## net.sf.picard.metrics.StringHeader
# net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=can_0_A.bam OUTPUT=can.metr.txt REFERENCE_SEQUENCE=aa.fasta VALIDATION_STRINGENCY=SILENT    ASSUME_SORTED=true MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false TMP_DIR=/tmp/xianggan VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
## net.sf.picard.metrics.StringHeader
# Started on: Thu Nov 04 17:47:28 GMT 2010

## METRICS CLASS	net.sf.picard.analysis.AlignmentSummaryMetrics
CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_HQ_ERROR_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER
FIRST_OF_PAIR	95838612	95838612	1	0	93573495	0.976365	67104880	2750436053	2564727506	0	0.011044	40.840735	91656299	0.979511	0	0.497274	0.009149	0.000085
SECOND_OF_PAIR	95838612	95838612	1	0	92485426	0.965012	66508022	2722883563	2476962635	0	0.013788	40.840735	91656326	0.991035	0	0.502809	0.009161	0.000043
PAIR	191677224	191677224	1	0	186058921	0.970689	133612902	5473319616	5041690141	0	0.012409	40.840735	183312625	0.98524	0	0.500025	0.009155	0.000064
UNPAIRED	31446396	31446396	1	0	30511536	0.970271	22777873	1156903058	1123231471	0	0.009557	51	0	0	0	0.472582	0	0.00001