## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics REF_FLAT=in/genes.refflat RIBOSOMAL_INTERVALS=in/ribosomal.interval_list STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=100 METRIC_ACCUMULATION_LEVEL=[ALL_READS, READ_GROUP, LIBRARY, SAMPLE] INPUT=in/sample.bam OUTPUT=picard/rna.rna_metrics    RRNA_FRAGMENT_PERCENTAGE=0.8 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 24 21:43:01 HST 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
148584	147105	1482	20891	3451	4005	117276	0	0	0	19	14	65	0.575758	0.424242	0.010074	0.142014	0.023459	0.027225	0.797226	0.165474	0.163827	0	0.477684	0.698277	0.455261	1.533796			
148584	147105	1482	20891	3451	4005	117276	0	0	0	19	14	65	0.575758	0.424242	0.010074	0.142014	0.023459	0.027225	0.797226	0.165474	0.163827	0	0.477684	0.698277	0.455261	1.533796	NA12891		
81842	80656	1057	12013	1765	2225	63596	0	0	0	14	5	37	0.736842	0.263158	0.013105	0.148941	0.021883	0.027586	0.788484	0.170824	0.168349	0	0.491819	0.773552	0.377371	2.049844	NA12891	Pond-492101	
66742	66449	425	8878	1686	1780	53680	0	0	0	5	9	28	0.357143	0.642857	0.006396	0.133606	0.025373	0.026787	0.807838	0.158979	0.158281	0	0.474283	0.600126	0.556822	1.07777	NA12891	NormPond-544932	
81842	80656	1057	12013	1765	2225	63596	0	0	0	14	5	37	0.736842	0.263158	0.013105	0.148941	0.021883	0.027586	0.788484	0.170824	0.168349	0	0.491819	0.773552	0.377371	2.049844	NA12891	Pond-492101	NA12891.r1
66742	66449	425	8878	1686	1780	53680	0	0	0	5	9	28	0.357143	0.642857	0.006396	0.133606	0.025373	0.026787	0.807838	0.158979	0.158281	0	0.474283	0.600126	0.556822	1.07777	NA12891	NormPond-544932	NA12891.r2

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage	NA12891.normalized_coverage	Pond-492101.normalized_coverage	NormPond-544932.normalized_coverage	NA12891.r1.normalized_coverage	NA12891.r2.normalized_coverage
0	0.365938	0.365938	0.440854	0.268255	0.440854	0.268255
1	0.382572	0.382572	0.470244	0.268255	0.470244	0.268255
2	0.425819	0.425819	0.534903	0.283584	0.534903	0.283584
3	0.45576	0.45576	0.558415	0.321907	0.558415	0.321907
4	0.46574	0.46574	0.558415	0.3449	0.558415	0.3449
5	0.46574	0.46574	0.558415	0.3449	0.558415	0.3449
6	0.47572	0.47572	0.576049	0.3449	0.576049	0.3449
7	0.502334	0.502334	0.617195	0.352564	0.617195	0.352564
8	0.568868	0.568868	0.646586	0.467531	0.646586	0.467531
9	0.625422	0.625422	0.699488	0.528847	0.699488	0.528847
10	0.632075	0.632075	0.705366	0.536511	0.705366	0.536511
11	0.645382	0.645382	0.705366	0.567169	0.705366	0.567169
12	0.671996	0.671996	0.734757	0.590162	0.734757	0.590162
13	0.715243	0.715243	0.793537	0.613155	0.793537	0.613155
14	0.731877	0.731877	0.822927	0.613155	0.822927	0.613155
15	0.751837	0.751837	0.858196	0.613155	0.858196	0.613155
16	0.765144	0.765144	0.881708	0.613155	0.881708	0.613155
17	0.778451	0.778451	0.881708	0.643813	0.881708	0.643813
18	0.811718	0.811718	0.881708	0.720458	0.881708	0.720458
19	0.851639	0.851639	0.899342	0.789438	0.899342	0.789438
20	0.94146	0.94146	0.981635	0.889075	0.981635	0.889075
21	0.978054	0.978054	1.022781	0.919733	1.022781	0.919733
22	1.001341	1.001341	1.046293	0.942726	1.046293	0.942726
23	1.047915	1.047915	1.075684	1.011706	1.075684	1.011706
24	1.101142	1.101142	1.110952	1.088351	1.110952	1.088351
25	1.151043	1.151043	1.163854	1.134337	1.163854	1.134337
26	1.137736	1.137736	1.163854	1.10368	1.163854	1.10368
27	1.134409	1.134409	1.205001	1.042364	1.205001	1.042364
28	1.151043	1.151043	1.222635	1.057693	1.222635	1.057693
29	1.151043	1.151043	1.193245	1.096015	1.193245	1.096015
30	1.197617	1.197617	1.205001	1.187989	1.205001	1.187989
31	1.267478	1.267478	1.222635	1.325949	1.222635	1.325949
32	1.264151	1.264151	1.228513	1.31062	1.228513	1.31062
33	1.260824	1.260824	1.216757	1.318284	1.216757	1.318284
