# HG changeset patch # User devteam # Date 1413831409 14400 # Node ID cd6eb75c9819b29bee432b0e2b3fca84128c1b3b Uploaded initial tool definition. diff -r 000000000000 -r cd6eb75c9819 samtools_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_stats.xml Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,227 @@ + + for a BAM or SAM file + + samtools + + samtools --version | head -n 1 | awk '{ print $2 }' + "${output}" + #if $split_output.split_output_selector == "yes": + #set outputs_to_split = str($split_output.generate_tables).split(',') + && mkdir split && echo ${split_output.generate_tables} && + #if 'sn' in $outputs_to_split: + grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- > "split/Summary numbers.tab" ; fi && + #end if + #if 'ffq' in $outputs_to_split: + grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- > "split/First Fragment Qualities.tab" ; fi && + #end if + #if 'lfq' in $outputs_to_split: + grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- > "split/Last Fragment Qualities.tab" ; fi && + #end if + #if 'mpc' in $outputs_to_split: + grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- > "split/Mismatches per cycle.tab" ; fi && + #end if + #if 'gcf' in $outputs_to_split: + grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- > "split/GC Content of first fragments.tab" ; fi && + #end if + #if 'gcl' in $outputs_to_split: + grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- > "split/GC Content of last fragments.tab" ; fi && + #end if + #if 'gcc' in $outputs_to_split: + grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- > "split/ACGT content per cycle.tab" ; fi && + #end if + #if 'is' in $outputs_to_split: + grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- > "split/Insert sizes.tab" ; fi && + #end if + #if 'rl' in $outputs_to_split: + grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- > "split/Read lengths.tab" ; fi && + #end if + #if 'id' in $outputs_to_split: + grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- > "split/Indel distribution.tab" ; fi && + #end if + #if 'ic' in $outputs_to_split: + grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- > "split/Indels per cycle.tab" ; fi && + #end if + #if 'cov' in $outputs_to_split: + grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- > "split/Coverage distribution.tab" ; fi && + #end if + #if 'gcd' in $outputs_to_split: + grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- > "split/GC depth.tab" ; fi + #end if + #end if + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool runs the ``samtools stats`` command in the SAMtools toolkit. + +Collects statistics from BAM files. The output can be visualized using plot-bamstats. + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + + diff -r 000000000000 -r cd6eb75c9819 test-data/phiX.bam Binary file test-data/phiX.bam has changed diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out1.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,951 @@ +# This file was produced by samtools stats (1.1+htslib-1.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 2000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 /tmp/tmptYfjRJ/tmpl0qHNN/database/files/000/dataset_929.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 76594422 342222f2 06e86208 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 1000 +SN filtered sequences: 0 +SN sequences: 1000 +SN is sorted: 1 +SN 1st fragments: 500 +SN last fragments: 500 +SN reads mapped: 972 +SN reads mapped and paired: 954 # paired-end technology bit set + both mates mapped +SN reads unmapped: 28 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 1000 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 0 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 70000 # ignores clipping +SN bases mapped: 68040 # ignores clipping +SN bases mapped (cigar): 68040 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 1237 # from NM fields +SN error rate: 1.818048e-02 # mismatches / bases mapped (cigar) +SN average length: 70 +SN maximum length: 70 +SN average quality: 17.0 +SN insert size average: 495.1 +SN insert size standard deviation: 48.9 +SN inward oriented pairs: 477 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 14.82 0 +GCF 31.16 2 +GCF 33.42 6 +GCF 34.92 4 +GCF 36.18 6 +GCF 37.44 12 +GCF 38.94 28 +GCF 40.45 34 +GCF 41.96 37 +GCF 43.47 46 +GCF 44.72 55 +GCF 45.98 57 +GCF 47.49 68 +GCF 48.99 60 +GCF 50.50 27 +GCF 52.01 18 +GCF 53.52 15 +GCF 54.77 9 +GCF 56.03 4 +GCF 57.54 3 +GCF 59.05 2 +GCF 60.55 4 +GCF 62.06 0 +GCF 63.32 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 14.07 0 +GCL 28.89 1 +GCL 30.40 3 +GCL 31.91 1 +GCL 33.42 2 +GCL 34.92 4 +GCL 36.18 8 +GCL 37.44 16 +GCL 38.94 31 +GCL 40.45 40 +GCL 41.96 39 +GCL 43.47 55 +GCL 44.72 