4	0.4969
5	0.544748
6	0.597102
7	0.647687
8	0.697908
9	0.745918
10	0.788676
11	0.837021
12	0.888475
13	0.937502
14	0.974284
15	1.0022
16	1.030302
17	1.052179
18	1.066833
19	1.075176
20	1.08538
21	1.096592
22	1.113992
23	1.127655
24	1.139903
25	1.147974
26	1.157444
27	1.161546
28	1.167812
29	1.174596
30	1.182189
31	1.185486
32	1.180201
33	1.178212
34	1.170637
35	1.179264
36	1.18704
37	1.184778
38	1.187302
39	1.185826
40	1.182569
41	1.179167
42	1.179924
43	1.189452
44	1.191441
45	1.202453
46	1.205739
47	1.210676
48	1.20829
49	1.211024
50	1.198752
51	1.192377
52	1.188772
53	1.188387
54	1.187546
55	1.173018
56	1.162342
57	1.151053
58	1.145672
59	1.140723
60	1.134618
61	1.133188
62	1.133557
63	1.128108
64	1.127953
65	1.127923
66	1.121063
67	1.116786
68	1.112596
69	1.107328
70	1.101322
71	1.092864
72	1.085445
73	1.076118
74	1.065903
75	1.057448
76	1.04848
77	1.035037
78	1.022015
79	1.009759
80	0.994632
81	0.980216
82	0.967754
83	0.952789
84	0.939208
85	0.927848
86	0.909552
87	0.896146
88	0.880104
89	0.861137
90	0.839008
91	0.812802
92	0.782318
93	0.753644
94	0.725551
95	0.698248
96	0.665246
97	0.63172
98	0.596099
99	0.559435
100	0.520967