Mercurial > repos > devteam > samtools_stats
annotate test-data/11.stats.g4.expected @ 12:541082d03bef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
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date | Sun, 08 Sep 2024 03:27:04 +0000 |
parents | e28839a4b932 |
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541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
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changeset
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1 # This file was produced by samtools stats (1.20+htslib-1.20) and can be plotted using plot-bamstats |
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e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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2 # This file contains statistics for all reads. |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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3 # The command line was: stats -g 4 -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56 |
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95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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diff
changeset
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6 CHK cb2d2d82 bcd83869 62ec814e |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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7 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. |
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e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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3
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changeset
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8 SN raw total sequences: 26 # excluding supplementary and secondary reads |
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95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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9 SN filtered sequences: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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10 SN sequences: 26 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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diff
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11 SN is sorted: 1 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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changeset
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12 SN 1st fragments: 14 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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13 SN last fragments: 12 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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diff
changeset
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14 SN reads mapped: 26 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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15 SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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16 SN reads unmapped: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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17 SN reads properly paired: 24 # proper-pair bit set |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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18 SN reads paired: 26 # paired-end technology bit set |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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changeset
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19 SN reads duplicated: 0 # PCR or optical duplicate bit set |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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20 SN reads MQ0: 1 # mapped and MQ=0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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changeset
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21 SN reads QC failed: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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22 SN non-primary alignments: 0 |
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e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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23 SN supplementary alignments: 0 |
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95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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changeset
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24 SN total length: 260 # ignores clipping |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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25 SN total first fragment length: 140 # ignores clipping |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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26 SN total last fragment length: 120 # ignores clipping |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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27 SN bases mapped: 260 # ignores clipping |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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28 SN bases mapped (cigar): 206 # more accurate |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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29 SN bases trimmed: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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30 SN bases duplicated: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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31 SN mismatches: 0 # from NM fields |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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32 SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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33 SN average length: 10 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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34 SN average first fragment length: 10 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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changeset
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35 SN average last fragment length: 10 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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36 SN maximum length: 10 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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37 SN maximum first fragment length: 10 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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38 SN maximum last fragment length: 10 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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39 SN average quality: 13.1 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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40 SN insert size average: 34.0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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41 SN insert size standard deviation: 0.0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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42 SN inward oriented pairs: 12 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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43 SN outward oriented pairs: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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44 SN pairs with other orientation: 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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45 SN pairs on different chromosomes: 1 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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46 SN percentage of properly paired reads (%): 92.3 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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47 SN bases inside the target: 42 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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48 SN percentage of target genome with coverage > 4 (%): 85.71 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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49 # First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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50 # Columns correspond to qualities and rows to cycles. First column is the cycle number. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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51 FFQ 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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52 FFQ 2 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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53 FFQ 3 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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54 FFQ 4 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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55 FFQ 5 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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56 FFQ 6 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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57 FFQ 7 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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58 FFQ 8 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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59 FFQ 9 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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60 FFQ 10 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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61 # Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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62 # Columns correspond to qualities and rows to cycles. First column is the cycle number. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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63 LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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64 LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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65 LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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66 LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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67 LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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68 LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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69 LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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70 LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
71 LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
72 LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
73 # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
74 GCF 19.85 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