46 +GCL 45.98 61 +GCL 47.49 53 +GCL 48.99 50 +GCL 50.50 32 +GCL 52.01 23 +GCL 53.52 11 +GCL 54.77 9 +GCL 56.03 8 +GCL 57.54 3 +GCL 61.06 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 21.50 23.30 24.50 30.70 +GCC 2 21.10 22.20 22.50 34.20 +GCC 3 22.20 20.50 26.80 30.50 +GCC 4 24.40 21.50 21.50 32.60 +GCC 5 23.50 21.10 25.60 29.80 +GCC 6 26.30 21.80 20.40 31.50 +GCC 7 25.40 20.50 22.00 32.10 +GCC 8 23.90 19.20 27.00 29.90 +GCC 9 23.70 22.70 22.00 31.60 +GCC 10 22.50 22.00 24.10 31.40 +GCC 11 22.40 21.50 22.10 34.00 +GCC 12 25.20 18.00 24.50 32.30 +GCC 13 23.70 20.80 21.70 33.80 +GCC 14 24.60 23.00 22.40 30.00 +GCC 15 25.50 22.30 22.50 29.70 +GCC 16 24.10 21.40 23.60 30.90 +GCC 17 24.30 21.00 23.90 30.80 +GCC 18 24.40 22.10 22.70 30.80 +GCC 19 25.60 20.50 24.70 29.20 +GCC 20 25.80 19.60 22.00 32.60 +GCC 21 23.20 22.90 23.00 30.90 +GCC 22 23.90 22.70 22.60 30.80 +GCC 23 25.80 21.30 22.40 30.50 +GCC 24 23.50 22.00 22.70 31.80 +GCC 25 22.40 21.80 23.10 32.70 +GCC 26 22.90 19.90 24.30 32.90 +GCC 27 23.10 22.10 24.20 30.60 +GCC 28 23.50 22.10 22.90 31.50 +GCC 29 24.40 21.80 21.30 32.50 +GCC 30 21.90 22.50 22.60 33.00 +GCC 31 23.10 20.90 24.20 31.80 +GCC 32 24.60 22.10 23.60 29.70 +GCC 33 22.80 21.10 22.00 34.10 +GCC 34 21.70 22.10 23.60 32.60 +GCC 35 24.30 23.20 20.60 31.90 +GCC 36 21.60 22.70 24.50 31.20 +GCC 37 22.20 23.50 22.20 32.10 +GCC 38 24.10 20.80 22.00 33.10 +GCC 39 22.20 21.10 26.80 29.90 +GCC 40 21.80 24.00 22.90 31.30 +GCC 41 25.10 22.90 23.10 28.90 +GCC 42 25.50 22.70 22.20 29.60 +GCC 43 22.60 23.00 24.10 30.30 +GCC 44 21.70 21.60 24.20 32.50 +GCC 45 21.80 22.70 21.20 34.30 +GCC 46 22.80 22.00 23.80 31.40 +GCC 47 23.70 22.30 23.90 30.10 +GCC 48 24.30 21.70 24.80 29.20 +GCC 49 23.90 22.00 22.90 31.20 +GCC 50 23.50 22.40 22.80 31.30 +GCC 51 23.30 20.40 24.70 31.60 +GCC 52 23.30 20.20 25.10 31.40 +GCC 53 23.70 22.00 22.30 32.00 +GCC 54 23.30 21.30 25.40 30.00 +GCC 55 25.30 21.40 22.60 30.70 +GCC 56 24.40 24.10 19.20 32.30 +GCC 57 22.00 21.50 24.50 32.00 +GCC 58 24.90 21.20 24.20 29.70 +GCC 59 24.10 21.70 24.50 29.70 +GCC 60 24.80 20.90 25.10 29.20 +GCC 61 21.30 21.60 28.10 29.00 +GCC 62 23.80 21.80 21.70 32.70 +GCC 63 23.30 22.80 23.50 30.40 +GCC 64 24.00 21.40 23.50 31.10 +GCC 65 24.40 22.80 22.50 30.30 +GCC 66 24.70 22.30 21.40 31.60 +GCC 67 22.40 21.10 24.60 31.90 +GCC 68 24.60 22.90 20.60 31.90 +GCC 69 22.40 23.00 23.10 31.50 +GCC 70 23.50 19.50 23.90 33.10 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs +IS 0 0 0 0 0 +IS 1 0 0 0 0 +IS 2 0 0 0 0 +IS 3 0 0 0 0 +IS 4 0 0 0 0 +IS 5 0 0 0 0 +IS 6 0 0 0 0 +IS 7 0 0 0 0 +IS 8 0 0 0 0 +IS 9 0 0 0 0 +IS 10 0 0 0 0 +IS 11 0 0 0 0 +IS 12 0 0 0 0 +IS 13 0 0 0 0 +IS 14 0 0 0 0 +IS 15 0 0 0 0 +IS 16 0 0 0 0 +IS 17 0 0 0 0 +IS 18 0 0 0 0 +IS 19 0 0 0 0 +IS 20 0 0 0 0 +IS 21 0 0 0 0 +IS 22 0 0 0 0 +IS 23 0 0 0 0 +IS 24 0 0 0 0 +IS 25 0 0 0 0 +IS 26 0 0 0 0 +IS 27 0 0 0 0 +IS 28 0 0 0 0 +IS 29 0 0 0 0 +IS 30 0 0 0 0 +IS 31 0 0 0 0 +IS 32 0 0 0 0 +IS 33 0 0 0 0 +IS 34 0 0 0 0 +IS 35 0 0 0 0 +IS 36 0 0 0 0 +IS 37 0 0 0 0 +IS 38 0 0 0 0 +IS 39 0 0 0 0 +IS 40 0 0 0 0 +IS 41 0 0 0 0 +IS 42 0 0 0 0 +IS 43 0 0 0 0 +IS 44 0 0 0 0 +IS 45 0 0 0 0 +IS 46 0 0 0 0 +IS 47 0 0 0 0 +IS 48 0 0 0 0 +IS 49 0 0 0 0 +IS 50 0 0 0 0 +IS 51 0 0 0 0 +IS 52 0 0 0 0 +IS 53 0 0 0 0 +IS 54 0 0 0 0 +IS 55 0 0 0 0 +IS 56 0 0 0 0 +IS 57 0 0 0 0 +IS 58 0 0 0 0 +IS 59 0 0 0 0 +IS 60 0 0 0 0 +IS 61 0 0 0 0 +IS 62 0 0 0 0 +IS 63 0 0 0 0 +IS 64 0 0 0 0 +IS 65 0 0 0 0 +IS 66 0 0 0 0 +IS 67 0 0 0 0 +IS 68 0 0 0 0 +IS 69 0 0 0 0 +IS 70 0 0 0 0 +IS 71 0 0 0 0 +IS 72 0 0 0 0 +IS 73 0 0 0 0 +IS 74 0 0 0 0 +IS 75 0 0 0 0 +IS 76 0 0 0 0 +IS 77 0 0 0 0 +IS 78 0 0 0 0 +IS 79 0 0 0 0 +IS 80 0 0 0 0 +IS 81 0 0 0 0 +IS 82 0 0 0 0 +IS 83 0 0 0 0 +IS 84 0 0 0 0 +IS 85 0 0 0 0 +IS 86 0 0 0 0 +IS 87 0 0 0 0 +IS 88 0 0 0 0 +IS 89 0 0 0 0 +IS 90 0 0 0 0 +IS 91 0 0 0 0 +IS 92 0 0 0 0 +IS 93 0 0 0 0 +IS 94 0 0 0 0 +IS 95 0 0 0 0 +IS 96 0 0 0 0 +IS 97 0 0 0 0 +IS 98 0 0 0 0 +IS 99 0 0 0 0 +IS 100 0 0 0 0 +IS 101 0 0 0 0 +IS 102 0 0 0 0 +IS 103 0 0 0 0 +IS 104 0 0 0 0 +IS 105 0 0 0 0 +IS 106 0 0 0 0 +IS 107 0 0 0 0 +IS 108 0 0 0 0 +IS 109 0 0 0 0 +IS 110 0 0 0 0 +IS 111 0 0 0 0 +IS 112 0 0 0 0 +IS 113 0 0 0 0 +IS 114 0 0 0 0 +IS 115 0 0 0 0 +IS 116 0 0 0 0 +IS 117 0 0 0 0 +IS 118 0 0 0 0 +IS 119 0 0 0 0 +IS 120 0 0 0 0 +IS 121 0 0 0 0 +IS 122 0 0 0 0 +IS 123 0 0 0 0 +IS 124 0 0 0 0 +IS 125 0 0 0 0 +IS 126 0 0 0 0 +IS 127 0 0 0 0 +IS 128 0 0 0 0 +IS 129 0 0 0 0 +IS 130 0 0 0 0 +IS 131 0 0 0 0 +IS 132 0 0 0 0 +IS 133 0 0 0 0 +IS 134 0 0 0 0 +IS 135 0 0 0 0 +IS 136 0 0 0 0 +IS 137 0 0 0 0 +IS 138 0 0 0 0 +IS 139 0 0 0 0 +IS 140 0 0 0 0 +IS 141 0 0 0 0 +IS 142 0 0 0 0 +IS 143 0 0 0 0 +IS 144 0 0 0 0 +IS 145 0 0 0 0 +IS 146 0 0 0 0 +IS 147 0 0 0 0 +IS 148 0 0 0 0 +IS 149 0 0 0 0 +IS 150 0 0 0 0 +IS 151 0 0 0 0 +IS 152 0 0 0 0 +IS 153 0 0 0 0 +IS 154 0 0 0 0 +IS 155 0 0 0 0 +IS 156 0 0 0 0 +IS 157 0 0 0 0 +IS 158 0 0 0 0 +IS 159 0 0 0 0 +IS 160 0 0 0 0 +IS 161 0 0 0 0 +IS 162 0 0 0 0 +IS 163 0 0 0 0 +IS 164 0 0 0 0 +IS 165 0 0 0 0 +IS 166 0 0 0 0 +IS 167 0 0 0 0 +IS 168 0 0 0 0 +IS 169 0 0 0 0 +IS 170 0 0 0 0 +IS 171 0 0 0 0 +IS 172 0 0 0 0 +IS 173 0 0 0 0 +IS 174 0 0 0 0 +IS 175 0 0 0 0 +IS 176 0 0 0 0 +IS 177 0 0 0 0 +IS 178 0 0 0 0 +IS 179 0 0 0 0 +IS 180 0 0 0 0 +IS 181 0 0 0 0 +IS 182 0 0 0 0 +IS 183 0 0 0 0 +IS 184 0 0 0 0 +IS 185 0 0 0 0 +IS 186 0 0 0 0 +IS 187 0 0 0 0 +IS 188 0 0 0 0 +IS 189 0 0 0 0 +IS 190 0 0 0 0 +IS 191 0 0 0 0 +IS 192 0 0 0 0 +IS 193 0 0 0 0 +IS 194 0 0 0 0 +IS 195 0 0 0 0 +IS 196 0 0 0 0 +IS 197 0 0 0 0 +IS 198 0 0 0 0 +IS 199 0 0 0 0 +IS 200 0 0 0 0 +IS 201 0 0 0 0 +IS 202 0 0 0 0 +IS 203 0 0 0 0 +IS 204 0 0 0 0 +IS 205 0 0 0 0 +IS 206 0 0 0 0 +IS 207 0 0 0 0 +IS 208 0 0 0 0 +IS 209 0 0 0 0 +IS 210 0 0 0 0 +IS 211 0 0 0 0 +IS 212 0 0 0 0 +IS 213 0 0 0 0 +IS 214 0 0 0 0 +IS 215 0 0 0 0 +IS 216 0 0 0 0 +IS 217 0 0 0 0 +IS 218 0 0 0 0 +IS 219 0 0 0 0 +IS 220 0 0 0 0 +IS 221 0 0 0 0 +IS 222 0 0 0 0 +IS 223 0 0 0 0 +IS 224 0 0 0 0 +IS 225 0 0 0 0 +IS 226 0 0 0 0 +IS 227 0 0 0 0 +IS 228 0 0 0 0 +IS 229 0 0 0 0 +IS 230 0 0 0 0 +IS 231 0 0 0 0 +IS 232 0 0 0 0 +IS 233 0 0 0 0 +IS 234 0 0 0 0 +IS 235 0 0 0 0 +IS 236 0 0 0 0 +IS 237 0 0 0 0 +IS 238 0 0 0 0 +IS 239 0 0 0 0 +IS 240 0 0 0 0 +IS 241 0 0 0 0 +IS 242 0 0 0 0 +IS 243 0 0 0 0 +IS 244 0 0 0 0 +IS 245 0 0 0 0 +IS 246 0 0 0 0 +IS 247 0 0 0 0 +IS 248 0 0 0 0 +IS 249 0 0 0 0 +IS 250 0 0 0 0 +IS 251 0 0 0 0 +IS 252 0 0 0 0 +IS 253 0 0 0 0 +IS 254 0 0 0 0 +IS 255 0 0 0 0 +IS 256 0 0 0 0 +IS 257 0 0 0 0 +IS 258 0 0 0 0 +IS 259 0 0 0 0 +IS 260 0 0 0 0 +IS 261 0 0 0 0 +IS 262 0 0 0 0 +IS 263 0 0 0 0 +IS 264 0 0 0 0 +IS 265 0 0 0 0 +IS 266 0 0 0 0 +IS 267 0 0 0 0 +IS 268 0 0 0 0 +IS 269 0 0 0 0 +IS 270 0 0 0 0 +IS 271 0 0 0 0 +IS 272 0 0 0 0 +IS 273 0 0 0 0 +IS 274 0 0 0 0 +IS 275 0 0 0 0 +IS 276 0 0 0 0 +IS 277 0 0 0 0 +IS 278 0 0 0 0 +IS 279 0 0 0 0 +IS 280 0 0 0 0 +IS 281 0 0 0 0 +IS 282 0 0 0 0 +IS 283 0 0 0 0 +IS 284 0 0 0 0 +IS 285 0 0 0 0 +IS 286 0 0 0 0 +IS 287 0 0 0 0 +IS 288 0 0 0 0 +IS 289 0 0 0 0 +IS 290 0 0 0 0 +IS 291 0 0 0 0 +IS 292 0 0 0 0 +IS 293 0 0 0 0 +IS 294 0 0 0 0 +IS 295 0 0 0 0 +IS 296 0 0 0 0 +IS 297 0 0 0 0 +IS 298 0 0 0 0 +IS 299 0 0 0 0 +IS 300 0 0 0 0 +IS 301 0 0 0 0 +IS 302 0 0 0 0 +IS 303 0 0 0 0 +IS 304 0 0 0 0 +IS 305 0 0 0 0 +IS 306 0 0 0 0 +IS 307 0 0 0 0 +IS 308 0 0 0 0 +IS 309 0 0 0 0 +IS 310 0 0 0 0 +IS 311 1 1 0 0 +IS 312 0 0 0 0 +IS 313 0 0 0 0 +IS 314 0 0 0 0 +IS 315 0 0 0 0 +IS 316 0 0 0 0 +IS 317 0 0 0 0 +IS 318 0 0 0 0 +IS 319 0 0 0 0 +IS 320 0 0 0 0 +IS 321 0 0 0 0 +IS 322 0 0 0 0 +IS 323 0 0 0 0 +IS 324 0 0 0 0 +IS 325 0 0 0 0 +IS 326 0 0 0 0 +IS 327 0 0 0 0 +IS 328 0 0 0 0 +IS 329 0 0 0 0 +IS 330 0 0 0 0 +IS 331 0 0 0 0 +IS 332 0 0 0 0 +IS 333 0 0 0 0 +IS 334 0 0 0 0 +IS 335 0 0 0 0 +IS 336 0 0 0 0 +IS 337 0 0 0 0 +IS 338 0 0 0 0 +IS 339 0 0 0 0 +IS 340 0 0 0 0 +IS 341 0 0 0 0 +IS 342 0 0 0 0 +IS 343 0 0 0 0 +IS 344 0 0 0 0 +IS 345 1 1 0 0 +IS 346 0 0 0 0 +IS 347 1 1 0 0 +IS 348 0 0 0 0 +IS 349 0 0 0 0 +IS 350 0 0 0 0 +IS 351 0 0 0 0 +IS 352 0 0 0 0 +IS 353 0 0 0 0 +IS 354 0 0 0 0 +IS 355 0 0 0 0 +IS 356 0 0 0 0 +IS 357 0 0 0 0 +IS 358 0 0 0 0 +IS 359 0 0 0 0 +IS 360 0 0 0 0 +IS 361 0 0 0 0 +IS 362 0 0 0 0 +IS 363 0 0 0 0 +IS 364 1 1 0 0 +IS 365 0 0 0 0 +IS 366 0 0 0 0 +IS 367 0 0 0 0 +IS 368 0 0 0 0 +IS 369 0 0 0 0 +IS 370 1 1 0 0 +IS 371 1 1 0 0 +IS 372 0 0 0 0 +IS 373 0 0 0 0 +IS 374 0 0 0 0 +IS 375 0 0 0 0 +IS 376 0 0 0 0 +IS 377 0 0 0 0 +IS 378 2 2 0 0 +IS 379 0 0 0 0 +IS 380 0 0 0 0 +IS 381 0 0 0 0 +IS 382 0 0 0 0 +IS 383 0 0 0 0 +IS 384 0 0 0 0 +IS 385 0 0 0 0 +IS 386 0 0 0 0 +IS 387 1 1 0 0 +IS 388 1 1 0 0 +IS 389 0 0 0 0 +IS 390 1 1 0 0 +IS 391 0 0 0 0 +IS 392 0 0 0 0 +IS 393 0 0 0 0 +IS 394 1 1 0 0 +IS 395 1 1 0 0 +IS 396 1 1 0 0 +IS 397 0 0 0 0 +IS 398 1 1 0 0 +IS 399 0 0 0 0 +IS 400 1 1 0 0 +IS 401 0 0 0 0 +IS 402 0 0 0 0 +IS 403 1 1 0 0 +IS 404 0 0 0 0 +IS 405 0 0 0 0 +IS 406 0 0 0 0 +IS 407 1 1 0 0 +IS 408 1 1 0 0 +IS 409 3 3 0 0 +IS 410 4 4 0 0 +IS 411 0 0 0 0 +IS 412 0 0 0 0 +IS 413 1 1 0 0 +IS 414 1 1 0 0 +IS 415 1 1 0 0 +IS 416 1 1 0 0 +IS 417 0 0 0 0 +IS 418 1 1 0 0 +IS 419 0 0 0 0 +IS 420 1 1 0 0 +IS 421 1 1 0 0 +IS 422 0 0 0 0 +IS 423 0 0 0 0 +IS 424 3 3 0 0 +IS 425 3 3 0 0 +IS 426 0 0 0 0 +IS 427 1 1 0 0 +IS 428 1 1 0 0 +IS 429 0 0 0 0 +IS 430 0 0 0 0 +IS 431 4 4 0 0 +IS 432 1 1 0 0 +IS 433 1 1 0 0 +IS 434 3 3 0 0 +IS 435 1 1 0 0 +IS 436 1 1 0 0 +IS 437 0 0 0 0 +IS 438 1 1 0 0 +IS 439 0 0 0 0 +IS 440 3 3 0 0 +IS 441 1 1 0 0 +IS 442 4 4 0 0 +IS 443 3 3 0 0 +IS 444 1 1 0 0 +IS 445 4 4 0 0 +IS 446 1 1 0 0 +IS 447 1 