## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=2000 ADAPTER_SEQUENCE=[] INPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/mapped/NaomicfDNA2_S2_R1.dedup.bam OUTPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/alignment-metrics/NaomicfDNA2_S2_R1.dedup.alignment_summary_metrics.txt REFERENCE_SEQUENCE=/mnt/data/pipeline_genome_data/hg19/male.hg19.fa    EXPECTED_PAIR_ORIENTATIONS=[FR] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Apr 03 03:42:04 PDT 2018

## 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	84686707	84686707	1	0	69660700	0.822569	4003694873	62055484	3610257426	3466826778	0	0.00624	0.004162	0.000206	59	68963766	0.989995	2643178	0.037944	0	0.500065	0.020994	0			
SECOND_OF_PAIR	84692538	84692538	1	0	69372325	0.819108	3979715838	61739126	3587404154	3399447304	0	0.006924	0.00486	0.000201	59	68963766	0.994111	2354803	0.033944	0	0.500418	0.02108	0			
PAIR	169379245	169379245	1	0	139033025	0.820839	7983410711	123794610	7197661580	6866274082	0	0.006581	0.00451	0.000203	59	137927532	0.992049	4997981	0.035948	0	0.500241	0.021037	0