# HG changeset patch # User iuc # Date 1538053510 14400 # Node ID 95a7ddf617e771d1e703f38618244be2d6ec797e # Parent 24c5d43cb545ce9cc36e0f7b49f71f7986841cf8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4 diff -r 24c5d43cb545 -r 95a7ddf617e7 macros.xml --- a/macros.xml Tue May 09 11:19:01 2017 -0400 +++ b/macros.xml Thu Sep 27 09:05:10 2018 -0400 @@ -1,11 +1,131 @@ - samtools + samtools - 1.3.1 + 1.9 + #set $flags = sum(map(int, str($filter).split(','))) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$ + + + + + + + + + @@ -49,21 +169,4 @@ - ------ - -.. class:: warningmark - -**No options available? How to re-detect metadata** - -If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: - -1. Click on the **pencil** icon adjacent to the dataset in the history -2. A new menu will appear in the center pane of the interface -3. Click **Datatype** tab -4. Set **New Type** to **BAM** -5. Click **Save** - -The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - diff -r 24c5d43cb545 -r 95a7ddf617e7 samtools_stats.xml --- a/samtools_stats.xml Tue May 09 11:19:01 2017 -0400 +++ b/samtools_stats.xml Thu Sep 27 09:05:10 2018 -0400 @@ -1,164 +1,103 @@ - + generate statistics for BAM dataset macros.xml - + + gnuplot + '${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 $outputs_to_split: - && echo "# Summary Numbers" > 'split/Summary numbers.tab' && - echo "" >> 'split/Summary numbers.tab' && - if grep -q ^SN '${output}'; then - grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab'; - fi + #if str($most_inserts): + --most-inserts ${most_inserts} #end if - - #if 'ffq' in $outputs_to_split: - && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' && - if grep -q ^FFQ '${output}'; then - grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab'; - fi - #end if - - #if 'lfq' in $outputs_to_split: - && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' && - if grep -q ^LFQ '${output}'; then - grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab'; - fi - #end if - - #if 'mpc' in $outputs_to_split: - && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' && - if grep -q ^MPC '${output}'; then - grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab'; - fi - #end if - - #if 'gcf' in $outputs_to_split: - && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' && - if grep -q ^GCF '${output}'; then - grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab'; - fi + #if str($trim_quality): + --trim-quality ${trim_quality} #end if - #if 'gcl' in $outputs_to_split: - && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' && - if grep -q ^GCL '${output}'; then - grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab'; - fi - #end if - - #if 'gcc' in $outputs_to_split: - && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' && - if grep -q ^GCC '${output}'; then - grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab'; - fi + #if $reffa != None: + --ref-seq '$reffa' #end if - - #if 'is' in $outputs_to_split: - && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' && - if grep -q ^IS '${output}'; then - grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab'; - fi + ## TODO currently not implemented in Galaxy + ## generates STR_VALUE.bamstat where STR is given by -P and VALUE is a value of the TAG given by -S + ## needs some discover data sets action... + ## -P, --split-prefix STR + ## -S, --split TAG + $sparse + @REGIONS_FILE@ + $remove_overlaps + #if str($cov_threshold): + -g $cov_threshold #end if + infile + @REGIONS_MANUAL@ + > '$output' - #if 'rl' in $outputs_to_split: - && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' && - if grep -q ^RL '${output}'; then - grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab'; - fi + #if $cond_plot.select_plot=='yes': + && plot-bamstats '$output' $cond_plot.log -p '${html_file.files_path}'/ + && mv '${html_file.files_path}'/index.html '${html_file}' #end if - #if 'id' in $outputs_to_split: - && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' && - if grep -q ^ID '${output}'; then - grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab'; - fi - #end if - - #if 'ic' in $outputs_to_split: - && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' && - if grep -q ^IC '${output}'; then - grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab'; - fi + #if $split_output_cond.split_output_selector == "yes": + #set outputs_to_split = str($split_output_cond.generate_tables).split(',') + && mkdir split + #for s in str($split_output_cond.generate_tables).split(','): + && name=`cat '$output' | grep '\^$s' | cut -d'.' -f 1 | sed 's/^# //'` + && awk '/\^/{out=0} /\^$s/{out=1} {if(out==1){print $0}}' '$output' | sed 's/Use `grep .*` to extract this part.//' | sed 's/$s\t//' > "split/\$name.tab" + #end for #end if - - #if 'cov' in $outputs_to_split: - && echo "# Coverage distribution" > 'split/Coverage distribution.tab' && - if grep -q ^COV '${output}'; then - grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab'; - fi - #end if - - #if 'gcd' in $outputs_to_split: - && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' && - if grep -q ^GCD '${output}'; then - grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab'; - fi - #end if - #end if - ]]> + ]]> - - - - - - + + + + + + + + + + + + + + + @@ -166,19 +105,23 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + @@ -189,111 +132,251 @@ - - - - - - - - - - - + - - - - - - - - - - - + - - + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + - - - - - - - - - - - - - - - - + - - - + + split_output_cond['split_output_selector'] == 'no' + + + + split_output_cond['split_output_selector'] == 'yes' + + + cond_plot['select_plot']=='yes' + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + + + + + 0 (%): 100.00 +# First Fragment Qualities. 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 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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +# Last Fragment Qualities. 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 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +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 +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 +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 +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 +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 +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 +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 +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 +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 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 19.85 0 +GCF 44.72 1 +GCF 54.77 4 +GCF 64.82 2 +GCF 74.87 4 +GCF 84.92 3 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 19.85 0 +GCL 44.72 2 +GCL 59.80 3 +GCL 74.87 4 +# 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 [%] +GCC 1 19.23 42.31 15.38 23.08 0.00 0.00 +GCC 2 19.23 19.23 46.15 15.38 0.00 0.00 +GCC 3 23.08 38.46 19.23 19.23 0.00 0.00 +GCC 4 23.08 23.08 38.46 15.38 0.00 0.00 +GCC 5 11.54 38.46 26.92 23.08 0.00 0.00 +GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 +GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 +GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 +GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 +GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 +# 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 [%] +FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 +FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 +FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 +FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 +FBC 5 14.29 35.71 35.71 14.29 0.00 0.00 +FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 +FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 +FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 +FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 +FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 +# 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 [%] +LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 +LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 +LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 +LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 +LBC 5 8.33 41.67 16.67 33.33 0.00 0.00 +LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 +LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 +LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 +LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 +LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 +# 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 +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 12 12 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 10 26 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 10 14 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 10 12 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +# 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) +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [2-2] 2 1 +COV [3-3] 3 2 +COV [4-4] 4 2 +COV [5-5] 5 23 +COV [6-6] 6 13 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/11.stats.g4.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.stats.g4.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,166 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK cb2d2d82 bcd83869 62ec814e +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 26 +SN filtered sequences: 0 +SN sequences: 26 +SN is sorted: 1 +SN 1st fragments: 14 +SN last fragments: 12 +SN reads mapped: 26 +SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 24 # proper-pair bit set +SN reads paired: 26 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 1 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 260 # ignores clipping +SN total first fragment length: 140 # ignores clipping +SN total last fragment length: 120 # ignores clipping +SN bases mapped: 260 # ignores clipping +SN bases mapped (cigar): 206 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 0 # from NM fields +SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) +SN average length: 10 +SN average first fragment length: 10 +SN average last fragment length: 10 +SN maximum length: 10 +SN maximum first fragment length: 10 +SN maximum last fragment length: 10 +SN average quality: 13.1 +SN insert size average: 34.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 12 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 1 +SN percentage of properly paired reads (%): 92.3 +SN bases inside the target: 42 +SN percentage of target genome with coverage > 4 (%): 85.71 +# First Fragment Qualities. 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 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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +# Last Fragment Qualities. 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 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +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 +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 +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 +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 +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 +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 +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 +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 +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 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 19.85 0 +GCF 44.72 1 +GCF 54.77 4 +GCF 64.82 2 +GCF 74.87 4 +GCF 84.92 3 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 19.85 0 +GCL 44.72 2 +GCL 59.80 3 +GCL 74.87 4 +# 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 [%] +GCC 1 19.23 42.31 15.38 23.08 0.00 0.00 +GCC 2 19.23 19.23 46.15 15.38 0.00 0.00 +GCC 3 23.08 38.46 19.23 19.23 0.00 0.00 +GCC 4 23.08 23.08 38.46 15.38 0.00 0.00 +GCC 5 11.54 38.46 26.92 23.08 0.00 0.00 +GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 +GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 +GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 +GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 +GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 +# 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 [%] +FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 +FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 +FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 +FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 +FBC 5 14.29 35.71 35.71 14.29 0.00 0.00 +FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 +FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 +FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 +FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 +FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 +# 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 [%] +LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 +LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 +LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 +LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 +LBC 5 8.33 41.67 16.67 33.33 0.00 0.00 +LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 +LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 +LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 +LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 +LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 +# 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 +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 12 12 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 10 26 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 10 14 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 10 12 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +# 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) +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 1 +COV [2-2] 2 1 +COV [3-3] 3 2 +COV [4-4] 4 2 +COV [5-5] 5 23 +COV [6-6] 6 13 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/11.stats.targets --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11.stats.targets Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,24 @@ +# The MIT License +# +# Copyright (c) 2014 Genome Research Ltd. +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +ref1 10 24 +ref1 30 46 +ref1 39 56 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/11_target.bam Binary file test-data/11_target.bam has changed diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/11_target.bam.bai Binary file test-data/11_target.bam.bai has changed diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/11_target.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/11_target.sam Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,59 @@ +@HD VN:1.4 SO:coordinate +@RG ID:s1_a_1 LB:1 SM:s1 +@RG ID:grp1 DS:Group 1 LB:Library 1 SM:Sample +@RG ID:grp2 DS:Group 2 LB:Library 2 SM:Sample +@RG ID:grp3 DS:Group 3 SM:Sample +@PG ID:prog1 PN:emacs CL:emacs VN:23.1.1 +@CO The MIT License +@CO +@CO Copyright (c) 2014 Genome Research Ltd. +@CO +@CO Permission is hereby granted, free of charge, to any person obtaining a copy +@CO of this software and associated documentation files (the "Software"), to deal +@CO in the Software without restriction, including without limitation the rights +@CO to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +@CO copies of the Software, and to permit persons to whom the Software is +@CO furnished to do so, subject to the following conditions: +@CO +@CO The above copyright notice and this permission notice shall be included in +@CO all copies or substantial portions of the Software. +@CO +@CO THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +@CO IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +@CO FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@CO AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +@CO LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +@CO OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +@CO THE SOFTWARE. +@SQ SN:alpha LN:100 +@SQ SN:ref1 LN:56 M5:08c04d512d4797d9ba2a156c1daba468 +@SQ SN:ref2 LN:60 M5:7c35feac7036c1cdef3bee0cc4b21437 +@SQ SN:ref3_unused LN:70 M5:5fdd18c2c6ecac4838996d029bf395b5 +r1 99 alpha 1 40 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * NM:i:0 RG:Z:s1_a_1 +r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * NM:i:0 RG:Z:s1_a_1 +ref1_grp1_p001 99 ref1 1 0 10M = 25 34 CGAGCTCGGT !!!!!!!!!! RG:Z:grp1 BC:Z:ACGT H0:i:1 aa:A:! ab:A:~ fa:f:3.14159 za:Z:Hello world! ha:H:DEADBEEF ba:B:c,-128,0,127 bb:B:C,0,127,255 bc:B:s,-32768,0,32767 bd:B:S,0,32768,65535 be:B:i,-2147483648,0,2147483647 bf:B:I,0,2147483648,4294967295 bg:B:f,2.71828,6.626e-34,2.9979e+09 NM:i:0 MD:Z:10 +ref1_grp2_p001 99 ref1 3 1 10M = 27 34 AGCTCGGTAC """""""""" RG:Z:grp2 BC:Z:TGCA H0:i:1 aa:A:A ab:A:Z fa:f:6.67e-11 za:Z:!"