34	1.300745	1.300745	1.269659	1.341277	1.269659	1.341277
35	1.320705	1.320705	1.293172	1.356606	1.293172	1.356606
36	1.340665	1.340665	1.293172	1.402593	1.293172	1.402593
37	1.340665	1.340665	1.257903	1.44858	1.257903	1.44858
38	1.477061	1.477061	1.493025	1.456244	1.493025	1.456244
39	1.566882	1.566882	1.581196	1.548217	1.581196	1.548217
40	1.596822	1.596822	1.587074	1.609533	1.587074	1.609533
41	1.593496	1.593496	1.581196	1.609533	1.581196	1.609533
42	1.653376	1.653376	1.628221	1.686177	1.628221	1.686177
43	1.69995	1.69995	1.722269	1.670848	1.722269	1.670848
44	1.686643	1.686643	1.745782	1.609533	1.745782	1.609533
45	1.646723	1.646723	1.75166	1.509895	1.75166	1.509895
46	1.633416	1.633416	1.734025	1.502231	1.734025	1.502231
47	1.65005	1.65005	1.728147	1.548217	1.728147	1.548217
48	1.633416	1.633416	1.698757	1.548217	1.698757	1.548217
49	1.606802	1.606802	1.681123	1.509895	1.681123	1.509895
50	1.580189	1.580189	1.645855	1.494566	1.645855	1.494566
51	1.583515	1.583515	1.59883	1.563546	1.59883	1.563546
52	1.576862	1.576862	1.563562	1.594204	1.563562	1.594204
53	1.590169	1.590169	1.563562	1.624862	1.563562	1.624862
54	1.583515	1.583515	1.557684	1.617197	1.557684	1.617197
55	1.553575	1.553575	1.54005	1.571211	1.54005	1.571211
56	1.477061	1.477061	1.516538	1.425586	1.516538	1.425586
57	1.440467	1.440467	1.487147	1.3796	1.487147	1.3796
58	1.440467	1.440467	1.493025	1.371935	1.493025	1.371935
59	1.43714	1.43714	1.475391	1.387264	1.475391	1.387264
60	1.453774	1.453774	1.463635	1.440915	1.463635	1.440915
61	1.487041	1.487041	1.493025	1.479237	1.493025	1.479237
62	1.490367	1.490367	1.516538	1.456244	1.516538	1.456244
63	1.483714	1.483714	1.510659	1.44858	1.510659	1.44858
64	1.463754	1.463754	1.469513	1.456244	1.469513	1.456244
65	1.460427	1.460427	1.463635	1.456244	1.463635	1.456244
66	1.41718	1.41718	1.38722	1.456244	1.38722	1.456244
67	1.380586	1.380586	1.322562	1.456244	1.322562	1.456244
68	1.357299	1.357299	1.287293	1.44858	1.287293	1.44858
69	1.330685	1.330685	1.263781	1.417922	1.263781	1.417922
70	1.310725	1.310725	1.240269	1.402593	1.240269	1.402593
71	1.284111	1.284111	1.222635	1.364271	1.222635	1.364271
72	1.244191	1.244191	1.199123	1.302955	1.199123	1.302955
73	1.180983	1.180983	1.128586	1.249304	1.128586	1.249304
74	1.101142	1.101142	1.028659	1.195653	1.028659	1.195653
75	1.034608	1.034608	0.928732	1.17266	0.928732	1.17266
76	0.924826	0.924826	0.811171	1.073022	0.811171	1.073022
77	0.848312	0.848312	0.752391	0.973384	0.752391	0.973384
78	0.828352	0.828352	0.728878	0.958055	0.728878	0.958055
79	0.788431	0.788431	0.687732	0.919733	0.687732	0.919733
80	0.705263	0.705263	0.617195	0.820095	0.617195	0.820095
81	0.665343	0.665343	0.558415	0.804766	0.558415	0.804766
82	0.645382	0.645382	0.523147	0.804766	0.523147	0.804766
83	0.598808	0.598808	0.45261	0.789438	0.45261	0.789438
84	0.568868	0.568868	0.440854	0.735786	0.440854	0.735786
85	0.532274	0.532274	0.42322	0.674471	0.42322	0.674471
86	0.50566	0.50566	0.411464	0.628484	0.411464	0.628484
87	0.482373	0.482373	0.39383	0.597827	0.39383	0.597827
88	0.432473	0.432473	0.382073	0.498189	0.382073	0.498189
89	0.405859	0.405859	0.370317	0.452202	0.370317	0.452202
90	0.352632	0.352632	0.311537	0.406215	0.311537	0.406215
91	0.316038	0.316038	0.27039	0.375558	0.27039	0.375558
92	0.299404	0.299404	0.264512	0.3449	0.264512	0.3449
93	0.289424	0.289424	0.246878	0.3449	0.246878	0.3449
94	0.269464	0.269464	0.21161	0.3449	0.21161	0.3449
95	0.249503	0.249503	0.176342	0.3449	0.176342	0.3449
96	0.219563	0.219563	0.135195	0.329571	0.135195	0.329571
97	0.169662	0.169662	0.088171	0.27592	0.088171	0.27592
98	0.109782	0.109782	0.047024	0.191611	0.047024	0.191611
99	0.043247	0.043247	0.023512	0.06898	0.023512	0.06898
100	0.012475	0.012475	0	0.028742	0	0.028742

