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aih-tih-sc-01eb49-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-01eb49-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:57 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-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-01eb49-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 20:33:04 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
77186172197	76217441612	2758	68951715091	5385062636	1645061482	235599645	0	0	0	8152717	236919951	1478916	0.033267	0.966733	0	0.904671	0.070654	0.021584	0.003091	0.975325	0.963084	0	0.523139	0.635645	0.672479	1.041947			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.277763
1	0.332303
2	0.410995
3	0.487122
4	0.564133
5	0.638294
6	0.708801
7	0.774212
8	0.842992
9	0.902595
10	0.951185
11	0.997841
12	1.043671
13	1.082781
14	1.112358
15	1.128876
16	1.1454
17	1.161467
18	1.169227
19	1.18086
20	1.201465
21	1.221603
22	1.233546
23	1.240659
24	1.242526
25	1.239942
26	1.238458
27	1.234043
28	1.231169
29	1.226455
30	1.223898
31	1.219906
32	1.20932
33	1.207684
34	1.199655
35	1.197521
36	1.198224
37	1.195055
38	1.195028
39	1.190101
40	1.18479
41	1.176917
42	1.179606
43	1.18672
44	1.182694
45	1.18876
46	1.187047
47	1.188743
48	1.186413
49	1.183248
50	1.180383
51	1.171391
52	1.157921
53	1.149689
54	1.148926
55	1.144443
56	1.137052
57	1.130926
58	1.120656
59	1.112368
60	1.108657
61	1.103762
62	1.102719
63	1.09094
64	1.082936
65	1.080204
66	1.066815
67	1.049051
68	1.042297
69	1.033982
70	1.024169
71	1.009464
72	1.001972
73	0.990884
74	0.978561
75	0.968629
76	0.956008
77	0.946035
78	0.941631
79	0.932524
80	0.911944
81	0.895222
82	0.884677
83	0.871554
84	0.856822
85	0.844978
86	0.828167
87	0.811792
88	0.790983
89	0.771297
90	0.749225
91	0.732471
92	0.711681
93	0.68651
94	0.658295
95	0.631658
96	0.605447
97	0.580614
98	0.551033
99	0.521081
100	0.489825