$%^&*() ha:H:CAFE NM:i:0 MD:Z:10 +ref1_grp1_p002 99 ref1 5 2 10M = 29 34 CTCGGTACCC ########## RG:Z:grp1 BC:Z:AATTCCGG H0:i:1 aa:A:a ab:A:z fa:f:4.3597e-18 za:Z:Another string ha:H:2000AD NM:i:0 MD:Z:10 +ref1_grp2_p002 99 ref1 7 3 10M = 31 34 CGGTACCCGG $$$$$$$$$$ fa:f:6.022e+23 RG:Z:grp2 NM:i:0 MD:Z:10 +ref1_grp1_p003 99 ref1 9 4 10M = 33 34 GTACCCGGGG %%%%%%%%%% fa:f:1.66e-27 RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p003 99 ref1 11 5 10M = 35 34 ACCCGGGGAT &&&&&&&&&& RG:Z:grp2 ia:i:4294967295 NM:i:0 MD:Z:10 +ref1_grp1_p004 99 ref1 13 6 10M = 37 34 CCGGGGATCC '''''''''' fa:f:1.38e-23 za:Z:xRG:Z:grp2 RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p004 99 ref1 15 7 10M = 39 34 GGGGATCCTC (((((((((( RG:Z:grp2 ia:i:-2147483648 NM:i:0 MD:Z:10 +ref1_grp1_p005 99 ref1 17 8 10M = 41 34 GGATCCTCTA )))))))))) RG:Z:grp1 ia:i:40000 NM:i:0 MD:Z:10 +ref1_grp2_p005 99 ref1 19 9 10M = 43 34 ATCCTCTAGA ********** RG:Z:grp2 ia:i:-1000 NM:i:0 MD:Z:10 +ref1_grp1_p006 99 ref1 21 10 10M = 45 34 CCTCTAGAGT ++++++++++ RG:Z:grp1 ia:i:255 NM:i:0 MD:Z:10 +ref1_grp2_p006 99 ref1 23 11 10M = 47 34 TCTAGAGTCG ,,,,,,,,,, RG:Z:grp2 ia:i:-1 NM:i:0 MD:Z:10 +ref1_grp1_p001 147 ref1 25 12 10M = 1 -34 TAGAGTCGAC ---------- RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p001 147 ref1 27 13 10M = 3 -34 GAGTCGACCT .......... RG:Z:grp2 NM:i:0 MD:Z:10 +ref1_grp1_p002 147 ref1 29 14 10M = 5 -34 GTCGACCTGC ////////// RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p002 147 ref1 31 15 10M = 7 -34 CGACCTGCAG 0000000000 RG:Z:grp2 NM:i:0 MD:Z:10 +ref1_grp1_p003 147 ref1 33 16 10M = 9 -34 ACCTGCAGGC 1111111111 RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p003 147 ref1 35 17 10M = 11 -34 CTGCAGGCAT 2222222222 RG:Z:grp2 NM:i:0 MD:Z:10 +ref12_grp1_p001 97 ref1 36 50 10M ref2 2 0 TGCAGGCATG AAAAAAAAAA RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp1_p004 147 ref1 37 18 10M = 13 -34 GCAGGCATGC 3333333333 RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p004 147 ref1 39 19 10M = 15 -34 AGGCATGCAA 4444444444 RG:Z:grp2 NM:i:0 MD:Z:10 +ref1_grp1_p005 147 ref1 41 20 10M = 17 -34 GCATGCAAGC 5555555555 RG:Z:grp1 NM:i:0 MD:Z:10 +ref1_grp2_p005 147 ref1 43 21 10M = 19 -34 ATGCAAGCTT 6666666666 RG:Z:grp2 NM:i:0 MD:Z:10 +ref1_grp1_p006 147 ref1 45 22 10M = 21 -34 GCAAGCTTGA 7777777777 RG:Z:grp1 NM:i:0 MD:Z:10 +ref12_grp2_p001 97 ref1 46 50 10M ref2 12 0 CAAGCTTGAG AAAAAAAAAA RG:Z:grp2 NM:i:0 MD:Z:10 +ref1_grp2_p006 147 ref1 47 23 10M = 23 -34 AAGCTTGAGT 8888888888 RG:Z:grp2 NM:i:0 MD:Z:10 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12.2reads.nooverlap.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12.2reads.nooverlap.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,740 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 5b31676a b0edee94 471895da +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 2 +SN filtered sequences: 0 +SN sequences: 2 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 1 +SN reads mapped: 2 +SN reads mapped and paired: 2 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 2 # proper-pair bit set +SN reads paired: 2 # 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: 200 # ignores clipping +SN total first fragment length: 100 # ignores clipping +SN total last fragment length: 100 # ignores clipping +SN bases mapped: 200 # ignores clipping +SN bases mapped (cigar): 168 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 6 # from NM fields +SN error rate: 3.571429e-02 # mismatches / bases mapped (cigar) +SN average length: 100 +SN average first fragment length: 100 +SN average last fragment length: 100 +SN maximum length: 100 +SN maximum first fragment length: 100 +SN maximum last fragment length: 100 +SN average quality: 36.2 +SN insert size average: 165.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +SN bases inside the target: 166 +SN percentage of target genome with coverage > 0 (%): 99.40 +# First Fragment Qualities. 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 10 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 17 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 21 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 1 0 0 0 0 0 0 +FFQ 22 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 1 0 0 0 0 0 +FFQ 23 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 1 0 0 0 0 +FFQ 24 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 1 0 0 0 0 0 +FFQ 25 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 1 0 0 0 0 0 0 0 +FFQ 26 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 1 0 0 0 0 0 0 0 +FFQ 27 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 1 0 0 0 0 0 +FFQ 28 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 1 0 0 0 0 +FFQ 29 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 1 0 0 0 0 0 0 0 0 +FFQ 30 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 1 0 0 0 0 0 +FFQ 31 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 1 0 0 0 0 0 +FFQ 32 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 1 0 0 0 0 0 +FFQ 33 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 1 0 0 0 0 0 +FFQ 34 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 1 0 0 0 0 +FFQ 35 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 40 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 43 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 45 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 48 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 51 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 1 0 0 0 0 +FFQ 52 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 1 0 0 0 0 +FFQ 53 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 1 0 0 0 0 0 +FFQ 54 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 1 0 0 0 0 +FFQ 55 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 57 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 1 0 0 0 0 0 0 +LFQ 93 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 1 0 0 0 0 0 0 0 +LFQ 94 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 1 0 0 0 0 0 0 +LFQ 95 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 1 0 0 0 0 0 +LFQ 96 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 1 0 0 0 0 0 0 0 +LFQ 97 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 1 0 0 0 0 0 0 0 0 +LFQ 98 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 1 0 0 0 0 0 +LFQ 99 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 100 0 0 0 0 0 0 1 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 17.34 0 +GCF 35.18 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.36 0 +GCL 43.22 1 +# 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 [%] +GCC 1 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 2 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 3 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 4 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 5 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 6 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 7 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 8 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 9 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 10 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 11 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 12 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 13 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 14 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 15 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 16 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 17 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 18 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 19 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 20 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 21 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 22 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 23 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 24 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 25 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 26 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 27 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 28 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 29 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 30 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 31 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 32 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 33 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 34 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 36 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 37 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 38 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 39 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 40 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 41 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 42 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 43 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 44 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 45 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 46 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 47 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 48 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 49 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 50 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 51 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 52 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 53 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 54 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 55 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 56 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 57 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 58 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 59 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 60 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 61 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 62 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 63 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 64 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 65 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 66 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 67 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 68 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 69 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 70 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 71 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 72 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 73 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 74 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 75 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 76 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 77 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 78 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 79 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 80 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 81 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 82 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 83 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 84 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 85 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 86 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 87 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 88 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 89 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 90 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 91 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 92 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 93 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 94 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 95 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 96 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 97 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 98 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 99 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# 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 [%] +FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 3 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 5 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 6 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 7 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 8 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 9 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 10 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 11 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 12 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 13 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 15 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 16 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 17 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 18 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 19 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 21 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 22 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 23 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 24 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 25 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 26 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 27 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 28 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 29 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 30 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 31 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 32 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 36 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 37 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 38 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 39 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 40 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 41 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 42 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 43 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 44 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 45 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 46 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 47 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 48 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 49 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 50 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 51 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 52 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 53 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 54 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 55 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 57 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 58 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 59 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 60 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 61 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 62 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 63 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 64 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 65 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 66 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 67 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 68 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 69 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 70 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 71 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 72 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 73 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 74 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 75 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 76 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 77 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 78 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 79 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 80 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 81 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 82 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 83 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 84 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 85 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 86 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 87 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 88 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 89 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 90 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 91 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 92 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 93 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 94 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 95 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 96 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 97 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 98 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# 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 [%] +LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 2 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 3 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 5 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 8 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 11 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 12 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 13 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 16 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 17 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 18 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 19 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 20 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 21 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 26 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 27 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 28 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 