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aih-tih-sc-67e6e5-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-67e6e5-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:31 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-67e6e5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-67e6e5-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 20:40:58 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
71896378629	70975117677	6730	62467229300	5903425632	2218573299	385882716	0	0	0	12723297	231371591	1235729	0.052124	0.947876	0	0.880129	0.083176	0.031258	0.005437	0.963305	0.950961	0	0.632295	0.586933	0.583093	1.088204			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.359668
1	0.405309
2	0.46585
3	0.531327
4	0.607924
5	0.685168
6	0.746879
7	0.808543
8	0.867217
9	0.919065
10	0.97792
11	1.036237
12	1.086102
13	1.122186
14	1.147918
15	1.161979
16	1.171516
17	1.183767
18	1.195999
19	1.20205
20	1.20755
21	1.218231
22	1.226597
23	1.231741
24	1.2348
25	1.239434
26	1.242191
27	1.239599
28	1.238996
29	1.238086
30	1.231887
31	1.221047
32	1.209037
33	1.203377
34	1.196268
35	1.190684
36	1.194043
37	1.187207
38	1.165727
39	1.146475
40	1.137062
41	1.127406
42	1.123528
43	1.123581
44	1.116507
45	1.127196
46	1.128563
47	1.133244
48	1.128664
49	1.133413
50	1.133975
51	1.135684
52	1.138661
53	1.135322
54	1.131185
55	1.122625
56	1.115448
57	1.107352
58	1.096966
59	1.085415
60	1.086698
61	1.095189
62	1.097797
63	1.079876
64	1.071759
65	1.074567
66	1.075661
67	1.067275
68	1.05544
69	1.040142
70	1.018544
71	0.999186
72	0.99174
73	0.984284
74	0.973411
75	0.961636
76	0.952193
77	0.943196
78	0.936473
79	0.929424
80	0.916487
81	0.904336
82	0.896855
83	0.884845
84	0.868267
85	0.848035
86	0.824987
87	0.810026
88	0.796553
89	0.779781
90	0.762931
91	0.749567
92	0.729911
93	0.702771
94	0.67276
95	0.648962
96	0.624785
97	0.599938
98	0.568548
99	0.538618
100	0.502488