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aih-tih-sc-d963a2-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-d963a2-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 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-d963a2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-d963a2-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 20:18:02 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
77379789033	76564954409	5672	67998688323	5741760813	2536372348	288127253	0	0	0	5264451	241361675	1378347	0.021346	0.978654	0	0.888118	0.074992	0.033127	0.003763	0.96311	0.952968	0	0.526606	0.589687	0.71083	0.9578			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.29759
1	0.350227
2	0.413651
3	0.48892
4	0.567889
5	0.645195
6	0.705304
7	0.763797
8	0.820473
9	0.861211
10	0.900626
11	0.941031
12	0.988594
13	1.024217
14	1.052253
15	1.07797
16	1.102182
17	1.126683
18	1.140511
19	1.158184
20	1.176418
21	1.185418
22	1.194454
23	1.202187
24	1.205806
25	1.204658
26	1.20529
27	1.201851
28	1.198662
29	1.187123
30	1.181533
31	1.174453
32	1.169691
33	1.167857
34	1.163563
35	1.159272
36	1.155236
37	1.156231
38	1.158128
39	1.152417
40	1.141232
41	1.13636
42	1.139256
43	1.143505
44	1.137221
45	1.136238
46	1.132008
47	1.129743
48	1.124846
49	1.124787
50	1.129709
51	1.122879
52	1.115416
53	1.121895
54	1.130452
55	1.129718
56	1.127145
57	1.124596
58	1.120635
59	1.117245
60	1.108246
61	1.107986
62	1.111791
63	1.109075
64	1.114848
65	1.11546
66	1.114325
67	1.11003
68	1.103991
69	1.095131
70	1.080228
71	1.066988
72	1.058374
73	1.051086
74	1.041542
75	1.030436
76	1.017281
77	0.99852
78	0.989179
79	0.984206
80	0.972176
81	0.960591
82	0.942096
83	0.924294
84	0.912474
85	0.894596
86	0.879059
87	0.866175
88	0.850312
89	0.83129
90	0.809031
91	0.794099
92	0.76901
93	0.738939
94	0.710536
95	0.680024
96	0.650975
97	0.621684
98	0.583032
99	0.546836
100	0.510388