29 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 30 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 32 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 33 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 36 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 37 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 38 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 39 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 40 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 41 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 42 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 43 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 44 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 45 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 46 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 47 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 48 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 49 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 50 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 51 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 52 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 53 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 54 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 55 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 57 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 58 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 59 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 60 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 61 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 62 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 63 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 64 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 65 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 66 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 67 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 68 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 69 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 70 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 71 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 72 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 73 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 74 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 75 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 76 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 77 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 78 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 79 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 80 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 81 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 82 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 83 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 84 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 85 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 86 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 87 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 88 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 89 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 90 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 91 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 92 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 93 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 94 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 95 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 96 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 97 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 98 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 99 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# 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 +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 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 100 2 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 100 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 100 1 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 2 0 1 +ID 3 1 0 +# 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 90 1 0 0 0 +IC 97 0 0 1 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 165 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12.2reads.overlap.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12.2reads.overlap.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,741 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 5b31676a b0edee94 471895da +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 2 +SN filtered sequences: 0 +SN sequences: 2 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 1 +SN reads mapped: 2 +SN reads mapped and paired: 2 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 2 # proper-pair bit set +SN reads paired: 2 # 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: 200 # ignores clipping +SN total first fragment length: 100 # ignores clipping +SN total last fragment length: 100 # ignores clipping +SN bases mapped: 200 # ignores clipping +SN bases mapped (cigar): 199 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 6 # from NM fields +SN error rate: 3.015075e-02 # mismatches / bases mapped (cigar) +SN average length: 100 +SN average first fragment length: 100 +SN average last fragment length: 100 +SN maximum length: 100 +SN maximum first fragment length: 100 +SN maximum last fragment length: 100 +SN average quality: 36.2 +SN insert size average: 165.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +SN bases inside the target: 166 +SN percentage of target genome with coverage > 0 (%): 99.40 +# First Fragment Qualities. 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 10 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 17 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 21 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 1 0 0 0 0 0 0 +FFQ 22 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 1 0 0 0 0 0 +FFQ 23 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 1 0 0 0 0 +FFQ 24 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 1 0 0 0 0 0 +FFQ 25 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 1 0 0 0 0 0 0 0 +FFQ 26 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 1 0 0 0 0 0 0 0 +FFQ 27 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 1 0 0 0 0 0 +FFQ 28 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 1 0 0 0 0 +FFQ 29 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 1 0 0 0 0 0 0 0 0 +FFQ 30 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 1 0 0 0 0 0 +FFQ 31 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 1 0 0 0 0 0 +FFQ 32 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 1 0 0 0 0 0 +FFQ 33 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 1 0 0 0 0 0 +FFQ 34 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 1 0 0 0 0 +FFQ 35 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 40 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 43 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 45 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 48 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 51 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 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0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 +LFQ 93 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 1 0 0 0 0 0 0 0 +LFQ 94 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 1 0 0 0 0 0 0 +LFQ 95 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 1 0 0 0 0 0 +LFQ 96 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 1 0 0 0 0 0 0 0 +LFQ 97 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 1 0 0 0 0 0 0 0 0 +LFQ 98 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 1 0 0 0 0 0 +LFQ 99 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 100 0 0 0 0 0 0 1 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 17.34 0 +GCF 35.18 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.36 0 +GCL 43.22 1 +# 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 [%] +GCC 1 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 2 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 3 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 4 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 5 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 6 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 7 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 8 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 9 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 10 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 11 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 12 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 13 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 14 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 15 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 16 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 17 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 18 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 19 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 20 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 21 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 22 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 23 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 24 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 25 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 26 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 27 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 28 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 29 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 30 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 31 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 32 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 33 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 34 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 36 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 37 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 38 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 39 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 40 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 41 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 42 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 43 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 44 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 45 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 46 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 47 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 48 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 49 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 50 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 51 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 52 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 53 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 54 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 55 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 56 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 57 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 58 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 59 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 60 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 61 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 62 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 63 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 64 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 65 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 66 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 67 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 68 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 69 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 70 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 71 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 72 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 73 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 74 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 75 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 76 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 77 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 78 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 79 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 80 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 81 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 82 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 83 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 84 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 85 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 86 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 87 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 88 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 89 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 90 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 91 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 92 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 93 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 94 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 95 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 96 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 97 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 98 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 99 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# 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 [%] +FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 3 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 5 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 6 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 7 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 8 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 9 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 10 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 11 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 12 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 13 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 15 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 16 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 17 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 18 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 19 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 21 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 22 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 23 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 24 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 25 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 26 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 27 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 28 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 29 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 30 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 31 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 32 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 36 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 37 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 38 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 39 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 40 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 41 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 42 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 43 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 44 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 45 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 46 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 47 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 48 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 49 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 50 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 51 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 52 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 53 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 54 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 55 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 57 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 58 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 59 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 60 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 61 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 62 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 63 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 64 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 65 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 66 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 67 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 68 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 69 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 70 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 71 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 72 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 73 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 74 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 75 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 76 