|
0
|
1 raw total sequences: 1000
|
|
|
2 filtered sequences: 0
|
|
|
3 sequences: 1000
|
|
|
4 is sorted: 1
|
|
|
5 1st fragments: 500
|
|
|
6 last fragments: 500
|
|
|
7 reads mapped: 972
|
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8 reads mapped and paired: 954 # paired-end technology bit set + both mates mapped
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|
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9 reads unmapped: 28
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10 reads properly paired: 0 # proper-pair bit set
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11 reads paired: 1000 # paired-end technology bit set
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12 reads duplicated: 0 # PCR or optical duplicate bit set
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13 reads MQ0: 0 # mapped and MQ=0
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14 reads QC failed: 0
|
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15 non-primary alignments: 0
|
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16 total length: 70000 # ignores clipping
|
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|
17 bases mapped: 68040 # ignores clipping
|
|
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18 bases mapped (cigar): 68040 # more accurate
|
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19 bases trimmed: 0
|
|
|
20 bases duplicated: 0
|
|
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21 mismatches: 1237 # from NM fields
|
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|
22 error rate: 1.818048e-02 # mismatches / bases mapped (cigar)
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23 average length: 70
|
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24 maximum length: 70
|
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25 average quality: 17.0
|
|
|
26 insert size average: 495.1
|
|
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27 insert size standard deviation: 48.9
|
|
|
28 inward oriented pairs: 477
|
|
|
29 outward oriented pairs: 0
|
|
|
30 pairs with other orientation: 0
|
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31 pairs on different chromosomes: 0
|
