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aih-tih-sc-f7ac14-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-f7ac14-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 6:22 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-f7ac14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f7ac14-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 22:40:35 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
63604727372	62699941302	9764	56893877417	3946183753	1590945080	268925288	0	0	0	7731116	229053385	926755	0.03265	0.96735	0	0.907399	0.062938	0.025374	0.004289	0.970337	0.956534	0	0.618465	0.515601	0.653259	0.854555			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.291511
1	0.327941
2	0.388966
3	0.456461
4	0.525299
5	0.595397
6	0.656928
7	0.712022
8	0.768501
9	0.819857
10	0.868689
11	0.920686
12	0.964632
13	0.998905
14	1.029551
15	1.042784
16	1.066408
17	1.086728
18	1.086825
19	1.104282
20	1.127815
21	1.143202
22	1.155931
23	1.16374
24	1.171073
25	1.168492
26	1.165683
27	1.176086
28	1.181437
29	1.171127
30	1.153258
31	1.150869
32	1.150713
33	1.159666
34	1.155748
35	1.152197
36	1.145156
37	1.13787
38	1.139044
39	1.143522
40	1.146745
41	1.154278
42	1.161947
43	1.16762
44	1.17021
45	1.180014
46	1.179996
47	1.18194
48	1.169998
49	1.167733
50	1.149331
51	1.140987
52	1.132572
53	1.128349
54	1.136616
55	1.136003
56	1.127993
57	1.127379
58	1.124979
59	1.12243
60	1.128278
61	1.139674
62	1.149835
63	1.138239
64	1.141289
65	1.140429
66	1.131014
67	1.121783
68	1.109747
69	1.104162
70	1.092967
71	1.07527
72	1.073257
73	1.06047
74	1.050987
75	1.046379
76	1.038571
77	1.026724
78	1.012528
79	0.992558
80	0.985339
81	0.979244
82	0.964003
83	0.953814
84	0.939441
85	0.926825
86	0.907703
87	0.899357
88	0.883198
89	0.861293
90	0.837012
91	0.822075
92	0.79367
93	0.759031
94	0.723536
95	0.691064
96	0.658303
97	0.62676
98	0.587782
99	0.548584
100	0.507757