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 77 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 78 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 79 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 80 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 81 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 82 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 83 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 84 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 85 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 86 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 87 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 88 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 89 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 90 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 91 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 92 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 93 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 94 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 95 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 96 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 97 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 98 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# 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 [%] +LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 2 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 3 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 5 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 8 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 11 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 12 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 13 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 16 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 17 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 18 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 19 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 20 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 21 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 26 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 27 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 28 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 29 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 30 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 32 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 33 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 36 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 37 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 38 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 39 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 40 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 41 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 42 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 43 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 44 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 45 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 46 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 47 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 48 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 49 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 50 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 51 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 52 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 53 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 54 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 55 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 57 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 58 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 59 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 60 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 61 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 62 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 63 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 64 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 65 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 66 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 67 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 68 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 69 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 70 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 71 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 72 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 73 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 74 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 75 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 76 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 77 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 78 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 79 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 80 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 81 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 82 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 83 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 84 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 85 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 86 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 87 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 88 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 89 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 90 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 91 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 92 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 93 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 94 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 95 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 96 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 97 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 98 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 99 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 100 100.00 0.00 0.00 0.00 0.00 0.00 +# 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 +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 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 100 2 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 100 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 100 1 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 2 0 1 +ID 3 1 0 +# 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 90 1 0 0 0 +IC 97 0 0 1 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 134 +COV [2-2] 2 31 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12.3reads.nooverlap.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12.3reads.nooverlap.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,758 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 09f8b87f 140798ec 2b989f07 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 3 +SN filtered sequences: 0 +SN sequences: 3 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 2 +SN reads mapped: 3 +SN reads mapped and paired: 3 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 3 # proper-pair bit set +SN reads paired: 3 # 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: 300 # ignores clipping +SN total first fragment length: 100 # ignores clipping +SN total last fragment length: 200 # ignores clipping +SN bases mapped: 300 # ignores clipping +SN bases mapped (cigar): 280 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 11 # from NM fields +SN error rate: 3.928572e-02 # mismatches / bases mapped (cigar) +SN average length: 100 +SN average first fragment length: 100 +SN average last fragment length: 100 +SN maximum length: 100 +SN maximum first fragment length: 100 +SN maximum last fragment length: 100 +SN average quality: 33.3 +SN insert size average: 180.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +SN bases inside the target: 180 +SN percentage of target genome with coverage > 0 (%): 99.44 +# First Fragment Qualities. 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 6 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 1 0 0 0 0 +FFQ 7 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 1 0 0 0 0 0 +FFQ 8 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 1 0 0 0 0 0 +FFQ 9 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 1 0 0 +FFQ 10 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 1 0 0 0 0 0 +FFQ 11 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 1 0 0 0 0 +FFQ 12 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 1 0 0 0 0 +FFQ 13 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +FFQ 15 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 1 0 0 0 0 +FFQ 16 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 1 0 0 0 +FFQ 17 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 1 0 0 0 0 +FFQ 18 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 1 0 0 0 0 +FFQ 19 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 1 0 0 0 0 +FFQ 20 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 1 0 0 0 +FFQ 21 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 1 0 0 0 0 +FFQ 22 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 1 0 0 0 +FFQ 23 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 1 0 0 +FFQ 24 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 1 0 0 0 +FFQ 25 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 1 0 0 0 0 0 0 0 +FFQ 26 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 1 0 0 0 0 0 +FFQ 27 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 1 0 0 0 +FFQ 28 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 1 0 0 +FFQ 29 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 1 0 0 0 0 0 0 +FFQ 30 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 1 0 0 0 +FFQ 31 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 1 0 0 0 +FFQ 32 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 1 0 0 0 +FFQ 33 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 1 0 0 0 +FFQ 34 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 1 0 +FFQ 35 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 37 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 39 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 1 0 0 0 +FFQ 40 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 1 0 0 0 0 +FFQ 41 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +FFQ 43 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 1 0 0 0 0 +FFQ 44 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 1 0 0 0 +FFQ 45 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 1 0 0 +FFQ 46 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 1 0 0 0 0 +FFQ 47 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +FFQ 49 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 1 0 0 0 0 +FFQ 50 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 1 0 0 +FFQ 51 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 53 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 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0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 97 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 98 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 2 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 99 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 1 0 0 0 1 0 0 0 +LFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 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 25.38 0 +GCF 51.26 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 24.87 0 +GCL 50.25 1 +GCL 51.26 0 +GCL 52.26 1 +# 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 [%] +GCC 1 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 2 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 3 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 4 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 5 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 6 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 7 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 8 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 9 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 10 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 11 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 12 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 13 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 14 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 15 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 16 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 17 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 18 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 19 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 20 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 21 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 22 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 23 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 24 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 25 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 26 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 27 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 28 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 29 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 30 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 31 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 32 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 33 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 34 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 35 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 36 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 37 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 38 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 39 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 40 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 41 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 42 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 43 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 44 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 45 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 46 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 47 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 48 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 49 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 50 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 51 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 52 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 53 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 54 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 55 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 56 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 57 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 58 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 59 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 60 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 61 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 62 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 63 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 64 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 65 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 66 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 67 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 68 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 69 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 70 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 71 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 72 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 73 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 74 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 75 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 76 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 77 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 78 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 79 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 80 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 81 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 82 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 83 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 84 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 85 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 86 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 87 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 88 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 89 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 90 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 91 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 92 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 93 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 94 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 95 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 96 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 97 33.33 33.33 0.00 33.33 0.00 0.00 +GCC 98 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 99 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 [%] +FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 2 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 3 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 5 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 8 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 