1 0 0 +IS 448 1 1 0 0 +IS 449 2 2 0 0 +IS 450 3 3 0 0 +IS 451 5 5 0 0 +IS 452 2 2 0 0 +IS 453 3 3 0 0 +IS 454 4 4 0 0 +IS 455 7 7 0 0 +IS 456 3 3 0 0 +IS 457 4 4 0 0 +IS 458 2 2 0 0 +IS 459 3 3 0 0 +IS 460 2 2 0 0 +IS 461 2 2 0 0 +IS 462 2 2 0 0 +IS 463 2 2 0 0 +IS 464 1 1 0 0 +IS 465 6 6 0 0 +IS 466 4 4 0 0 +IS 467 6 6 0 0 +IS 468 1 1 0 0 +IS 469 1 1 0 0 +IS 470 1 1 0 0 +IS 471 3 3 0 0 +IS 472 8 8 0 0 +IS 473 4 4 0 0 +IS 474 2 2 0 0 +IS 475 2 2 0 0 +IS 476 4 4 0 0 +IS 477 6 6 0 0 +IS 478 3 3 0 0 +IS 479 6 6 0 0 +IS 480 7 7 0 0 +IS 481 3 3 0 0 +IS 482 2 2 0 0 +IS 483 1 1 0 0 +IS 484 6 6 0 0 +IS 485 6 6 0 0 +IS 486 6 6 0 0 +IS 487 2 2 0 0 +IS 488 4 4 0 0 +IS 489 3 3 0 0 +IS 490 6 6 0 0 +IS 491 3 3 0 0 +IS 492 5 5 0 0 +IS 493 2 2 0 0 +IS 494 4 4 0 0 +IS 495 0 0 0 0 +IS 496 7 7 0 0 +IS 497 5 5 0 0 +IS 498 4 4 0 0 +IS 499 6 6 0 0 +IS 500 0 0 0 0 +IS 501 2 2 0 0 +IS 502 2 2 0 0 +IS 503 4 4 0 0 +IS 504 3 3 0 0 +IS 505 3 3 0 0 +IS 506 2 2 0 0 +IS 507 4 4 0 0 +IS 508 3 3 0 0 +IS 509 1 1 0 0 +IS 510 7 7 0 0 +IS 511 2 2 0 0 +IS 512 3 3 0 0 +IS 513 7 7 0 0 +IS 514 4 4 0 0 +IS 515 2 2 0 0 +IS 516 2 2 0 0 +IS 517 1 1 0 0 +IS 518 0 0 0 0 +IS 519 2 2 0 0 +IS 520 2 2 0 0 +IS 521 5 5 0 0 +IS 522 6 6 0 0 +IS 523 4 4 0 0 +IS 524 2 2 0 0 +IS 525 1 1 0 0 +IS 526 5 5 0 0 +IS 527 6 6 0 0 +IS 528 0 0 0 0 +IS 529 5 5 0 0 +IS 530 7 7 0 0 +IS 531 4 4 0 0 +IS 532 5 5 0 0 +IS 533 1 1 0 0 +IS 534 5 5 0 0 +IS 535 3 3 0 0 +IS 536 2 2 0 0 +IS 537 3 3 0 0 +IS 538 2 2 0 0 +IS 539 4 4 0 0 +IS 540 2 2 0 0 +IS 541 2 2 0 0 +IS 542 3 3 0 0 +IS 543 4 4 0 0 +IS 544 2 2 0 0 +IS 545 1 1 0 0 +IS 546 2 2 0 0 +IS 547 2 2 0 0 +IS 548 3 3 0 0 +IS 549 5 5 0 0 +IS 550 1 1 0 0 +IS 551 0 0 0 0 +IS 552 0 0 0 0 +IS 553 4 4 0 0 +IS 554 1 1 0 0 +IS 555 5 5 0 0 +IS 556 5 5 0 0 +IS 557 2 2 0 0 +IS 558 2 2 0 0 +IS 559 3 3 0 0 +IS 560 1 1 0 0 +IS 561 1 1 0 0 +IS 562 4 4 0 0 +IS 563 1 1 0 0 +IS 564 1 1 0 0 +IS 565 0 0 0 0 +IS 566 1 1 0 0 +IS 567 1 1 0 0 +IS 568 0 0 0 0 +IS 569 2 2 0 0 +IS 570 1 1 0 0 +IS 571 2 2 0 0 +IS 572 4 4 0 0 +IS 573 0 0 0 0 +IS 574 0 0 0 0 +IS 575 0 0 0 0 +IS 576 1 1 0 0 +IS 577 2 2 0 0 +IS 578 1 1 0 0 +IS 579 2 2 0 0 +IS 580 0 0 0 0 +IS 581 1 1 0 0 +IS 582 0 0 0 0 +IS 583 1 1 0 0 +IS 584 2 2 0 0 +IS 585 0 0 0 0 +IS 586 3 3 0 0 +IS 587 0 0 0 0 +IS 588 0 0 0 0 +IS 589 0 0 0 0 +IS 590 0 0 0 0 +IS 591 0 0 0 0 +IS 592 0 0 0 0 +IS 593 0 0 0 0 +IS 594 2 2 0 0 +IS 595 0 0 0 0 +IS 596 0 0 0 0 +IS 597 1 1 0 0 +IS 598 0 0 0 0 +IS 599 0 0 0 0 +IS 600 1 1 0 0 +IS 601 1 1 0 0 +IS 602 0 0 0 0 +IS 603 0 0 0 0 +IS 604 0 0 0 0 +IS 605 1 1 0 0 +IS 606 0 0 0 0 +IS 607 1 1 0 0 +IS 608 0 0 0 0 +IS 609 0 0 0 0 +IS 610 0 0 0 0 +IS 611 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 70 1000 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 0 1 +# 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) +IC 8 0 0 1 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 42 +COV [2-2] 2 59 +COV [3-3] 3 73 +COV [4-4] 4 98 +COV [5-5] 5 128 +COV [6-6] 6 142 +COV [7-7] 7 226 +COV [8-8] 8 241 +COV [9-9] 9 281 +COV [10-10] 10 400 +COV [11-11] 11 450 +COV [12-12] 12 444 +COV [13-13] 13 433 +COV [14-14] 14 423 +COV [15-15] 15 392 +COV [16-16] 16 434 +COV [17-17] 17 294 +COV [18-18] 18 229 +COV [19-19] 19 143 +COV [20-20] 20 143 +COV [21-21] 21 149 +COV [22-22] 22 90 +COV [23-23] 23 41 +COV [24-24] 24 14 +# 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 +GCD 0.0 50.000 0.000 0.000 0.000 0.000 0.000 +GCD 44.0 75.000 14.875 14.875 14.875 14.875 14.875 +GCD 46.0 100.000 11.900 11.900 11.900 11.900 11.900 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,951 @@ +# This file was produced by samtools stats (1.1+htslib-1.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 2000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 /tmp/tmpFDCqQD/tmprMv9KZ/database/files/000/dataset_893.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 76594422 342222f2 06e86208 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 1000 +SN filtered sequences: 0 +SN sequences: 1000 +SN is sorted: 1 +SN 1st fragments: 500 +SN last fragments: 500 +SN reads mapped: 972 +SN reads mapped and paired: 954 # paired-end technology bit set + both mates mapped +SN reads unmapped: 28 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 1000 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 0 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 70000 # ignores clipping +SN bases mapped: 68040 # ignores clipping +SN bases mapped (cigar): 68040 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 1237 # from NM fields +SN error rate: 1.818048e-02 # mismatches / bases mapped (cigar) +SN average length: 70 +SN maximum length: 70 +SN average quality: 17.0 +SN insert size average: 495.1 +SN insert size standard deviation: 48.9 +SN inward oriented pairs: 477 