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aih-tih-sc-885658-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-885658-R1_A23YTGFLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:43 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-885658-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-885658-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 20:37:55 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
67599429522	66807350786	9559	59107033368	5106511738	2288389450	305406671	0	0	0	9339740	214534327	1002266	0.041719	0.958281	0	0.884738	0.076436	0.034254	0.004571	0.961175	0.949913	0	0.565581	0.504819	0.741851	0.801959			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.316057
1	0.353074
2	0.407242
3	0.464167
4	0.517464
5	0.5699
6	0.618617
7	0.664447
8	0.710465
9	0.749002
10	0.786313
11	0.831662
12	0.87415
13	0.907722
14	0.935274
15	0.954949
16	0.979625
17	0.998561
18	1.014598
19	1.028288
20	1.04697
21	1.068228
22	1.087094
23	1.105994
24	1.118851
25	1.127465
26	1.128386
27	1.132111
28	1.138663
29	1.139478
30	1.136629
31	1.143445
32	1.143767
33	1.146058
34	1.137315
35	1.137032
36	1.126504
37	1.119583
38	1.120654
39	1.116429
40	1.11545
41	1.113405
42	1.117236
43	1.121288
44	1.12398
45	1.134342
46	1.133934
47	1.13984
48	1.138716
49	1.137339
50	1.141116
51	1.137137
52	1.138543
53	1.14113
54	1.145496
55	1.145401
56	1.146779
57	1.142619
58	1.138301
59	1.138371
60	1.142144
61	1.146778
62	1.151551
63	1.143337
64	1.147603
65	1.157647
66	1.160282
67	1.158512
68	1.156501
69	1.152764
70	1.139647
71	1.132195
72	1.131126
73	1.127004
74	1.118475
75	1.113274
76	1.104483
77	1.092466
78	1.081606
79	1.078629
80	1.067349
81	1.057358
82	1.04175
83	1.026205
84	1.012855
85	0.994629
86	0.969465
87	0.952252
88	0.935625
89	0.919898
90	0.899406
91	0.880024
92	0.848686
93	0.811894
94	0.775367
95	0.741067
96	0.704862
97	0.665993
98	0.626025
99	0.585961
100	0.54175