10 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 12 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 13 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 14 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 15 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 16 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 17 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 19 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 21 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 23 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 24 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 26 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 27 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 28 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 29 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 30 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 31 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 32 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 33 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 34 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 36 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 37 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 38 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 39 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 40 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 41 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 42 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 43 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 44 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 45 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 46 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 47 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 48 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 49 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 50 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 51 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 52 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 53 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 54 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 55 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 57 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 58 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 59 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 60 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 61 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 62 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 63 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 64 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 65 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 66 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 67 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 68 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 69 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 70 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 71 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 72 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 73 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 74 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 75 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 76 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 77 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 78 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 79 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 80 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 81 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 82 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 83 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 84 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 85 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 86 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 87 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 88 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 89 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 90 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 91 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 92 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 93 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 94 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 95 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 96 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 97 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 98 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 [%] +LBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 2 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 3 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 5 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 8 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 11 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 12 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 13 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 14 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 16 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 17 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 18 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 19 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 20 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 21 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 25 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 26 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 27 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 28 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 29 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 30 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 32 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 34 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 35 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 36 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 37 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 38 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 39 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 40 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 41 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 42 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 43 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 44 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 45 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 46 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 47 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 48 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 49 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 50 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 51 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 52 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 53 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 54 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 55 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 57 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 58 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 59 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 60 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 61 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 62 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 63 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 64 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 65 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 66 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 67 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 68 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 69 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 70 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 71 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 72 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 73 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 74 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 75 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 76 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 77 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 78 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 79 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 80 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 81 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 82 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 83 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 84 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 85 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 86 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 87 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 88 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 89 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 90 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 91 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 92 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 93 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 94 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 95 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 96 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 97 50.00 0.00 0.00 50.00 0.00 0.00 +LBC 98 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 99 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 +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 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 100 3 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 100 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 100 2 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 2 +# 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 19 0 0 1 0 +IC 92 0 0 1 0 +IC 98 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 79 +COV [2-2] 2 100 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12.3reads.overlap.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12.3reads.overlap.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,759 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 09f8b87f 140798ec 2b989f07 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 3 +SN filtered sequences: 0 +SN sequences: 3 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 2 +SN reads mapped: 3 +SN reads mapped and paired: 3 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 3 # proper-pair bit set +SN reads paired: 3 # 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: 300 # ignores clipping +SN total first fragment length: 100 # ignores clipping +SN total last fragment length: 200 # ignores clipping +SN bases mapped: 300 # ignores clipping +SN bases mapped (cigar): 300 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 11 # from NM fields +SN error rate: 3.666667e-02 # mismatches / bases mapped (cigar) +SN average length: 100 +SN average first fragment length: 100 +SN average last fragment length: 100 +SN maximum length: 100 +SN maximum first fragment length: 100 +SN maximum last fragment length: 100 +SN average quality: 33.3 +SN insert size average: 180.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +SN bases inside the target: 180 +SN percentage of target genome with coverage > 0 (%): 99.44 +# First Fragment Qualities. 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 6 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 1 0 0 0 0 +FFQ 7 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 1 0 0 0 0 0 +FFQ 8 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 1 0 0 0 0 0 +FFQ 9 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 1 0 0 +FFQ 10 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 1 0 0 0 0 0 +FFQ 11 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 1 0 0 0 0 +FFQ 12 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 1 0 0 0 0 +FFQ 13 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +FFQ 15 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 1 0 0 0 0 +FFQ 16 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 1 0 0 0 +FFQ 17 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 1 0 0 0 0 +FFQ 18 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 1 0 0 0 0 +FFQ 19 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 1 0 0 0 0 +FFQ 20 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 1 0 0 0 +FFQ 21 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 1 0 0 0 0 +FFQ 22 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 1 0 0 0 +FFQ 23 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 1 0 0 +FFQ 24 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 1 0 0 0 +FFQ 25 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 1 0 0 0 0 0 0 0 +FFQ 26 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 1 0 0 0 0 0 +FFQ 27 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 1 0 0 0 +FFQ 28 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 1 0 0 +FFQ 29 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 1 0 0 0 0 0 0 +FFQ 30 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 1 0 0 0 +FFQ 31 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 1 0 0 0 +FFQ 32 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 1 0 0 0 +FFQ 33 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 1 0 0 0 +FFQ 34 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 1 0 +FFQ 35 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 37 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 +FFQ 39 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 1 0 0 0 +FFQ 40 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 1 0 0 0 0 +FFQ 41 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +FFQ 43 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 1 0 0 0 0 +FFQ 44 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 1 0 0 0 +FFQ 45 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 1 0 0 +FFQ 46 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 1 0 0 0 0 +FFQ 47 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 +FFQ 49 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 1 0 0 0 0 +FFQ 50 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 1 0 0 +FFQ 51 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +FFQ 53 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 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0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 97 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 98 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 2 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 99 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 1 0 0 0 1 0 0 0 +LFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 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 25.38 0 +GCF 51.26 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 24.87 0 +GCL 50.25 1 +GCL 51.26 0 +GCL 52.26 1 +# 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 [%] +GCC 1 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 2 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 3 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 4 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 5 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 6 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 7 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 8 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 9 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 10 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 11 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 12 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 13 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 14 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 15 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 16 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 17 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 18 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 19 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 20 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 21 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 22 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 23 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 24 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 25 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 26 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 27 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 28 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 29 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 30 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 31 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 32 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 33 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 34 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 35 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 36 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 37 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 38 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 39 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 40 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 41 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 42 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 43 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 44 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 