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 +FFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 +LFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 500 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 14.82 0 +GCF 31.16 2 +GCF 33.42 6 +GCF 34.92 4 +GCF 36.18 6 +GCF 37.44 12 +GCF 38.94 28 +GCF 40.45 34 +GCF 41.96 37 +GCF 43.47 46 +GCF 44.72 55 +GCF 45.98 57 +GCF 47.49 68 +GCF 48.99 60 +GCF 50.50 27 +GCF 52.01 18 +GCF 53.52 15 +GCF 54.77 9 +GCF 56.03 4 +GCF 57.54 3 +GCF 59.05 2 +GCF 60.55 4 +GCF 62.06 0 +GCF 63.32 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 14.07 0 +GCL 28.89 1 +GCL 30.40 3 +GCL 31.91 1 +GCL 33.42 2 +GCL 34.92 4 +GCL 36.18 8 +GCL 37.44 16 +GCL 38.94 31 +GCL 40.45 40 +GCL 41.96 39 +GCL 43.47 55 +GCL 44.72 46 +GCL 45.98 61 +GCL 47.49 53 +GCL 48.99 50 +GCL 50.50 32 +GCL 52.01 23 +GCL 53.52 11 +GCL 54.77 9 +GCL 56.03 8 +GCL 57.54 3 +GCL 61.06 1 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 21.50 23.30 24.50 30.70 +GCC 2 21.10 22.20 22.50 34.20 +GCC 3 22.20 20.50 26.80 30.50 +GCC 4 24.40 21.50 21.50 32.60 +GCC 5 23.50 21.10 25.60 29.80 +GCC 6 26.30 21.80 20.40 31.50 +GCC 7 25.40 20.50 22.00 32.10 +GCC 8 23.90 19.20 27.00 29.90 +GCC 9 23.70 22.70 22.00 31.60 +GCC 10 22.50 22.00 24.10 31.40 +GCC 11 22.40 21.50 22.10 34.00 +GCC 12 25.20 18.00 24.50 32.30 +GCC 13 23.70 20.80 21.70 33.80 +GCC 14 24.60 23.00 22.40 30.00 +GCC 15 25.50 22.30 22.50 29.70 +GCC 16 24.10 21.40 23.60 30.90 +GCC 17 24.30 21.00 23.90 30.80 +GCC 18 24.40 22.10 22.70 30.80 +GCC 19 25.60 20.50 24.70 29.20 +GCC 20 25.80 19.60 22.00 32.60 +GCC 21 23.20 22.90 23.00 30.90 +GCC 22 23.90 22.70 22.60 30.80 +GCC 23 25.80 21.30 22.40 30.50 +GCC 24 23.50 22.00 22.70 31.80 +GCC 25 22.40 21.80 23.10 32.70 +GCC 26 22.90 19.90 24.30 32.90 +GCC 27 23.10 22.10 24.20 30.60 +GCC 28 23.50 22.10 22.90 31.50 +GCC 29 24.40 21.80 21.30 32.50 +GCC 30 21.90 22.50 22.60 33.00 +GCC 31 23.10 20.90 24.20 31.80 +GCC 32 24.60 22.10 23.60 29.70 +GCC 33 22.80 21.10 22.00 34.10 +GCC 34 21.70 22.10 23.60 32.60 +GCC 35 24.30 23.20 20.60 31.90 +GCC 36 21.60 22.70 24.50 31.20 +GCC 37 22.20 23.50 22.20 32.10 +GCC 38 24.10 20.80 22.00 33.10 +GCC 39 22.20 21.10 26.80 29.90 +GCC 40 21.80 24.00 22.90 31.30 +GCC 41 25.10 22.90 23.10 28.90 +GCC 42 25.50 22.70 22.20 29.60 +GCC 43 22.60 23.00 24.10 30.30 +GCC 44 21.70 21.60 24.20 32.50 +GCC 45 21.80 22.70 21.20 34.30 +GCC 46 22.80 22.00 23.80 31.40 +GCC 47 23.70 22.30 23.90 30.10 +GCC 48 24.30 21.70 24.80 29.20 +GCC 49 23.90 22.00 22.90 31.20 +GCC 50 23.50 22.40 22.80 31.30 +GCC 51 23.30 20.40 24.70 31.60 +GCC 52 23.30 20.20 25.10 31.40 +GCC 53 23.70 22.00 22.30 32.00 +GCC 54 23.30 21.30 25.40 30.00 +GCC 55 25.30 21.40 22.60 30.70 +GCC 56 24.40 24.10 19.20 32.30 +GCC 57 22.00 21.50 24.50 32.00 +GCC 58 24.90 21.20 24.20 29.70 +GCC 59 24.10 21.70 24.50 29.70 +GCC 60 24.80 20.90 25.10 29.20 +GCC 61 21.30 21.60 28.10 29.00 +GCC 62 23.80 21.80 21.70 32.70 +GCC 63 23.30 22.80 23.50 30.40 +GCC 64 24.00 21.40 23.50 31.10 +GCC 65 24.40 22.80 22.50 30.30 +GCC 66 24.70 22.30 21.40 31.60 +GCC 67 22.40 21.10 24.60 31.90 +GCC 68 24.60 22.90 20.60 31.90 +GCC 69 22.40 23.00 23.10 31.50 +GCC 70 23.50 19.50 23.90 33.10 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs +IS 0 0 0 0 0 +IS 1 0 0 0 0 +IS 2 0 0 0 0 +IS 3 0 0 0 0 +IS 4 0 0 0 0 +IS 5 0 0 0 0 +IS 6 0 0 0 0 +IS 7 0 0 0 0 +IS 8 0 0 0 0 +IS 9 0 0 0 0 +IS 10 0 0 0 0 +IS 11 0 0 0 0 +IS 12 0 0 0 0 +IS 13 0 0 0 0 +IS 14 0 0 0 0 +IS 15 0 0 0 0 +IS 16 0 0 0 0 +IS 17 0 0 0 0 +IS 18 0 0 0 0 +IS 19 0 0 0 0 +IS 20 0 0 0 0 +IS 21 0 0 0 0 +IS 22 0 0 0 0 +IS 23 0 0 0 0 +IS 24 0 0 0 0 +IS 25 0 0 0 0 +IS 26 0 0 0 0 +IS 27 0 0 0 0 +IS 28 0 0 0 0 +IS 29 0 0 0 0 +IS 30 0 0 0 0 +IS 31 0 0 0 0 +IS 32 0 0 0 0 +IS 33 0 0 0 0 +IS 34 0 0 0 0 +IS 35 0 0 0 0 +IS 36 0 0 0 0 +IS 37 0 0 0 0 +IS 38 0 0 0 0 +IS 39 0 0 0 0 +IS 40 0 0 0 0 +IS 41 0 0 0 0 +IS 42 0 0 0 0 +IS 43 0 0 0 0 +IS 44 0 0 0 0 +IS 45 0 0 0 0 +IS 46 0 0 0 0 +IS 47 0 0 0 0 +IS 48 0 0 0 0 +IS 49 0 0 0 0 +IS 50 0 0 0 0 +IS 51 0 0 0 0 +IS 52 0 0 0 0 +IS 53 0 0 0 0 +IS 54 0 0 0 0 +IS 55 0 0 0 0 +IS 56 0 0 0 0 +IS 57 0 0 0 0 +IS 58 0 0 0 0 +IS 59 0 0 0 0 +IS 60 0 0 0 0 +IS 61 0 0 0 0 +IS 62 0 0 0 0 +IS 63 0 0 0 0 +IS 64 0 0 0 0 +IS 65 0 0 0 0 +IS 66 0 0 0 0 +IS 67 0 0 0 0 +IS 68 0 0 0 0 +IS 69 0 0 0 0 +IS 70 0 0 0 0 +IS 71 0 0 0 0 +IS 72 0 0 0 0 +IS 73 0 0 0 0 +IS 74 0 0 0 0 +IS 75 0 0 0 0 +IS 76 0 0 0 0 +IS 77 0 0 0 0 +IS 78 0 0 0 0 +IS 79 0 0 0 0 +IS 80 0 0 0 0 +IS 81 0 0 0 0 +IS 82 0 0 0 0 +IS 83 0 0 0 0 +IS 84 0 0 0 0 +IS 85 0 0 0 0 +IS 86 0 0 0 0 +IS 87 0 0 0 0 +IS 88 0 0 0 0 +IS 89 0 0 0 0 +IS 90 0 0 0 0 +IS 91 0 0 0 0 +IS 92 0 0 0 0 +IS 93 0 0 0 0 +IS 94 0 0 0 0 +IS 95 0 0 0 0 +IS 96 0 0 0 0 +IS 97 0 0 0 0 +IS 98 0 0 0 0 +IS 99 0 0 0 0 +IS 100 0 0 0 0 +IS 101 0 0 0 0 +IS 102 