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aih-tih-sc-b6fd19-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-b6fd19-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:47 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-b6fd19-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-b6fd19-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 20:40:02 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
77442799878	76636229839	1774	68667659258	5534079786	2133718980	300770041	0	0	0	6447544	240221795	1260640	0.026138	0.973862	0	0.896021	0.072212	0.027842	0.003925	0.968233	0.958149	0	0.511604	0.587501	0.725626	0.935106			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294369
1	0.335827
2	0.394614
3	0.456746
4	0.5225
5	0.590274
6	0.65166
7	0.710719
8	0.767562
9	0.810037
10	0.85968
11	0.909225
12	0.96064
13	1.009384
14	1.038744
15	1.063685
16	1.089855
17	1.110559
18	1.123536
19	1.14206
20	1.151314
21	1.168
22	1.183455
23	1.19845
24	1.207491
25	1.212288
26	1.217065
27	1.21999
28	1.218258
29	1.208615
30	1.206885
31	1.207774
32	1.191501
33	1.187203
34	1.183853
35	1.179361
36	1.173514
37	1.167327
38	1.163758
39	1.159995
40	1.15427
41	1.155215
42	1.158228
43	1.159553
44	1.153536
45	1.163243
46	1.160565
47	1.157671
48	1.151294
49	1.151361
50	1.154155
51	1.14669
52	1.139749
53	1.13546
54	1.140286
55	1.136492
56	1.132687
57	1.121833
58	1.115648
59	1.110569
60	1.106204
61	1.104827
62	1.10756
63	1.093834
64	1.089395
65	1.091065
66	1.095792
67	1.095739
68	1.096463
69	1.085003
70	1.076072
71	1.061512
72	1.057992
73	1.047238
74	1.030426
75	1.020975
76	1.012448
77	1.000631
78	0.991908
79	0.975784
80	0.962202
81	0.951602
82	0.941917
83	0.929946
84	0.916569
85	0.906285
86	0.887773
87	0.878783
88	0.863314
89	0.845556
90	0.825918
91	0.808055
92	0.786002
93	0.757359
94	0.726933
95	0.697385
96	0.669091
97	0.635768
98	0.602272
99	0.567501
100	0.52661