## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=in/sample.bam OUTPUT=picard/cmm METRIC_ACCUMULATION_LEVEL=[ALL_READS, LIBRARY, SAMPLE, READ_GROUP] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectGcBiasMetrics, CollectInsertSizeMetrics, CollectQualityYieldMetrics, CollectSequencingArtifactMetrics, MeanQualityByCycle, QualityScoreDistribution] REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false DO_NOT_CREATE_PLOTS=false 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 21:42:13 HST 2026

## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	SD_READ_LENGTH	MEDIAN_READ_LENGTH	MAD_READ_LENGTH	MIN_READ_LENGTH	MAX_READ_LENGTH	MEAN_ALIGNED_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	PCT_SOFTCLIP	PCT_HARDCLIP	AVG_POS_3PRIME_SOFTCLIP_LENGTH	SAMPLE	LIBRARY	READ_GROUP
FIRST_OF_PAIR	495	495	1	0	495	1	74547	495	74547	71396	0	0.006425	0.006425	0.000054	151	0	151	0	151	151	150.6	491	0.991919	4	0.008081	0	0.723232	0	0	0.002649	0	16.5			
SECOND_OF_PAIR	489	489	1	0	486	0.993865	72558	486	72558	65189	1	0.010474	0.010474	0.000041	151	0	151	0	151	151	148.384458	486	1	0	0	0	0.720165	0.002058	0	0.011187	0	24.363636			
PAIR	984	984	1	0	981	0.996951	147105	981	147105	136585	1	0.008423	0.008423	0.000048	151	0	151	0	151	151	149.498984	977	0.995923	4	0.004077	0	0.721713	0.001019	0	0.006892	0	22.266667			
FIRST_OF_PAIR	495	495	1	0	495	1	74547	495	74547	71396	0	0.006425	0.006425	0.000054	151	0	151	0	151	151	150.6	491	0.991919	4	0.008081	0	0.723232	0	0	0.002649	0	16.5	NA12891		
SECOND_OF_PAIR	489	489	1	0	486	0.993865	72558	486	72558	65189	1	0.010474	0.010474	0.000041	151	0	151	0	151	151	148.384458	486	1	0	0	0	0.720165	0.002058	0	0.011187	0	24.363636	NA12891		
PAIR	984	984	1	0	981	0.996951	147105	981	147105	136585	1	0.008423	0.008423	0.000048	151	0	151	0	151	151	149.498984	977	0.995923	4	0.004077	0	0.721713	0.001019	0	0.006892	0	22.266667	NA12891		
FIRST_OF_PAIR	264	264	1	0	264	1	39716	264	39716	37638	1	0.007805	0.007805	0.000025	151	0	151	0	151	151	150.439394	260	0.984848	4	0.015152	0	0.712121	0	0	0.003713	0	18.5	NA12891	Pond-492101	
SECOND_OF_PAIR	278	278	1	0	275	0.989209	40940	275	40940	36745	1	0.0117	0.0117	0	151	0	151	0	151	151	147.266187	275	1	0	0	0	0.709091	0.003636	0	0.013936	0	25.681818	NA12891	Pond-492101	
PAIR	542	542	1	0	539	0.994465	80656	539	80656	74383	1	0.009782	0.009782	0.000012	151	0	151	0	151	151	148.811808	535	0.992579	4	0.007421	0	0.710575	0.001855	0	0.008956	0	23.766667	NA12891	Pond-492101	
FIRST_OF_PAIR	231	231	1	0	231	1	34831	231	34831	33758	0	0.004852	0.004852	0.000086	151	0	151	0	151	151	150.78355	231	1	0	0	0	0.735931	0	0	0.001433	0	12.5	NA12891	NormPond-544932	
SECOND_OF_PAIR	211	211	1	0	211	1	31618	211	31618	28444	1	0.008887	0.008887	0.000095	151	0	151	0	151	151	149.85782	211	1	0	0	0	0.734597	0	0	0.007564	0	21.727273	NA12891	NormPond-544932	
PAIR	442	442	1	0	442	1	66449	442	66449	62202	1	0.006772	0.006772	0.00009	151	0	151	0	151	151	150.341629	442	1	0	0	0	0.735294	0	0	0.00436	0	19.266667	NA12891	NormPond-544932	
FIRST_OF_PAIR	264	264	1	0	264	1	39716	264	39716	37638	1	0.007805	0.007805	0.000025	151	0	151	0	151	151	150.439394	260	0.984848	4	0.015152	0	0.712121	0	0	0.003713	0	18.5	NA12891	Pond-492101	NA12891.r1
SECOND_OF_PAIR	278	278	1	0	275	0.989209	40940	275	40940	36745	1	0.0117	0.0117	0	151	0	151	0	151	151	147.266187	275	1	0	0	0	0.709091	0.003636	0	0.013936	0	25.681818	NA12891	Pond-492101	NA12891.r1
PAIR	542	542	1	0	539	0.994465	80656	539	80656	74383	1	0.009782	0.009782	0.000012	151	0	151	0	151	151	148.811808	535	0.992579	4	0.007421	0	0.710575	0.001855	0	0.008956	0	23.766667	NA12891	Pond-492101	NA12891.r1
FIRST_OF_PAIR	231	231	1	0	231	1	34831	231	34831	33758	0	0.004852	0.004852	0.000086	151	0	151	0	151	151	150.78355	231	1	0	0	0	0.735931	0	0	0.001433	0	12.5	NA12891	NormPond-544932	NA12891.r2
SECOND_OF_PAIR	211	211	1	0	211	1	31618	211	31618	28444	1	0.008887	0.008887	0.000095	151	0	151	0	151	151	149.85782	211	1	0	0	0	0.734597	0	0	0.007564	0	21.727273	NA12891	NormPond-544932	NA12891.r2
PAIR	442	442	1	0	442	1	66449	442	66449	62202	1	0.006772	0.006772	0.00009	151	0	151	0	151	151	150.341629	442	1	0	0	0	0.735294	0	0	0.00436	0	19.266667	NA12891	NormPond-544932	NA12891.r2

## HISTOGRAM	java.lang.Integer
READ_LENGTH	PAIRED_TOTAL_LENGTH_COUNT	PAIRED_ALIGNED_LENGTH_COUNT
0	0	3
49	0	1
61	0	1
92	0	1
96	0	1
98	0	1
106	0	1
109	0	1
111	0	1
112	0	1
115	0	1
118	0	1
126	0	2
127	0	1
128	0	3
129	0	1
130	0	1
131	0	2
134	0	1
135	0	1
136	0	2
137	0	3
140	0	1
141	0	1
142	0	1
143	0	1
144	0	2
145	0	1
146	0	4
147	0	2
148	0	1
149	0	5
151	984	934