45 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 46 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 47 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 48 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 49 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 50 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 51 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 52 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 53 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 54 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 55 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 56 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 57 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 58 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 59 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 60 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 61 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 62 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 63 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 64 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 65 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 66 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 67 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 68 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 69 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 70 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 71 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 72 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 73 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 74 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 75 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 76 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 77 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 78 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 79 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 80 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 81 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 82 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 83 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 84 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 85 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 86 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 87 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 88 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 89 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 90 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 91 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 92 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 93 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 94 0.00 33.33 0.00 66.67 0.00 0.00 +GCC 95 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 96 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 97 33.33 33.33 0.00 33.33 0.00 0.00 +GCC 98 0.00 66.67 0.00 33.33 0.00 0.00 +GCC 99 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 [%] +FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 2 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 3 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 5 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 8 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 10 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 12 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 13 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 14 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 15 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 16 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 17 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 19 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 21 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 23 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 24 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 26 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 27 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 28 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 29 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 30 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 31 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 32 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 33 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 34 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 36 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 37 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 38 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 39 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 40 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 41 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 42 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 43 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 44 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 45 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 46 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 47 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 48 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 49 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 50 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 51 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 52 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 53 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 54 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 55 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 57 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 58 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 59 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 60 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 61 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 62 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 63 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 64 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 65 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 66 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 67 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 68 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 69 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 70 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 71 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 72 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 73 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 74 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 75 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 76 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 77 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 78 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 79 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 80 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 81 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 82 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 83 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 84 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 85 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 86 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 87 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 88 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 89 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 90 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 91 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 92 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 93 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 94 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 95 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 96 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 97 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 98 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 [%] +LBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 2 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 3 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 5 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 8 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 11 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 12 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 13 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 14 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 16 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 17 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 18 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 19 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 20 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 21 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 25 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 26 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 27 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 28 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 29 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 30 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 32 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 34 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 35 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 36 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 37 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 38 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 39 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 40 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 41 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 42 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 43 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 44 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 45 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 46 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 47 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 48 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 49 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 50 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 51 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 52 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 53 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 54 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 55 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 56 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 57 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 58 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 59 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 60 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 61 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 62 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 63 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 64 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 65 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 66 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 67 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 68 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 69 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 70 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 71 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 72 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 73 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 74 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 75 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 76 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 77 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 78 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 79 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 80 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 81 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 82 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 83 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 84 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 85 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 86 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 87 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 88 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 89 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 90 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 91 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 92 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 93 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 94 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 95 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 96 0.00 50.00 0.00 50.00 0.00 0.00 +LBC 97 50.00 0.00 0.00 50.00 0.00 0.00 +LBC 98 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 99 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 100 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 +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 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 100 3 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 100 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 100 2 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 2 +# 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 19 0 0 1 0 +IC 92 0 0 1 0 +IC 98 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 79 +COV [2-2] 2 80 +COV [3-3] 3 20 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12_2reads.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_2reads.bed Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,1 @@ +14 38169880 38170045 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12_3reads.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_3reads.bed Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,1 @@ +16 89701235 89701414 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/12_overlaps.bam Binary file test-data/12_overlaps.bam has changed diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/1_map_cigar.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_map_cigar.sam Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,5 @@ +@HD VN:1.4 +@SQ SN:alpha LN:100 +@RG ID:s1_a_1 LB:1 SM:s1 +r1 99 alpha 1 40 35M = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:s1_a_1 NM:i:0 +r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/2.stats.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.stats.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,383 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1a1c1362 29c426ae 7bab45da +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 2 +SN filtered sequences: 0 +SN sequences: 2 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 1 +SN reads mapped: 2 +SN reads mapped and paired: 2 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 2 # proper-pair bit set +SN reads paired: 2 # 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: 70 # ignores clipping +SN total first fragment length: 35 # ignores clipping +SN total last fragment length: 35 # ignores clipping +SN bases mapped: 70 # ignores clipping +SN bases mapped (cigar): 70 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 0 # from NM fields +SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) +SN average length: 35 +SN average first fragment length: 35 +SN average last fragment length: 35 +SN maximum length: 35 +SN maximum first fragment length: 35 +SN maximum last fragment length: 35 +SN average quality: 255.0 +SN insert size average: 100.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +# First Fragment Qualities. 