## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics    --INPUT data/TP53.primerclipped.bam --OUTPUT data/alignment_metrics.txt --ASSUME_SORTED false --VALIDATION_STRINGENCY STRICT --REFERENCE_SEQUENCE data/hs_b37_chr17_upto_TP53.fasta.gz  --MAX_INSERT_SIZE 100000 --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Dec 19 15:11:03 UTC 2019

## 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	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	SAMPLE	LIBRARY	READ_GROUP
FIRST_OF_PAIR	667	667	1	0	661	0.991004	63496	661	63496	60832	0	0.005591	0.005591	0.000283	150.563718	643	0.972769	309	0.467474	0	0.567322	0.972769	0			
SECOND_OF_PAIR	667	667	1	0	649	0.973013	60647	649	60647	57020	0	0.006101	0.006101	0.000264	149.82009	643	0.990755	297	0.457627	0	0.440678	0.990755	0			
PAIR	1334	1334	1	0	1310	0.982009	124143	1310	124143	117852	0	0.00584	0.00584	0.000274	150.191904	1286	0.981679	606	0.462595	0	0.50458	0.981679	0			


