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tih_rna_sample_00081_23KKJ7LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0007/A23KKJ7LT4/nfcore_rnafusion_100M__5f1fa79--20260304-102235/QC/picard/tih_rna_sample_00081_23KKJ7LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0007-5f1fa79
Published
Mar 05, 2026 1:29 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 tih_rna_sample_00081_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00081_23KKJ7LT4_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: Thu Mar 05 20:23:26 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
24815415357	24387668904	49778	17587983638	2427919189	3974686466	397029833	0	0	0	952559	67872710	273617	0.01384	0.98616	0.000002	0.721183	0.099555	0.162979	0.01628	0.820739	0.806591	0	0.551339	0.51182	0.703843	0.88879			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.304798
1	0.3411
2	0.394762
3	0.456521
4	0.513546
5	0.559771
6	0.623851
7	0.683491
8	0.740629
9	0.790583
10	0.83901
11	0.883643
12	0.93227
13	0.969106
14	0.998371
15	1.022847
16	1.049187
17	1.071935
18	1.086906
19	1.096263
20	1.112679
21	1.128722
22	1.145539
23	1.160024
24	1.169291
25	1.169211
26	1.166774
27	1.165375
28	1.166024
29	1.162274
30	1.165309
31	1.164297
32	1.164533
33	1.168956
34	1.172797
35	1.18208
36	1.178642
37	1.172785
38	1.17156
39	1.17126
40	1.166365
41	1.163888
42	1.172531
43	1.18302
44	1.181512
45	1.185479
46	1.186414
47	1.184016
48	1.186866
49	1.192894
50	1.180723
51	1.175237
52	1.166349
53	1.157883
54	1.153845
55	1.147609
56	1.142768
57	1.137989
58	1.125792
59	1.112436
60	1.104122
61	1.09871
62	1.096523
63	1.093353
64	1.091615
65	1.087416
66	1.083708
67	1.077726
68	1.07332
69	1.069273
70	1.065578
71	1.058625
72	1.058775
73	1.050801
74	1.043847
75	1.040068
76	1.037193
77	1.032892
78	1.030326
79	1.017761
80	1.009752
81	0.994047
82	0.984816
83	0.971548
84	0.962891
85	0.951827
86	0.932666
87	0.913754
88	0.891586
89	0.871389
90	0.850871
91	0.823645
92	0.800697
93	0.770707
94	0.737874
95	0.710822
96	0.682531
97	0.651458
98	0.615734
99	0.580081
100	0.53931