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 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 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 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 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 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 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 1 +FFQ 2 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 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 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 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 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 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 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 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 +MPC 30 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 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 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 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 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 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 0 0 0 0 +MPC 31 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 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 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 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 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 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 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 +MPC 34 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 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 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 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 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 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 0 0 0 0 +MPC 35 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 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 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 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 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 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 0 0 0 0 +MPC 36 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 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 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 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 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 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 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 28.39 0 +GCF 58.29 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.36 0 +GCL 43.97 1 +# 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 [%] +GCC 1 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 2 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 3 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 4 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 5 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 6 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 7 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 8 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 9 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 10 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 11 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 12 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 13 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 14 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 15 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 16 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 17 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 18 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 19 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 20 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 21 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 22 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 23 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 24 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 25 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 26 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 27 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 28 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 29 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 30 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 31 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 32 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 33 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 34 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +# 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 [%] +FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 3 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 5 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 6 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 7 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 8 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 10 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 12 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 13 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 14 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 15 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 16 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 17 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 19 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 21 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 22 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 24 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 25 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 26 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 27 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 28 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 29 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 30 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 32 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 34 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +# 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 [%] +LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 3 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 5 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 7 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 8 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 12 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 13 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 16 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 17 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 19 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 20 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 21 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 26 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 27 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 28 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 29 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 30 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 32 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 +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 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 35 2 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 35 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 35 1 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +# 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) +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 70 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/2_equal_cigar_full_seq.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_equal_cigar_full_seq.sam Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,5 @@ +@HD VN:1.4 +@SQ SN:alpha LN:100 +@RG ID:s1_a_1 LB:1 SM:s1 +r1 99 alpha 1 40 35= = 66 100 TGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAGG * RG:Z:s1_a_1 NM:i:0 +r1 147 alpha 66 40 35= = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/5_insert_cigar.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/5_insert_cigar.sam Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,5 @@ +@HD VN:1.4 +@SQ SN:alpha LN:100 +@RG ID:s1_a_1 LB:1 SM:s1 +r1 99 alpha 1 40 1M1I33M = 66 100 TGGGGGTGTCATAGTAATCCGGTTGGGAGTCCGAG * RG:Z:s1_a_1 NM:i:0 +r1 147 alpha 66 40 35M = 1 -100 TATCCAGAACTTTGCAGCCATATCTCCAAGACATG * RG:Z:s1_a_1 NM:i:0 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/6.stats.expected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6.stats.expected Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,385 @@ +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 1a1c1362 32507d92 7bab45da +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 2 +SN filtered sequences: 0 +SN sequences: 2 +SN is sorted: 1 +SN 1st fragments: 1 +SN last fragments: 1 +SN reads mapped: 2 +SN reads mapped and paired: 2 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 2 # proper-pair bit set +SN reads paired: 2 # 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: 70 # ignores clipping +SN total first fragment length: 35 # ignores clipping +SN total last fragment length: 35 # ignores clipping +SN bases mapped: 70 # ignores clipping +SN bases mapped (cigar): 70 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 0 # from NM fields +SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) +SN average length: 35 +SN average first fragment length: 35 +SN average last fragment length: 35 +SN maximum length: 35 +SN maximum first fragment length: 35 +SN maximum last fragment length: 35 +SN average quality: 255.0 +SN insert size average: 100.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 1 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +SN percentage of properly paired reads (%): 100.0 +# First Fragment Qualities. 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 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 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 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 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 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 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 1 +FFQ 2 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 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 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 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 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 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 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 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 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 0 0 0 0 0 +MPC 36 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 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 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 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 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 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 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 28.39 0 +GCF 58.29 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 21.36 0 +GCL 43.97 1 +# 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 [%] +GCC 1 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 2 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 3 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 4 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 5 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 6 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 7 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 8 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 9 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 10 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 11 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 12 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 13 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 14 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 15 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 16 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 17 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 18 0.00 50.00 0.00 50.00 0.00 0.00 +GCC 19 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 20 50.00 50.00 0.00 0.00 0.00 0.00 +GCC 21 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 22 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 23 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 24 0.00 0.00 0.00 100.00 0.00 0.00 +GCC 25 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 26 0.00 50.00 50.00 0.00 0.00 0.00 +GCC 27 50.00 0.00 50.00 0.00 0.00 0.00 +GCC 28 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 29 0.00 0.00 100.00 0.00 0.00 0.00 +GCC 30 50.00 0.00 0.00 50.00 0.00 0.00 +GCC 31 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 32 0.00 100.00 0.00 0.00 0.00 0.00 +GCC 33 0.00 0.00 50.00 50.00 0.00 0.00 +GCC 34 100.00 0.00 0.00 0.00 0.00 0.00 +GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 +# 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 [%] +FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 3 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 5 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 6 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 7 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 8 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 9 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 10 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 11 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 12 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 13 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 14 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 15 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 16 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 17 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 18 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 19 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 20 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 21 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 22 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 24 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 25 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 26 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 27 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 28 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 29 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 30 0.00 0.00 0.00 100.00 0.00 0.00 +FBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 32 0.00 100.00 0.00 0.00 0.00 0.00 +FBC 33 0.00 0.00 100.00 0.00 0.00 0.00 +FBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 +# 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 [%] +LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 3 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 5 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 6 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 7 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 8 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 10 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 11 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 12 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 13 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 14 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 15 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 16 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 17 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 18 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 19 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 20 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 21 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 22 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 24 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 25 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 26 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 27 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 28 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 29 0.00 0.00 100.00 0.00 0.00 0.00 +LBC 30 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 32 0.00 100.00 0.00 0.00 0.00 0.00 +LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 +LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 +LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 +# 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 +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 1 1 0 0 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 35 2 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 35 1 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 35 1 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 1 0 +# 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 2 1 0 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 69 +# 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/samtools_stats_out1.tab --- a/test-data/samtools_stats_out1.tab Tue May 09 11:19:01 2017 -0400 +++ b/test-data/samtools_stats_out1.tab Thu Sep 27 09:05:10 2018 -0400 @@ -1,6 +1,6 @@ -# This file was produced by samtools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-bamstats +# This file was produced by samtools stats (1.9+htslib-1.9) and can be plotted using plot-bamstats # This file contains statistics for all reads. -# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /tmp/tmpO1aTrb/files/000/dataset_2.dat /tmp/tmpO1aTrb/files/000/dataset_1.dat +# The command line was: stats --ref-seq reference.fa infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 1bd20fd8 58ad2167 29883386 @@ -21,6 +21,8 @@ SN reads QC failed: 0 SN non-primary alignments: 0 SN total length: 50200 # ignores clipping +SN total first fragment length: 25100 # ignores clipping +SN total last fragment length: 25100 # ignores clipping SN bases mapped: 6275 # ignores clipping SN bases mapped (cigar): 6275 # more accurate SN bases trimmed: 0 @@ -28,7 +30,11 @@ SN mismatches: 591 # from NM fields SN error rate: 9.418327e-02 # mismatches / bases mapped (cigar) SN average length: 251 +SN average first fragment length: 251 +SN average last fragment length: 251 SN maximum length: 251 +SN maximum first fragment length: 251 +SN maximum last fragment length: 251 SN average quality: 34.7 SN insert size average: 0.0 SN insert size standard deviation: 0.0 @@ -36,7 +42,8 @@ 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. +SN percentage of properly paired reads (%): 0.0 +# First Fragment Qualities. 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 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3 2 0 20 38 32 1 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 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 18 36 36 6 0 0 0 0 0 0 @@ -289,8 +296,7 @@ FFQ 249 0 0 0 0 0 0 0 0 0 0 0 0 5 6 20 8 0 0 0 0 0 0 0 0 5 7 10 0 1 0 0 0 1 15 0 2 0 20 0 0 0 0 FFQ 250 0 0 0 0 0 0 0 0 0 0 0 0 2 10 15 10 0 0 0 0 0 0 0 0 9 5 8 1 0 0 0 2 6 10 0 0 2 20 0 0 0 0 FFQ 251 0 0 0 0 0 0 0 0 0 0 0 0 7 20 21 17 0 0 0 0 0 0 0 0 7 7 6 0 0 0 0 1 2 4 0 0 0 8 0 0 0 0 -FFQ 252 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. +# Last Fragment Qualities. 