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1 ## net.sf.picard.metrics.StringHeader
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2 # net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=picard_input_tiny.sam OUTPUT=AsMetrics REFERENCE_SEQUENCE=picard_input_hg18.trimmed.fasta 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
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3 ## net.sf.picard.metrics.StringHeader
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4 # Started on: Tue Feb 11 21:51:51 EST 2014
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5
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6 ## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics
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7 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
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8 FIRST_OF_PAIR 4 4 1 0 4 1 404 4 404 28 78 0,777228 0,777228 0 101 3 0,75 63 0,25 0 0
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9 SECOND_OF_PAIR 4 4 1 0 3 0,75 298 3 298 45 75 0,758389 0,758389 0,006711 101 3 1 7 0,666667 0 0
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10 PAIR 8 8 1 0 7 0,875 702 7 702 73 78 0,769231 0,769231 0,002849 101 6 0,857143 70 0,428571 0 0
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11
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12
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