## 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$BaitBiasSummaryMetrics
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	AAG	29	CAN	44	NAA	100	NA
NA12891	Pond-492101	A	G	27	CAT	19	CAN	24	NAT	24	NA
NA12891	Pond-492101	A	T	100	AAA	100	AAN	100	NAA	100	NA
NA12891	Pond-492101	C	A	100	TCC	31	TCN	36	NCC	36	Cref
NA12891	Pond-492101	C	G	25	TCT	15	TCN	20	NCT	20	NA
NA12891	Pond-492101	C	T	24	ACG	6	ACN	19	NCG	11	NA
NA12891	Pond-492101	G	A	100	GGC	29	GGN	34	NGC	34	NA
NA12891	Pond-492101	G	C	100	GGT	29	GGN	37	NGT	35	NA
NA12891	Pond-492101	G	T	34	TGG	23	TGN	28	NGG	27	Gref
NA12891	Pond-492101	T	A	43	GTG	31	GTN	35	NTG	37	NA
NA12891	Pond-492101	T	C	100	CTG	31	CTN	43	NTA	100	NA
NA12891	Pond-492101	T	G	33	TTA	26	TTN	28	NTC	30	NA
NA12891	NormPond-544932	A	C	36	CAA	21	CAN	27	NAA	29	NA
NA12891	NormPond-544932	A	G	29	CAT	19	CAN	24	NAT	24	NA
NA12891	NormPond-544932	A	T	100	TAA	30	CAN	53	NAA	100	NA
NA12891	NormPond-544932	C	A	100	CCC	29	GCN	34	NCT	40	Cref
NA12891	NormPond-544932	C	G	25	TCT	14	TCN	20	NCT	20	NA
NA12891	NormPond-544932	C	T	23	ACG	6	ACN	19	NCG	11	NA
NA12891	NormPond-544932	G	A	100	GGT	28	GGN	36	NGA	34	NA
NA12891	NormPond-544932	G	C	100	AGA	100	AGN	100	NGA	100	NA
NA12891	NormPond-544932	G	T	34	TGG	22	TGN	28	NGG	27	Gref
NA12891	NormPond-544932	T	A	46	ATA	30	TTN	42	NTA	56	NA
NA12891	NormPond-544932	T	C	100	ATA	30	ATN	100	NTA	35	NA
NA12891	NormPond-544932	T	G	100	GTA	27	CTN	34	NTA	32	NA


