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aih-tih-sc-7f9674-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-7f9674-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:34 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-7f9674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-7f9674-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 20:17:01 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
73156460709	72395962925	4310	65817175964	4516910113	1855687794	206184744	0	0	0	10175169	238049520	1009628	0.040992	0.959008	0	0.909128	0.062392	0.025632	0.002848	0.971519	0.96142	0	0.540099	0.516435	0.712439	0.831833			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294812
1	0.331943
2	0.385641
3	0.445593
4	0.499614
5	0.548486
6	0.608868
7	0.670015
8	0.722249
9	0.771131
10	0.821275
11	0.867467
12	0.918501
13	0.962448
14	0.999343
15	1.032737
16	1.054469
17	1.065997
18	1.078175
19	1.093712
20	1.114332
21	1.128017
22	1.14916
23	1.164382
24	1.170767
25	1.174908
26	1.178964
27	1.183959
28	1.189761
29	1.194093
30	1.195507
31	1.196643
32	1.190938
33	1.186057
34	1.177268
35	1.182614
36	1.182548
37	1.178738
38	1.180355
39	1.175859
40	1.169213
41	1.16431
42	1.166317
43	1.171591
44	1.169743
45	1.168366
46	1.158548
47	1.1607
48	1.155357
49	1.157816
50	1.159584
51	1.156691
52	1.154418
53	1.148532
54	1.141808
55	1.137428
56	1.133065
57	1.125618
58	1.117383
59	1.112465
60	1.104108
61	1.104402
62	1.109578
63	1.10931
64	1.108973
65	1.106666
66	1.102727
67	1.101439
68	1.100092
69	1.097736
70	1.093219
71	1.081772
72	1.077921
73	1.06943
74	1.061624
75	1.0579
76	1.053794
77	1.043954
78	1.03845
79	1.028666
80	1.016683
81	1.004262
82	0.992552
83	0.975906
84	0.958639
85	0.939896
86	0.918401
87	0.910753
88	0.89315
89	0.869419
90	0.840058
91	0.811846
92	0.782942
93	0.751176
94	0.727172
95	0.702643
96	0.672949
97	0.639881
98	0.604742
99	0.569433
100	0.536354