## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectAlignmentSummaryMetrics INPUT=genome.bam OUTPUT=picard_alignment_summary_v1124_01.txt REFERENCE_SEQUENCE=hg19_nohap.fa    MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] 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
## htsjdk.samtools.metrics.StringHeader
# Started on: Sun Jul 19 15:42:28 CEST 2015

## 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	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	SAMPLE	LIBRARY	READ_GROUP
FIRST_OF_PAIR	35691	35691	1	0	35557	0.996246	3501223	33864	3346832	3334799	0	0.002714	0.001829	0.000208	99.003895	35535	0.999381	0	0.500464	0.007275	0.000224			
SECOND_OF_PAIR	35698	35698	1	0	35549	0.995826	3444468	33837	3291466	3272670	0	0.002978	0.002061	0.000187	97.424225	35535	0.999606	0	0.499789	0.007275	0.000224			
PAIR	71389	71389	1	0	71106	0.996036	6945691	67701	6638298	6607469	0	0.002845	0.001944	0.000197	98.213983	71070	0.999494	0	0.500127	0.007275	0.000224			