75 GCF 44.72 1 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
76 GCF 54.77 4 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
77 GCF 64.82 2 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
78 GCF 74.87 4 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
79 GCF 84.92 3 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
80 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
81 GCL 19.85 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
82 GCL 44.72 2 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
83 GCL 59.80 3 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
84 GCL 74.87 4 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
85 # ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
86 GCC 1 19.23 42.31 15.38 23.08 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
87 GCC 2 19.23 19.23 46.15 15.38 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
88 GCC 3 23.08 38.46 19.23 19.23 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
89 GCC 4 23.08 23.08 38.46 15.38 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
90 GCC 5 11.54 38.46 26.92 23.08 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
91 GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
92 GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
93 GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
94 GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
95 GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 |
8
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
96 # ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%] |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
97 GCT 1 26.92 26.92 30.77 15.38 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
98 GCT 2 7.69 38.46 26.92 26.92 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
99 GCT 3 26.92 26.92 30.77 15.38 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
100 GCT 4 11.54 34.62 26.92 26.92 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
101 GCT 5 23.08 26.92 38.46 11.54 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
102 GCT 6 11.54 34.62 23.08 30.77 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
103 GCT 7 19.23 23.08 38.46 19.23 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
104 GCT 8 11.54 38.46 23.08 26.92 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
105 GCT 9 23.08 19.23 34.62 23.08 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
106 GCT 10 11.54 34.62 26.92 26.92 |
3
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
107 # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
108 FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
109 FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
110 FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
111 FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
112 FBC 5 14.29 35.71 35.71 14.29 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
113 FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
114 FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
115 FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
116 FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
117 FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 |
8
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
118 # ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
119 FTC 24 43 45 28 0 |
3
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
120 # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
121 LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
122 LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
123 LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
124 LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
125 LBC 5 8.33 41.67 16.67 33.33 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
126 LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
127 LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
128 LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
129 LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
130 LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 |
8
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
131 # ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
132 LTC 30 33 36 21 0 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
133 # ACGT content per cycle for barcodes. Use `grep ^BCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N counts as a percentage of all A/C/G/T bases [%] |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
134 BCC1 1 50.00 0.00 0.00 50.00 0.00 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
135 BCC1 2 0.00 50.00 50.00 0.00 0.00 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
136 BCC1 3 0.00 50.00 50.00 0.00 0.00 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
137 BCC1 4 50.00 0.00 0.00 50.00 0.00 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
138 # Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
139 # Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
140 QTQ1 1 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
141 QTQ1 2 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
142 QTQ1 3 |
e28839a4b932
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
3
diff
changeset
|
143 QTQ1 4 |
3
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
144 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
145 IS 0 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
146 IS 1 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
147 IS 2 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
148 IS 3 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
149 IS 4 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
150 IS 5 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
151 IS 6 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
152 IS 7 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
153 IS 8 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
154 IS 9 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
155 IS 10 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
156 IS 11 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
157 IS 12 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
158 IS 13 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
159 IS 14 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
160 IS 15 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
161 IS 16 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
162 IS 17 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
163 IS 18 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
164 IS 19 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
165 IS 20 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
166 IS 21 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
167 IS 22 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
168 IS 23 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
169 IS 24 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
170 IS 25 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
171 IS 26 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
172 IS 27 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
173 IS 28 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
174 IS 29 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
175 IS 30 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
176 IS 31 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
177 IS 32 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
178 IS 33 0 0 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
179 IS 34 12 12 0 0 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
180 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
181 RL 10 26 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
182 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
183 FRL 10 14 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
184 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
185 LRL 10 12 |
12
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
186 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
187 MAPQ 0 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
188 MAPQ 1 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
189 MAPQ 2 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
190 MAPQ 3 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
191 MAPQ 4 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
192 MAPQ 5 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
193 MAPQ 6 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
194 MAPQ 7 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
195 MAPQ 8 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
196 MAPQ 9 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
197 MAPQ 10 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
198 MAPQ 11 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
199 MAPQ 12 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
200 MAPQ 13 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
201 MAPQ 14 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
202 MAPQ 15 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
203 MAPQ 16 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
204 MAPQ 17 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
205 MAPQ 18 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
206 MAPQ 19 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
207 MAPQ 20 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
208 MAPQ 21 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
209 MAPQ 22 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
210 MAPQ 23 1 |
541082d03bef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents:
8
diff
changeset
|
211 MAPQ 50 2 |
3
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
212 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
|
213 # Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff
changeset
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214 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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215 COV [1-1] 1 1 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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216 COV [2-2] 2 1 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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217 COV [3-3] 3 2 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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218 COV [4-4] 4 2 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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219 COV [5-5] 5 23 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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220 COV [6-6] 6 13 |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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221 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile |
95a7ddf617e7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
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222 GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000 |