0 0 0 0 +IS 103 0 0 0 0 +IS 104 0 0 0 0 +IS 105 0 0 0 0 +IS 106 0 0 0 0 +IS 107 0 0 0 0 +IS 108 0 0 0 0 +IS 109 0 0 0 0 +IS 110 0 0 0 0 +IS 111 0 0 0 0 +IS 112 0 0 0 0 +IS 113 0 0 0 0 +IS 114 0 0 0 0 +IS 115 0 0 0 0 +IS 116 0 0 0 0 +IS 117 0 0 0 0 +IS 118 0 0 0 0 +IS 119 0 0 0 0 +IS 120 0 0 0 0 +IS 121 0 0 0 0 +IS 122 0 0 0 0 +IS 123 0 0 0 0 +IS 124 0 0 0 0 +IS 125 0 0 0 0 +IS 126 0 0 0 0 +IS 127 0 0 0 0 +IS 128 0 0 0 0 +IS 129 0 0 0 0 +IS 130 0 0 0 0 +IS 131 0 0 0 0 +IS 132 0 0 0 0 +IS 133 0 0 0 0 +IS 134 0 0 0 0 +IS 135 0 0 0 0 +IS 136 0 0 0 0 +IS 137 0 0 0 0 +IS 138 0 0 0 0 +IS 139 0 0 0 0 +IS 140 0 0 0 0 +IS 141 0 0 0 0 +IS 142 0 0 0 0 +IS 143 0 0 0 0 +IS 144 0 0 0 0 +IS 145 0 0 0 0 +IS 146 0 0 0 0 +IS 147 0 0 0 0 +IS 148 0 0 0 0 +IS 149 0 0 0 0 +IS 150 0 0 0 0 +IS 151 0 0 0 0 +IS 152 0 0 0 0 +IS 153 0 0 0 0 +IS 154 0 0 0 0 +IS 155 0 0 0 0 +IS 156 0 0 0 0 +IS 157 0 0 0 0 +IS 158 0 0 0 0 +IS 159 0 0 0 0 +IS 160 0 0 0 0 +IS 161 0 0 0 0 +IS 162 0 0 0 0 +IS 163 0 0 0 0 +IS 164 0 0 0 0 +IS 165 0 0 0 0 +IS 166 0 0 0 0 +IS 167 0 0 0 0 +IS 168 0 0 0 0 +IS 169 0 0 0 0 +IS 170 0 0 0 0 +IS 171 0 0 0 0 +IS 172 0 0 0 0 +IS 173 0 0 0 0 +IS 174 0 0 0 0 +IS 175 0 0 0 0 +IS 176 0 0 0 0 +IS 177 0 0 0 0 +IS 178 0 0 0 0 +IS 179 0 0 0 0 +IS 180 0 0 0 0 +IS 181 0 0 0 0 +IS 182 0 0 0 0 +IS 183 0 0 0 0 +IS 184 0 0 0 0 +IS 185 0 0 0 0 +IS 186 0 0 0 0 +IS 187 0 0 0 0 +IS 188 0 0 0 0 +IS 189 0 0 0 0 +IS 190 0 0 0 0 +IS 191 0 0 0 0 +IS 192 0 0 0 0 +IS 193 0 0 0 0 +IS 194 0 0 0 0 +IS 195 0 0 0 0 +IS 196 0 0 0 0 +IS 197 0 0 0 0 +IS 198 0 0 0 0 +IS 199 0 0 0 0 +IS 200 0 0 0 0 +IS 201 0 0 0 0 +IS 202 0 0 0 0 +IS 203 0 0 0 0 +IS 204 0 0 0 0 +IS 205 0 0 0 0 +IS 206 0 0 0 0 +IS 207 0 0 0 0 +IS 208 0 0 0 0 +IS 209 0 0 0 0 +IS 210 0 0 0 0 +IS 211 0 0 0 0 +IS 212 0 0 0 0 +IS 213 0 0 0 0 +IS 214 0 0 0 0 +IS 215 0 0 0 0 +IS 216 0 0 0 0 +IS 217 0 0 0 0 +IS 218 0 0 0 0 +IS 219 0 0 0 0 +IS 220 0 0 0 0 +IS 221 0 0 0 0 +IS 222 0 0 0 0 +IS 223 0 0 0 0 +IS 224 0 0 0 0 +IS 225 0 0 0 0 +IS 226 0 0 0 0 +IS 227 0 0 0 0 +IS 228 0 0 0 0 +IS 229 0 0 0 0 +IS 230 0 0 0 0 +IS 231 0 0 0 0 +IS 232 0 0 0 0 +IS 233 0 0 0 0 +IS 234 0 0 0 0 +IS 235 0 0 0 0 +IS 236 0 0 0 0 +IS 237 0 0 0 0 +IS 238 0 0 0 0 +IS 239 0 0 0 0 +IS 240 0 0 0 0 +IS 241 0 0 0 0 +IS 242 0 0 0 0 +IS 243 0 0 0 0 +IS 244 0 0 0 0 +IS 245 0 0 0 0 +IS 246 0 0 0 0 +IS 247 0 0 0 0 +IS 248 0 0 0 0 +IS 249 0 0 0 0 +IS 250 0 0 0 0 +IS 251 0 0 0 0 +IS 252 0 0 0 0 +IS 253 0 0 0 0 +IS 254 0 0 0 0 +IS 255 0 0 0 0 +IS 256 0 0 0 0 +IS 257 0 0 0 0 +IS 258 0 0 0 0 +IS 259 0 0 0 0 +IS 260 0 0 0 0 +IS 261 0 0 0 0 +IS 262 0 0 0 0 +IS 263 0 0 0 0 +IS 264 0 0 0 0 +IS 265 0 0 0 0 +IS 266 0 0 0 0 +IS 267 0 0 0 0 +IS 268 0 0 0 0 +IS 269 0 0 0 0 +IS 270 0 0 0 0 +IS 271 0 0 0 0 +IS 272 0 0 0 0 +IS 273 0 0 0 0 +IS 274 0 0 0 0 +IS 275 0 0 0 0 +IS 276 0 0 0 0 +IS 277 0 0 0 0 +IS 278 0 0 0 0 +IS 279 0 0 0 0 +IS 280 0 0 0 0 +IS 281 0 0 0 0 +IS 282 0 0 0 0 +IS 283 0 0 0 0 +IS 284 0 0 0 0 +IS 285 0 0 0 0 +IS 286 0 0 0 0 +IS 287 0 0 0 0 +IS 288 0 0 0 0 +IS 289 0 0 0 0 +IS 290 0 0 0 0 +IS 291 0 0 0 0 +IS 292 0 0 0 0 +IS 293 0 0 0 0 +IS 294 0 0 0 0 +IS 295 0 0 0 0 +IS 296 0 0 0 0 +IS 297 0 0 0 0 +IS 298 0 0 0 0 +IS 299 0 0 0 0 +IS 300 0 0 0 0 +IS 301 0 0 0 0 +IS 302 0 0 0 0 +IS 303 0 0 0 0 +IS 304 0 0 0 0 +IS 305 0 0 0 0 +IS 306 0 0 0 0 +IS 307 0 0 0 0 +IS 308 0 0 0 0 +IS 309 0 0 0 0 +IS 310 0 0 0 0 +IS 311 1 1 0 0 +IS 312 0 0 0 0 +IS 313 0 0 0 0 +IS 314 0 0 0 0 +IS 315 0 0 0 0 +IS 316 0 0 0 0 +IS 317 0 0 0 0 +IS 318 0 0 0 0 +IS 319 0 0 0 0 +IS 320 0 0 0 0 +IS 321 0 0 0 0 +IS 322 0 0 0 0 +IS 323 0 0 0 0 +IS 324 0 0 0 0 +IS 325 0 0 0 0 +IS 326 0 0 0 0 +IS 327 0 0 0 0 +IS 328 0 0 0 0 +IS 329 0 0 0 0 +IS 330 0 0 0 0 +IS 331 0 0 0 0 +IS 332 0 0 0 0 +IS 333 0 0 0 0 +IS 334 0 0 0 0 +IS 335 0 0 0 0 +IS 336 0 0 0 0 +IS 337 0 0 0 0 +IS 338 0 0 0 0 +IS 339 0 0 0 0 +IS 340 0 0 0 0 +IS 341 0 0 0 0 +IS 342 0 0 0 0 +IS 343 0 0 0 0 +IS 344 0 0 0 0 +IS 345 1 1 0 0 +IS 346 0 0 0 0 +IS 347 1 1 0 0 +IS 348 0 0 0 0 +IS 349 0 0 0 0 +IS 350 0 0 0 0 +IS 351 0 0 0 0 +IS 352 0 0 0 0 +IS 353 0 0 0 0 +IS 354 0 0 0 0 +IS 355 0 0 0 0 +IS 356 0 0 0 0 +IS 357 0 0 0 0 +IS 358 0 0 0 0 +IS 359 0 0 0 0 +IS 360 0 0 0 0 +IS 361 0 0 0 0 +IS 362 0 0 0 0 +IS 363 0 0 0 0 +IS 364 1 1 0 0 +IS 365 0 0 0 0 +IS 366 0 0 0 0 +IS 367 0 0 0 0 +IS 368 0 0 0 0 +IS 369 0 0 0 0 +IS 370 1 1 0 0 +IS 371 1 1 0 0 +IS 372 0 0 0 0 +IS 373 0 0 0 0 +IS 374 0 0 0 0 +IS 375 0 0 0 0 +IS 376 0 0 0 0 +IS 377 0 0 0 0 +IS 378 2 2 0 0 +IS 379 0 0 0 0 +IS 380 0 0 0 0 +IS 381 0 0 0 0 +IS 382 0 0 0 0 +IS 383 0 0 0 0 +IS 384 0 0 0 0 +IS 385 0 0 0 0 +IS 386 0 0 0 0 +IS 387 1 1 0 0 +IS 388 1 1 0 0 +IS 389 0 0 0 0 +IS 390 1 1 0 0 +IS 391 0 0 0 0 +IS 392 0 0 0 0 +IS 393 0 0 0 0 +IS 394 1 1 0 0 +IS 395 1 1 0 0 +IS 396 1 1 0 0 +IS 397 0 0 0 0 +IS 398 1 1 0 0 +IS 399 0 0 0 0 +IS 