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1 # Summary Numbers
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2
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3 raw total sequences: 200
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4 filtered sequences: 0
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5 sequences: 200
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6 is sorted: 1
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7 1st fragments: 100
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8 last fragments: 100
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9 reads mapped: 25
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10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
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11 reads unmapped: 175
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12 reads properly paired: 0 # proper-pair bit set
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13 reads paired: 200 # paired-end technology bit set
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14 reads duplicated: 0 # PCR or optical duplicate bit set
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15 reads MQ0: 6 # mapped and MQ=0
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16 reads QC failed: 0
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17 non-primary alignments: 0
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18 total length: 50200 # ignores clipping
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19 bases mapped: 6275 # ignores clipping
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20 bases mapped (cigar): 6275 # more accurate
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21 bases trimmed: 0
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22 bases duplicated: 0
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23 mismatches: 591 # from NM fields
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24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
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25 average length: 251
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26 maximum length: 251
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27 average quality: 34.7
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28 insert size average: 0.0
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29 insert size standard deviation: 0.0
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30 inward oriented pairs: 0
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31 outward oriented pairs: 0
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32 pairs with other orientation: 0
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33 pairs on different chromosomes: 0
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