## 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.artifacts.SequencingArtifactMetrics$PreAdapterSummaryMetrics
SAMPLE_ALIAS	LIBRARY	REF_BASE	ALT_BASE	TOTAL_QSCORE	WORST_CXT	WORST_CXT_QSCORE	WORST_PRE_CXT	WORST_PRE_CXT_QSCORE	WORST_POST_CXT	WORST_POST_CXT_QSCORE	ARTIFACT_NAME
NA12891	Pond-492101	A	C	100	GAG	29	AAN	38	NAG	33	NA
NA12891	Pond-492101	A	G	46	GAA	30	GAN	32	NAG	35	NA
NA12891	Pond-492101	A	T	46	CAC	33	CAN	40	NAC	38	NA
NA12891	Pond-492101	C	A	100	CCT	35	ACN	100	NCT	40	NA
NA12891	Pond-492101	C	G	100	ACC	31	ACN	38	NCC	40	NA
NA12891	Pond-492101	C	T	36	ACG	14	ACN	29	NCG	21	Deamination
NA12891	Pond-492101	G	A	100	AGA	35	AGN	40	NGA	37	NA
NA12891	Pond-492101	G	C	37	AGA	28	AGN	32	NGA	32	NA
NA12891	Pond-492101	G	T	38	TGG	28	TGN	33	NGG	34	OxoG
NA12891	Pond-492101	T	A	100	ATA	100	ATN	100	NTA	100	NA
NA12891	Pond-492101	T	C	100	ATG	29	ATN	34	NTG	35	NA
NA12891	Pond-492101	T	G	39	TTG	27	TTN	32	NTA	34	NA
NA12891	NormPond-544932	A	C	100	AAA	33	AAN	37	NAA	37	NA
NA12891	NormPond-544932	A	G	100	TAT	32	TAN	38	NAA	100	NA
NA12891	NormPond-544932	A	T	100	AAA	100	AAN	100	NAA	100	NA
NA12891	NormPond-544932	C	A	100	TCA	33	TCN	39	NCA	100	NA
NA12891	NormPond-544932	C	G	39	TCT	30	TCN	34	NCT	34	NA
NA12891	NormPond-544932	C	T	39	ACG	22	TCN	36	NCG	29	Deamination
NA12891	NormPond-544932	G	A	100	TGT	34	TGN	39	NGA	100	NA
NA12891	NormPond-544932	G	C	100	AGA	100	AGN	100	NGA	100	NA
NA12891	NormPond-544932	G	T	44	TGC	32	TGN	39	NGC	37	OxoG
NA12891	NormPond-544932	T	A	39	ATA	32	ATN	36	NTA	35	NA
NA12891	NormPond-544932	T	C	39	ATG	29	ATN	36	NTG	35	NA
NA12891	NormPond-544932	T	G	42	GTA	30	ATN	35	NTA	35	NA