400 1 1 0 0 +IS 401 0 0 0 0 +IS 402 0 0 0 0 +IS 403 1 1 0 0 +IS 404 0 0 0 0 +IS 405 0 0 0 0 +IS 406 0 0 0 0 +IS 407 1 1 0 0 +IS 408 1 1 0 0 +IS 409 3 3 0 0 +IS 410 4 4 0 0 +IS 411 0 0 0 0 +IS 412 0 0 0 0 +IS 413 1 1 0 0 +IS 414 1 1 0 0 +IS 415 1 1 0 0 +IS 416 1 1 0 0 +IS 417 0 0 0 0 +IS 418 1 1 0 0 +IS 419 0 0 0 0 +IS 420 1 1 0 0 +IS 421 1 1 0 0 +IS 422 0 0 0 0 +IS 423 0 0 0 0 +IS 424 3 3 0 0 +IS 425 3 3 0 0 +IS 426 0 0 0 0 +IS 427 1 1 0 0 +IS 428 1 1 0 0 +IS 429 0 0 0 0 +IS 430 0 0 0 0 +IS 431 4 4 0 0 +IS 432 1 1 0 0 +IS 433 1 1 0 0 +IS 434 3 3 0 0 +IS 435 1 1 0 0 +IS 436 1 1 0 0 +IS 437 0 0 0 0 +IS 438 1 1 0 0 +IS 439 0 0 0 0 +IS 440 3 3 0 0 +IS 441 1 1 0 0 +IS 442 4 4 0 0 +IS 443 3 3 0 0 +IS 444 1 1 0 0 +IS 445 4 4 0 0 +IS 446 1 1 0 0 +IS 447 1 1 0 0 +IS 448 1 1 0 0 +IS 449 2 2 0 0 +IS 450 3 3 0 0 +IS 451 5 5 0 0 +IS 452 2 2 0 0 +IS 453 3 3 0 0 +IS 454 4 4 0 0 +IS 455 7 7 0 0 +IS 456 3 3 0 0 +IS 457 4 4 0 0 +IS 458 2 2 0 0 +IS 459 3 3 0 0 +IS 460 2 2 0 0 +IS 461 2 2 0 0 +IS 462 2 2 0 0 +IS 463 2 2 0 0 +IS 464 1 1 0 0 +IS 465 6 6 0 0 +IS 466 4 4 0 0 +IS 467 6 6 0 0 +IS 468 1 1 0 0 +IS 469 1 1 0 0 +IS 470 1 1 0 0 +IS 471 3 3 0 0 +IS 472 8 8 0 0 +IS 473 4 4 0 0 +IS 474 2 2 0 0 +IS 475 2 2 0 0 +IS 476 4 4 0 0 +IS 477 6 6 0 0 +IS 478 3 3 0 0 +IS 479 6 6 0 0 +IS 480 7 7 0 0 +IS 481 3 3 0 0 +IS 482 2 2 0 0 +IS 483 1 1 0 0 +IS 484 6 6 0 0 +IS 485 6 6 0 0 +IS 486 6 6 0 0 +IS 487 2 2 0 0 +IS 488 4 4 0 0 +IS 489 3 3 0 0 +IS 490 6 6 0 0 +IS 491 3 3 0 0 +IS 492 5 5 0 0 +IS 493 2 2 0 0 +IS 494 4 4 0 0 +IS 495 0 0 0 0 +IS 496 7 7 0 0 +IS 497 5 5 0 0 +IS 498 4 4 0 0 +IS 499 6 6 0 0 +IS 500 0 0 0 0 +IS 501 2 2 0 0 +IS 502 2 2 0 0 +IS 503 4 4 0 0 +IS 504 3 3 0 0 +IS 505 3 3 0 0 +IS 506 2 2 0 0 +IS 507 4 4 0 0 +IS 508 3 3 0 0 +IS 509 1 1 0 0 +IS 510 7 7 0 0 +IS 511 2 2 0 0 +IS 512 3 3 0 0 +IS 513 7 7 0 0 +IS 514 4 4 0 0 +IS 515 2 2 0 0 +IS 516 2 2 0 0 +IS 517 1 1 0 0 +IS 518 0 0 0 0 +IS 519 2 2 0 0 +IS 520 2 2 0 0 +IS 521 5 5 0 0 +IS 522 6 6 0 0 +IS 523 4 4 0 0 +IS 524 2 2 0 0 +IS 525 1 1 0 0 +IS 526 5 5 0 0 +IS 527 6 6 0 0 +IS 528 0 0 0 0 +IS 529 5 5 0 0 +IS 530 7 7 0 0 +IS 531 4 4 0 0 +IS 532 5 5 0 0 +IS 533 1 1 0 0 +IS 534 5 5 0 0 +IS 535 3 3 0 0 +IS 536 2 2 0 0 +IS 537 3 3 0 0 +IS 538 2 2 0 0 +IS 539 4 4 0 0 +IS 540 2 2 0 0 +IS 541 2 2 0 0 +IS 542 3 3 0 0 +IS 543 4 4 0 0 +IS 544 2 2 0 0 +IS 545 1 1 0 0 +IS 546 2 2 0 0 +IS 547 2 2 0 0 +IS 548 3 3 0 0 +IS 549 5 5 0 0 +IS 550 1 1 0 0 +IS 551 0 0 0 0 +IS 552 0 0 0 0 +IS 553 4 4 0 0 +IS 554 1 1 0 0 +IS 555 5 5 0 0 +IS 556 5 5 0 0 +IS 557 2 2 0 0 +IS 558 2 2 0 0 +IS 559 3 3 0 0 +IS 560 1 1 0 0 +IS 561 1 1 0 0 +IS 562 4 4 0 0 +IS 563 1 1 0 0 +IS 564 1 1 0 0 +IS 565 0 0 0 0 +IS 566 1 1 0 0 +IS 567 1 1 0 0 +IS 568 0 0 0 0 +IS 569 2 2 0 0 +IS 570 1 1 0 0 +IS 571 2 2 0 0 +IS 572 4 4 0 0 +IS 573 0 0 0 0 +IS 574 0 0 0 0 +IS 575 0 0 0 0 +IS 576 1 1 0 0 +IS 577 2 2 0 0 +IS 578 1 1 0 0 +IS 579 2 2 0 0 +IS 580 0 0 0 0 +IS 581 1 1 0 0 +IS 582 0 0 0 0 +IS 583 1 1 0 0 +IS 584 2 2 0 0 +IS 585 0 0 0 0 +IS 586 3 3 0 0 +IS 587 0 0 0 0 +IS 588 0 0 0 0 +IS 589 0 0 0 0 +IS 590 0 0 0 0 +IS 591 0 0 0 0 +IS 592 0 0 0 0 +IS 593 0 0 0 0 +IS 594 2 2 0 0 +IS 595 0 0 0 0 +IS 596 0 0 0 0 +IS 597 1 1 0 0 +IS 598 0 0 0 0 +IS 599 0 0 0 0 +IS 600 1 1 0 0 +IS 601 1 1 0 0 +IS 602 0 0 0 0 +IS 603 0 0 0 0 +IS 604 0 0 0 0 +IS 605 1 1 0 0 +IS 606 0 0 0 0 +IS 607 1 1 0 0 +IS 608 0 0 0 0 +IS 609 0 0 0 0 +IS 610 0 0 0 0 +IS 611 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 70 1000 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 0 1 +# 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) +IC 8 0 0 1 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 42 +COV [2-2] 2 59 +COV [3-3] 3 73 +COV [4-4] 4 98 +COV [5-5] 5 128 +COV [6-6] 6 142 +COV [7-7] 7 226 +COV [8-8] 8 241 +COV [9-9] 9 281 +COV [10-10] 10 400 +COV [11-11] 11 450 +COV [12-12] 12 444 +COV [13-13] 13 433 +COV [14-14] 14 423 +COV [15-15] 15 392 +COV [16-16] 16 434 +COV [17-17] 17 294 +COV [18-18] 18 229 +COV [19-19] 19 143 +COV [20-20] 20 143 +COV [21-21] 21 149 +COV [22-22] 22 90 +COV [23-23] 23 41 +COV [24-24] 24 14 +# 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 +GCD 0.0 50.000 0.000 0.000 0.000 0.000 0.000 +GCD 44.0 75.000 14.875 14.875 14.875 14.875 14.875 +GCD 46.0 100.000 11.900 11.900 11.900 11.900 11.900 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2/cov.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/cov.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,24 @@ +[1-1] 1 42 +[2-2] 2 59 +[3-3] 3 73 +[4-4] 4 98 +[5-5] 5 128 +[6-6] 6 142 +[7-7] 7 226 +[8-8] 8 241 +[9-9] 9 281 +[10-10] 10 400 +[11-11] 11 450 +[12-12] 12 444 +[13-13] 13 433 +[14-14] 14 423 +[15-15] 15 392 +[16-16] 16 434 +[17-17] 17 294 +[18-18] 18 229 +[19-19] 19 143 +[20-20] 20 143 +[21-21] 21 149 +[22-22] 22 90 +[23-23] 23 41 +[24-24] 24 14 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2/gcc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/gcc.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,70 @@ +1 21.50 23.30 24.50 30.70 +2 21.10 22.20 22.50 34.20 +3 22.20 20.50 26.80 30.50 +4 24.40 21.50 21.50 32.60 +5 23.50 21.10 25.60 29.80 +6 26.30 21.80 20.40 31.50 +7 25.40 20.50 22.00 32.10 +8 23.90 19.20 27.00 29.90 +9 23.70 22.70 22.00 31.60 +10 22.50 22.00 24.10 31.40 +11 22.40 21.50 22.10 34.00 +12 25.20 18.00 24.50 32.30 +13 23.70 20.80 21.70 33.80 +14 24.60 23.00 22.40 30.00 +15 25.50 22.30 22.50 29.70 +16 24.10 21.40 23.60 30.90 +17 24.30 21.00 23.90 30.80 +18 24.40 22.10 22.70 30.80 +19 25.60 20.50 24.70 29.20 +20 25.80 19.60 22.00 32.60 +21 23.20 22.90 23.00 30.90 +22 23.90 22.70 22.60 30.80 +23 25.80 21.30 22.40 30.50 +24 23.50 22.00 22.70 31.80 +25 22.40 21.80 23.10 32.70 +26 22.90 19.90 24.30 32.90 +27 23.10 22.10 24.20 30.60 +28 23.50 22.10 22.90 31.50 +29 24.40 21.80 21.30 32.50 +30 21.90 22.50 22.60 33.00 +31 23.10 20.90 24.20 31.80 +32 24.60 22.10 23.60 29.70 +33 22.80 21.10 22.00 34.10 +34 21.70 22.10 23.60 32.60 +35 24.30 23.20 20.60 31.90 +36 21.60 22.70 24.50 31.20 +37 22.20 23.50 22.20 32.10 +38 24.10 20.80 22.00 33.10 +39 22.20 21.10 26.80 29.90 +40 21.80 24.00 22.90 31.30 +41 25.10 22.90 23.10 28.90 +42 25.50 22.70 22.20 29.60 +43 22.60 23.00 24.10 30.30 +44 21.70 21.60 24.20 32.50 +45 21.80 22.70 21.20 34.30 +46 22.80 22.00 23.80 31.40 +47 23.70 22.30 23.90 30.10 +48 24.30 21.70 24.80 29.20 +49 23.90 22.00 22.90 31.20 +50 23.50 22.40 22.80 31.30 +51 23.30 20.40 24.70 31.60 +52 23.30 20.20 25.10 31.40 +53 23.70 22.00 22.30 32.00 +54 23.30 21.30 25.40 30.00 +55 25.30 21.40 22.60 30.70 +56 24.40 24.10 19.20 32.30 +57 22.00 21.50 24.50 32.00 +58 24.90 21.20 24.20 29.70 +59 24.10 21.70 24.50 29.70 +60 24.80 20.90 25.10 29.20 +61 21.30 21.60 28.10 29.00 +62 23.80 21.80 21.70 32.70 +63 23.30 22.80 23.50 30.40 +64 24.00 21.40 23.50 31.10 +65 24.40 22.80 22.50 30.30 +66 24.70 22.30 21.40 31.60 +67 22.40 21.10 24.60 31.90 +68 24.60 22.90 20.60 31.90 +69 22.40 23.00 23.10 31.50 +70 23.50 19.50 23.90 33.10 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2/gcd.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/gcd.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,3 @@ +0.0 50.000 0.000 0.000 0.000 0.000 0.000 +44.0 75.000 14.875 14.875 14.875 14.875 14.875 +46.0 100.000 11.900 11.900 11.900 11.900 11.900 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2/gcf.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/gcf.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,24 @@ +14.82 0 +31.16 2 +33.42 6 +34.92 4 +36.18 6 +37.44 12 +38.94 28 +40.45 34 +41.96 37 +43.47 46 +44.72 55 +45.98 57 +47.49 68 +48.99 60 +50.50 27 +52.01 18 +53.52 15 +54.77 9 +56.03 4 +57.54 3 +59.05 2 +60.55 4 +62.06 0 +63.32 1 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2/gcl.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/gcl.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,23 @@ +14.07 0 +28.89 1 +30.40 3 +31.91 1 +33.42 2 +34.92 4 +36.18 8 +37.44 16 +38.94 31 +40.45 40 +41.96 39 +43.47 55 +44.72 46 +45.98 61 +47.49 53 +48.99 50 +50.50 32 +52.01 23 +53.52 11 +54.77 9 +56.03 8 +57.54 3 +61.06 1 diff -r 000000000000 -r cd6eb75c9819 test-data/samtools_stats_out2/sn.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out2/sn.tab Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,31 @@ +raw total sequences: 1000 +filtered sequences: 0 +sequences: 1000 +is sorted: 1 +1st fragments: 500 +last fragments: 500 +reads mapped: 972 +reads mapped and paired: 954 # paired-end technology bit set + both mates mapped +reads unmapped: 28 +reads properly paired: 0 # proper-pair bit set +reads paired: 1000 # paired-end technology bit set +reads duplicated: 0 # PCR or optical duplicate bit set +reads MQ0: 0 # mapped and MQ=0 +reads QC failed: 0 +non-primary alignments: 0 +total length: 70000 # ignores clipping +bases mapped: 68040 # ignores clipping +bases mapped (cigar): 68040 # more accurate +bases trimmed: 0 +bases duplicated: 0 +mismatches: 1237 # from NM fields +error rate: 1.818048e-02 # mismatches / bases mapped (cigar) +average length: 70 +maximum length: 70 +average quality: 17.0 +insert size average: 495.1 +insert size standard deviation: 48.9 +inward oriented pairs: 477 +outward oriented pairs: 0 +pairs with other orientation: 0 +pairs on different chromosomes: 0 diff -r 000000000000 -r cd6eb75c9819 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa diff -r 000000000000 -r cd6eb75c9819 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r cd6eb75c9819 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Oct 20 14:56:49 2014 -0400 @@ -0,0 +1,6 @@ + + + + + +