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 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 3 2 0 20 38 32 1 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 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 18 36 36 6 0 0 0 0 0 0 @@ -543,7 +549,6 @@ LFQ 249 0 0 0 0 0 0 0 0 0 0 0 0 5 6 20 8 0 0 0 0 0 0 0 0 5 7 10 0 1 0 0 0 1 15 0 2 0 20 0 0 0 0 LFQ 250 0 0 0 0 0 0 0 0 0 0 0 0 2 10 15 10 0 0 0 0 0 0 0 0 9 5 8 1 0 0 0 2 6 10 0 0 2 20 0 0 0 0 LFQ 251 0 0 0 0 0 0 0 0 0 0 0 0 7 20 21 17 0 0 0 0 0 0 0 0 7 7 6 0 0 0 0 1 2 4 0 0 0 8 0 0 0 0 -LFQ 252 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 # Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part. # Columns correspond to qualities, rows to cycles. First column is the cycle number, second # is the number of N's and the rest is the number of mismatches @@ -1089,9 +1094,517 @@ GCC 249 25.00 23.00 21.00 31.00 0.00 0.00 GCC 250 27.50 22.50 17.50 32.50 0.00 0.00 GCC 251 13.50 20.50 36.50 29.50 0.00 0.00 +# 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 [%] +FBC 1 21.43 27.55 36.73 14.29 2.04 0.00 +FBC 2 34.00 15.00 12.00 39.00 0.00 0.00 +FBC 3 32.00 25.00 9.00 34.00 0.00 0.00 +FBC 4 21.00 26.00 16.00 37.00 0.00 0.00 +FBC 5 37.00 20.00 14.00 29.00 0.00 0.00 +FBC 6 28.00 26.00 17.00 29.00 0.00 0.00 +FBC 7 31.00 14.00 31.00 24.00 0.00 0.00 +FBC 8 52.00 13.00 21.00 14.00 0.00 0.00 +FBC 9 15.00 31.00 20.00 34.00 0.00 0.00 +FBC 10 39.00 15.00 20.00 26.00 0.00 0.00 +FBC 11 23.00 14.00 30.00 33.00 0.00 0.00 +FBC 12 32.00 24.00 22.00 22.00 0.00 0.00 +FBC 13 25.00 13.00 23.00 39.00 0.00 0.00 +FBC 14 27.27 20.20 28.28 24.24 1.01 0.00 +FBC 15 28.00 21.00 24.00 27.00 0.00 0.00 +FBC 16 27.00 15.00 20.00 38.00 0.00 0.00 +FBC 17 27.00 24.00 15.00 34.00 0.00 0.00 +FBC 18 30.00 27.00 21.00 22.00 0.00 0.00 +FBC 19 28.00 26.00 21.00 25.00 0.00 0.00 +FBC 20 22.00 26.00 15.00 37.00 0.00 0.00 +FBC 21 35.00 17.00 20.00 28.00 0.00 0.00 +FBC 22 36.00 26.00 18.00 20.00 0.00 0.00 +FBC 23 32.32 17.17 15.15 35.35 1.01 0.00 +FBC 24 38.00 10.00 24.00 28.00 0.00 0.00 +FBC 25 33.00 22.00 18.00 27.00 0.00 0.00 +FBC 26 31.00 16.00 18.00 35.00 0.00 0.00 +FBC 27 37.00 11.00 29.00 23.00 0.00 0.00 +FBC 28 32.00 15.00 23.00 30.00 0.00 0.00 +FBC 29 30.00 26.00 25.00 19.00 0.00 0.00 +FBC 30 28.00 19.00 15.00 38.00 0.00 0.00 +FBC 31 34.00 30.00 13.00 23.00 0.00 0.00 +FBC 32 47.00 21.00 19.00 13.00 0.00 0.00 +FBC 33 24.00 24.00 14.00 38.00 0.00 0.00 +FBC 34 36.00 16.00 21.00 27.00 0.00 0.00 +FBC 35 30.00 24.00 21.00 25.00 0.00 0.00 +FBC 36 43.00 25.00 16.00 16.00 0.00 0.00 +FBC 37 38.00 16.00 20.00 26.00 0.00 0.00 +FBC 38 25.00 26.00 25.00 24.00 0.00 0.00 +FBC 39 23.00 42.00 18.00 17.00 0.00 0.00 +FBC 40 35.00 18.00 19.00 28.00 0.00 0.00 +FBC 41 37.00 29.00 18.00 16.00 0.00 0.00 +FBC 42 32.00 24.00 21.00 23.00 0.00 0.00 +FBC 43 32.00 30.00 14.00 24.00 0.00 0.00 +FBC 44 19.00 28.00 21.00 32.00 0.00 0.00 +FBC 45 43.00 18.00 25.00 14.00 0.00 0.00 +FBC 46 26.00 20.00 23.00 31.00 0.00 0.00 +FBC 47 37.00 31.00 15.00 17.00 0.00 0.00 +FBC 48 30.00 27.00 15.00 28.00 0.00 0.00 +FBC 49 31.00 32.00 11.00 26.00 0.00 0.00 +FBC 50 44.00 21.00 9.00 26.00 0.00 0.00 +FBC 51 40.00 28.00 14.00 18.00 0.00 0.00 +FBC 52 40.00 25.00 19.00 16.00 0.00 0.00 +FBC 53 21.00 29.00 25.00 25.00 0.00 0.00 +FBC 54 38.00 19.00 24.00 19.00 0.00 0.00 +FBC 55 29.00 23.00 16.00 32.00 0.00 0.00 +FBC 56 31.00 25.00 11.00 33.00 0.00 0.00 +FBC 57 18.00 24.00 23.00 35.00 0.00 0.00 +FBC 58 27.00 35.00 21.00 17.00 0.00 0.00 +FBC 59 35.00 25.00 22.00 18.00 0.00 0.00 +FBC 60 28.00 30.00 15.00 27.00 0.00 0.00 +FBC 61 28.00 24.00 24.00 24.00 0.00 0.00 +FBC 62 28.00 26.00 13.00 33.00 0.00 0.00 +FBC 63 29.00 32.00 22.00 17.00 0.00 0.00 +FBC 64 37.00 23.00 24.00 16.00 0.00 0.00 +FBC 65 33.00 22.00 16.00 29.00 0.00 0.00 +FBC 66 35.00 24.00 16.00 25.00 0.00 0.00 +FBC 67 39.00 25.00 17.00 19.00 0.00 0.00 +FBC 68 34.00 31.00 12.00 23.00 0.00 0.00 +FBC 69 39.00 21.00 19.00 21.00 0.00 0.00 +FBC 70 37.00 20.00 15.00 28.00 0.00 0.00 +FBC 71 22.00 36.00 24.00 18.00 0.00 0.00 +FBC 72 25.00 32.00 22.00 21.00 0.00 0.00 +FBC 73 34.00 23.00 19.00 24.00 0.00 0.00 +FBC 74 26.00 33.00 12.00 29.00 0.00 0.00 +FBC 75 37.00 15.00 16.00 32.00 0.00 0.00 +FBC 76 26.00 31.00 22.00 21.00 0.00 0.00 +FBC 77 37.00 22.00 17.00 24.00 0.00 0.00 +FBC 78 25.00 38.00 18.00 19.00 0.00 0.00 +FBC 79 19.00 28.00 24.00 29.00 0.00 0.00 +FBC 80 28.00 20.00 27.00 25.00 0.00 0.00 +FBC 81 16.00 26.00 26.00 32.00 0.00 0.00 +FBC 82 32.00 35.00 18.00 15.00 0.00 0.00 +FBC 83 27.00 28.00 11.00 34.00 0.00 0.00 +FBC 84 16.00 43.00 19.00 22.00 0.00 0.00 +FBC 85 33.00 29.00 12.00 26.00 0.00 0.00 +FBC 86 18.00 49.00 14.00 19.00 0.00 0.00 +FBC 87 37.00 17.00 17.00 29.00 0.00 0.00 +FBC 88 21.00 31.00 24.00 24.00 0.00 0.00 +FBC 89 27.00 30.00 24.00 19.00 0.00 0.00 +FBC 90 13.00 25.00 23.00 39.00 0.00 0.00 +FBC 91 25.00 34.00 20.00 21.00 0.00 0.00 +FBC 92 25.00 22.00 23.00 30.00 0.00 0.00 +FBC 93 22.00 35.00 18.00 25.00 0.00 0.00 +FBC 94 24.00 18.00 23.00 35.00 0.00 0.00 +FBC 95 22.22 40.40 12.12 25.25 1.01 0.00 +FBC 96 25.00 24.00 18.00 33.00 0.00 0.00 +FBC 97 26.00 35.00 17.00 22.00 0.00 0.00 +FBC 98 15.15 35.35 20.20 29.29 1.01 0.00 +FBC 99 22.00 30.00 28.00 20.00 0.00 0.00 +FBC 100 20.00 18.00 23.00 39.00 0.00 0.00 +FBC 101 23.00 46.00 13.00 18.00 0.00 0.00 +FBC 102 15.00 21.00 29.00 35.00 0.00 0.00 +FBC 103 30.00 26.00 16.00 28.00 0.00 0.00 +FBC 104 23.00 31.00 19.00 27.00 0.00 0.00 +FBC 105 33.00 31.00 23.00 13.00 0.00 0.00 +FBC 106 24.00 30.00 27.00 19.00 0.00 0.00 +FBC 107 16.16 38.38 21.21 24.24 1.01 0.00 +FBC 108 22.22 28.28 26.26 23.23 1.01 0.00 +FBC 109 15.00 33.00 20.00 32.00 0.00 0.00 +FBC 110 12.12 39.39 20.20 28.28 1.01 0.00 +FBC 111 23.23 31.31 24.24 21.21 1.01 0.00 +FBC 112 35.35 28.28 16.16 20.20 1.01 0.00 +FBC 113 18.18 21.21 34.34 26.26 1.01 0.00 +FBC 114 15.00 31.00 35.00 19.00 0.00 0.00 +FBC 115 27.00 26.00 22.00 25.00 0.00 0.00 +FBC 116 24.00 31.00 33.00 12.00 0.00 0.00 +FBC 117 23.00 25.00 17.00 35.00 0.00 0.00 +FBC 118 26.00 15.00 34.00 25.00 0.00 0.00 +FBC 119 24.00 38.00 17.00 21.00 0.00 0.00 +FBC 120 16.00 25.00 26.00 33.00 0.00 0.00 +FBC 121 31.31 31.31 25.25 12.12 1.01 0.00 +FBC 122 16.00 21.00 27.00 36.00 0.00 0.00 +FBC 123 22.00 45.00 13.00 20.00 0.00 0.00 +FBC 124 8.00 33.00 33.00 26.00 0.00 0.00 +FBC 125 21.00 30.00 16.00 33.00 0.00 0.00 +FBC 126 28.00 15.00 30.00 27.00 0.00 0.00 +FBC 127 27.00 17.00 21.00 35.00 0.00 0.00 +FBC 128 20.00 33.00 32.00 15.00 0.00 0.00 +FBC 129 27.00 24.00 29.00 20.00 0.00 0.00 +FBC 130 25.00 21.00 21.00 33.00 0.00 0.00 +FBC 131 18.00 39.00 25.00 18.00 0.00 0.00 +FBC 132 22.00 29.00 22.00 27.00 0.00 0.00 +FBC 133 12.00 29.00 38.00 21.00 0.00 0.00 +FBC 134 27.00 20.00 30.00 23.00 0.00 0.00 +FBC 135 16.00 19.00 35.00 30.00 0.00 0.00 +FBC 136 31.00 31.00 16.00 22.00 0.00 0.00 +FBC 137 24.00 21.00 31.00 24.00 0.00 0.00 +FBC 138 14.00 39.00 20.00 27.00 0.00 0.00 +FBC 139 22.00 27.00 27.00 24.00 0.00 0.00 +FBC 140 15.00 22.00 31.00 32.00 0.00 0.00 +FBC 141 20.00 23.00 26.00 31.00 0.00 0.00 +FBC 142 19.00 26.00 41.00 14.00 0.00 0.00 +FBC 143 21.00 25.00 26.00 28.00 0.00 0.00 +FBC 144 23.00 28.00 29.00 20.00 0.00 0.00 +FBC 145 24.00 16.00 34.00 26.00 0.00 0.00 +FBC 146 24.00 17.00 38.00 21.00 0.00 0.00 +FBC 147 30.00 22.00 31.00 17.00 0.00 0.00 +FBC 148 13.00 25.00 40.00 22.00 0.00 0.00 +FBC 149 26.00 23.00 24.00 27.00 0.00 0.00 +FBC 150 16.00 26.00 27.00 31.00 0.00 0.00 +FBC 151 17.00 32.00 31.00 20.00 0.00 0.00 +FBC 152 21.00 14.00 33.00 32.00 0.00 0.00 +FBC 153 21.00 25.00 29.00 25.00 0.00 0.00 +FBC 154 19.00 20.00 30.00 31.00 0.00 0.00 +FBC 155 21.00 24.00 21.00 34.00 0.00 0.00 +FBC 156 13.00 24.00 35.00 28.00 0.00 0.00 +FBC 157 21.00 28.00 26.00 25.00 0.00 0.00 +FBC 158 24.00 26.00 28.00 22.00 0.00 0.00 +FBC 159 16.00 10.00 49.00 25.00 0.00 0.00 +FBC 160 25.00 22.00 31.00 22.00 0.00 0.00 +FBC 161 13.00 18.00 50.00 19.00 0.00 0.00 +FBC 162 30.00 14.00 25.00 31.00 0.00 0.00 +FBC 163 16.00 17.00 40.00 27.00 0.00 0.00 +FBC 164 25.00 17.00 22.00 36.00 0.00 0.00 +FBC 165 16.00 19.00 34.00 31.00 0.00 0.00 +FBC 166 15.00 39.00 27.00 19.00 0.00 0.00 +FBC 167 16.00 15.00 38.00 31.00 0.00 0.00 +FBC 168 12.00 26.00 29.00 33.00 0.00 0.00 +FBC 169 16.00 18.00 26.00 40.00 0.00 0.00 +FBC 170 16.00 22.00 29.00 33.00 0.00 0.00 +FBC 171 17.00 26.00 35.00 22.00 0.00 0.00 +FBC 172 14.00 18.00 34.00 34.00 0.00 0.00 +FBC 173 25.00 16.00 34.00 25.00 0.00 0.00 +FBC 174 14.00 23.00 34.00 29.00 0.00 0.00 +FBC 175 33.00 16.00 37.00 14.00 0.00 0.00 +FBC 176 16.00 28.00 33.00 23.00 0.00 0.00 +FBC 177 14.00 20.00 29.00 37.00 0.00 0.00 +FBC 178 13.00 26.00 30.00 31.00 0.00 0.00 +FBC 179 12.00 16.00 24.00 48.00 0.00 0.00 +FBC 180 20.00 19.00 37.00 24.00 0.00 0.00 +FBC 181 20.00 22.00 33.00 25.00 0.00 0.00 +FBC 182 30.00 16.00 25.00 29.00 0.00 0.00 +FBC 183 21.00 12.00 30.00 37.00 0.00 0.00 +FBC 184 13.00 28.00 31.00 28.00 0.00 0.00 +FBC 185 14.00 32.00 33.00 21.00 0.00 0.00 +FBC 186 24.00 25.00 33.00 18.00 0.00 0.00 +FBC 187 14.00 15.00 39.00 32.00 0.00 0.00 +FBC 188 26.00 24.00 25.00 25.00 0.00 0.00 +FBC 189 15.00 21.00 35.00 29.00 0.00 0.00 +FBC 190 22.00 32.00 21.00 25.00 0.00 0.00 +FBC 191 22.00 23.00 27.00 28.00 0.00 0.00 +FBC 192 32.00 24.00 14.00 30.00 0.00 0.00 +FBC 193 19.00 25.00 26.00 30.00 0.00 0.00 +FBC 194 16.00 33.00 25.00 26.00 0.00 0.00 +FBC 195 16.00 24.00 25.00 35.00 0.00 0.00 +FBC 196 20.00 28.00 22.00 30.00 0.00 0.00 +FBC 197 22.00 22.00 22.00 34.00 0.00 0.00 +FBC 198 19.00 23.00 35.00 23.00 0.00 0.00 +FBC 199 18.00 20.00 24.00 38.00 0.00 0.00 +FBC 200 17.00 31.00 19.00 33.00 0.00 0.00 +FBC 201 28.00 23.00 21.00 28.00 0.00 0.00 +FBC 202 20.00 26.00 18.00 36.00 0.00 0.00 +FBC 203 22.00 30.00 21.00 27.00 0.00 0.00 +FBC 204 28.00 29.00 24.00 19.00 0.00 0.00 +FBC 205 23.00 20.00 24.00 33.00 0.00 0.00 +FBC 206 25.00 24.00 22.00 29.00 0.00 0.00 +FBC 207 23.00 21.00 20.00 36.00 0.00 0.00 +FBC 208 16.00 38.00 26.00 20.00 0.00 0.00 +FBC 209 14.00 26.00 9.00 51.00 0.00 0.00 +FBC 210 19.00 24.00 36.00 21.00 0.00 0.00 +FBC 211 24.00 26.00 16.00 34.00 0.00 0.00 +FBC 212 19.00 35.00 14.00 32.00 0.00 0.00 +FBC 213 26.00 18.00 28.00 28.00 0.00 0.00 +FBC 214 19.00 25.00 25.00 31.00 0.00 0.00 +FBC 215 24.00 26.00 21.00 29.00 0.00 0.00 +FBC 216 25.00 18.00 25.00 32.00 0.00 0.00 +FBC 217 25.00 28.00 18.00 29.00 0.00 0.00 +FBC 218 22.00 30.00 18.00 30.00 0.00 0.00 +FBC 219 15.00 24.00 18.00 43.00 0.00 0.00 +FBC 220 23.00 24.00 23.00 30.00 0.00 0.00 +FBC 221 23.00 23.00 21.00 33.00 0.00 0.00 +FBC 222 21.00 22.00 18.00 39.00 0.00 0.00 +FBC 223 21.00 32.00 23.00 24.00 0.00 0.00 +FBC 224 26.00 25.00 22.00 27.00 0.00 0.00 +FBC 225 15.00 39.00 27.00 19.00 0.00 0.00 +FBC 226 20.00 26.00 23.00 31.00 0.00 0.00 +FBC 227 24.00 27.00 21.00 28.00 0.00 0.00 +FBC 228 32.00 18.00 27.00 23.00 0.00 0.00 +FBC 229 23.00 22.00 21.00 34.00 0.00 0.00 +FBC 230 19.00 31.00 17.00 33.00 0.00 0.00 +FBC 231 26.00 29.00 29.00 16.00 0.00 0.00 +FBC 232 22.00 20.00 14.00 44.00 0.00 0.00 +FBC 233 20.00 29.00 23.00 28.00 0.00 0.00 +FBC 234 19.00 28.00 22.00 31.00 0.00 0.00 +FBC 235 23.00 19.00 24.00 34.00 0.00 0.00 +FBC 236 27.00 26.00 18.00 29.00 0.00 0.00 +FBC 237 25.00 20.00 22.00 33.00 0.00 0.00 +FBC 238 21.00 34.00 20.00 25.00 0.00 0.00 +FBC 239 22.00 8.00 17.00 53.00 0.00 0.00 +FBC 240 29.00 22.00 18.00 31.00 0.00 0.00 +FBC 241 24.00 23.00 16.00 37.00 0.00 0.00 +FBC 242 32.00 22.00 16.00 30.00 0.00 0.00 +FBC 243 20.00 16.00 23.00 41.00 0.00 0.00 +FBC 244 26.00 23.00 17.00 34.00 0.00 0.00 +FBC 245 32.00 23.00 19.00 26.00 0.00 0.00 +FBC 246 24.00 33.00 21.00 22.00 0.00 0.00 +FBC 247 34.00 15.00 12.00 39.00 0.00 0.00 +FBC 248 14.00 19.00 24.00 43.00 0.00 0.00 +FBC 249 25.00 24.00 20.00 31.00 0.00 0.00 +FBC 250 30.00 25.00 15.00 30.00 0.00 0.00 +FBC 251 14.00 24.00 33.00 29.00 0.00 0.00 +# 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 [%] +LBC 1 22.45 32.65 31.63 13.27 2.04 0.00 +LBC 2 26.00 17.00 10.00 47.00 0.00 0.00 +LBC 3 34.00 25.00 9.00 32.00 0.00 0.00 +LBC 4 13.00 32.00 10.00 45.00 0.00 0.00 +LBC 5 37.00 24.00 10.00 29.00 0.00 0.00 +LBC 6 44.00 26.00 17.00 13.00 0.00 0.00 +LBC 7 28.00 13.00 32.00 27.00 0.00 0.00 +LBC 8 49.00 16.00 18.00 17.00 0.00 0.00 +LBC 9 19.00 35.00 16.00 30.00 0.00 0.00 +LBC 10 35.00 13.00 22.00 30.00 0.00 0.00 +LBC 11 18.00 15.00 29.00 38.00 0.00 0.00 +LBC 12 28.00 24.00 22.00 26.00 0.00 0.00 +LBC 13 29.00 17.00 19.00 35.00 0.00 0.00 +LBC 14 21.21 24.24 24.24 30.30 1.01 0.00 +LBC 15 23.00 20.00 25.00 32.00 0.00 0.00 +LBC 16 35.00 15.00 20.00 30.00 0.00 0.00 +LBC 17 29.00 26.00 13.00 32.00 0.00 0.00 +LBC 18 31.00 30.00 18.00 21.00 0.00 0.00 +LBC 19 30.00 26.00 21.00 23.00 0.00 0.00 +LBC 20 23.00 21.00 20.00 36.00 0.00 0.00 +LBC 21 36.00 18.00 19.00 27.00 0.00 0.00 +LBC 22 39.00 31.00 13.00 17.00 0.00 0.00 +LBC 23 30.30 21.21 11.11 37.37 1.01 0.00 +LBC 24 36.00 14.00 20.00 30.00 0.00 0.00 +LBC 25 38.00 23.00 17.00 22.00 0.00 0.00 +LBC 26 36.00 21.00 13.00 30.00 0.00 0.00 +LBC 27 32.00 18.00 22.00 28.00 0.00 0.00 +LBC 28 30.00 13.00 25.00 32.00 0.00 0.00 +LBC 29 30.00 28.00 23.00 19.00 0.00 0.00 +LBC 30 34.00 21.00 13.00 32.00 0.00 0.00 +LBC 31 33.00 29.00 14.00 24.00 0.00 0.00 +LBC 32 38.00 20.00 20.00 22.00 0.00 0.00 +LBC 33 27.00 23.00 15.00 35.00 0.00 0.00 +LBC 34 43.00 17.00 20.00 20.00 0.00 0.00 +LBC 35 35.00 23.00 22.00 20.00 0.00 0.00 +LBC 36 41.00 25.00 16.00 18.00 0.00 0.00 +LBC 37 38.00 18.00 18.00 26.00 0.00 0.00 +LBC 38 23.00 26.00 25.00 26.00 0.00 0.00 +LBC 39 22.00 41.00 19.00 18.00 0.00 0.00 +LBC 40 29.00 14.00 23.00 34.00 0.00 0.00 +LBC 41 29.00 27.00 20.00 24.00 0.00 0.00 +LBC 42 29.00 27.00 18.00 26.00 0.00 0.00 +LBC 43 38.00 28.00 16.00 18.00 0.00 0.00 +LBC 44 21.00 26.00 23.00 30.00 0.00 0.00 +LBC 45 38.00 25.00 18.00 19.00 0.00 0.00 +LBC 46 27.00 21.00 22.00 30.00 0.00 0.00 +LBC 47 40.00 28.00 18.00 14.00 0.00 0.00 +LBC 48 25.00 22.00 20.00 33.00 0.00 0.00 +LBC 49 26.00 33.00 10.00 31.00 0.00 0.00 +LBC 50 49.00 20.00 10.00 21.00 0.00 0.00 +LBC 51 29.00 29.00 13.00 29.00 0.00 0.00 +LBC 52 43.00 22.00 22.00 13.00 0.00 0.00 +LBC 53 19.00 27.00 27.00 27.00 0.00 0.00 +LBC 54 25.00 18.00 25.00 32.00 0.00 0.00 +LBC 55 32.00 22.00 17.00 29.00 0.00 0.00 +LBC 56 36.00 20.00 16.00 28.00 0.00 0.00 +LBC 57 28.00 24.00 23.00 25.00 0.00 0.00 +LBC 58 23.00 39.00 17.00 21.00 0.00 0.00 +LBC 59 33.00 21.00 26.00 20.00 0.00 0.00 +LBC 60 30.00 26.00 19.00 25.00 0.00 0.00 +LBC 61 23.00 23.00 25.00 29.00 0.00 0.00 +LBC 62 35.00 19.00 20.00 26.00 0.00 0.00 +LBC 63 26.00 25.00 29.00 20.00 0.00 0.00 +LBC 64 30.00 20.00 27.00 23.00 0.00 0.00 +LBC 65 38.00 17.00 21.00 24.00 0.00 0.00 +LBC 66 33.00 26.00 14.00 27.00 0.00 0.00 +LBC 67 35.00 21.00 21.00 23.00 0.00 0.00 +LBC 68 39.00 28.00 15.00 18.00 0.00 0.00 +LBC 69 38.00 18.00 22.00 22.00 0.00 0.00 +LBC 70 40.00 13.00 22.00 25.00 0.00 0.00 +LBC 71 29.00 41.00 19.00 11.00 0.00 0.00 +LBC 72 33.00 26.00 28.00 13.00 0.00 0.00 +LBC 73 31.00 18.00 24.00 27.00 0.00 0.00 +LBC 74 31.00 32.00 13.00 24.00 0.00 0.00 +LBC 75 46.00 10.00 21.00 23.00 0.00 0.00 +LBC 76 23.00 28.00 25.00 24.00 0.00 0.00 +LBC 77 35.00 20.00 19.00 26.00 0.00 0.00 +LBC 78 29.00 30.00 26.00 15.00 0.00 0.00 +LBC 79 24.00 25.00 27.00 24.00 0.00 0.00 +LBC 80 40.00 18.00 29.00 13.00 0.00 0.00 +LBC 81 18.00 26.00 26.00 30.00 0.00 0.00 +LBC 82 30.00 25.00 28.00 17.00 0.00 0.00 +LBC 83 36.00 25.00 14.00 25.00 0.00 0.00 +LBC 84 22.00 39.00 23.00 16.00 0.00 0.00 +LBC 85 42.00 20.00 21.00 17.00 0.00 0.00 +LBC 86 12.00 47.00 16.00 25.00 0.00 0.00 +LBC 87 45.00 15.00 19.00 21.00 0.00 0.00 +LBC 88 26.00 24.00 31.00 19.00 0.00 0.00 +LBC 89 26.00 25.00 29.00 20.00 0.00 0.00 +LBC 90 24.00 22.00 26.00 28.00 0.00 0.00 +LBC 91 29.00 30.00 24.00 17.00 0.00 0.00 +LBC 92 22.00 13.00 32.00 33.00 0.00 0.00 +LBC 93 29.00 40.00 13.00 18.00 0.00 0.00 +LBC 94 30.00 16.00 25.00 29.00 0.00 0.00 +LBC 95 31.31 35.35 17.17 16.16 1.01 0.00 +LBC 96 34.00 27.00 15.00 24.00 0.00 0.00 +LBC 97 32.00 27.00 25.00 16.00 0.00 0.00 +LBC 98 21.21 31.31 24.24 23.23 1.01 0.00 +LBC 99 27.00 37.00 21.00 15.00 0.00 0.00 +LBC 100 29.00 15.00 26.00 30.00 0.00 0.00 +LBC 101 27.00 34.00 25.00 14.00 0.00 0.00 +LBC 102 20.00 14.00 36.00 30.00 0.00 0.00 +LBC 103 32.00 26.00 16.00 26.00 0.00 0.00 +LBC 104 30.00 28.00 22.00 20.00 0.00 0.00 +LBC 105 35.00 35.00 19.00 11.00 0.00 0.00 +LBC 106 22.00 32.00 25.00 21.00 0.00 0.00 +LBC 107 19.19 33.33 26.26 21.21 1.01 0.00 +LBC 108 27.27 33.33 21.21 18.18 1.01 0.00 +LBC 109 19.00 29.00 24.00 28.00 0.00 0.00 +LBC 110 20.20 31.31 28.28 20.20 1.01 0.00 +LBC 111 25.25 33.33 22.22 19.19 1.01 0.00 +LBC 112 39.39 28.28 16.16 16.16 1.01 0.00 +LBC 113 21.21 24.24 31.31 23.23 1.01 0.00 +LBC 114 19.00 31.00 35.00 15.00 0.00 0.00 +LBC 115 32.00 23.00 25.00 20.00 0.00 0.00 +LBC 116 20.00 29.00 35.00 16.00 0.00 0.00 +LBC 117 31.00 21.00 21.00 27.00 0.00 0.00 +LBC 118 25.00 14.00 35.00 26.00 0.00 0.00 +LBC 119 21.00 31.00 24.00 24.00 0.00 0.00 +LBC 120 19.00 24.00 27.00 30.00 0.00 0.00 +LBC 121 24.24 36.36 20.20 19.19 1.01 0.00 +LBC 122 18.00 25.00 23.00 34.00 0.00 0.00 +LBC 123 25.00 48.00 10.00 17.00 0.00 0.00 +LBC 124 10.00 31.00 35.00 24.00 0.00 0.00 +LBC 125 27.00 24.00 22.00 27.00 0.00 0.00 +LBC 126 24.00 19.00 26.00 31.00 0.00 0.00 +LBC 127 26.00 16.00 22.00 36.00 0.00 0.00 +LBC 128 16.00 35.00 30.00 19.00 0.00 0.00 +LBC 129 24.00 27.00 26.00 23.00 0.00 0.00 +LBC 130 25.00 19.00 23.00 33.00 0.00 0.00 +LBC 131 17.00 40.00 24.00 19.00 0.00 0.00 +LBC 132 20.00 27.00 24.00 29.00 0.00 0.00 +LBC 133 15.00 34.00 33.00 18.00 0.00 0.00 +LBC 134 22.00 19.00 31.00 28.00 0.00 0.00 +LBC 135 17.00 28.00 26.00 29.00 0.00 0.00 +LBC 136 25.00 33.00 14.00 28.00 0.00 0.00 +LBC 137 21.00 22.00 30.00 27.00 0.00 0.00 +LBC 138 15.00 30.00 29.00 26.00 0.00 0.00 +LBC 139 19.00 32.00 22.00 27.00 0.00 0.00 +LBC 140 19.00 24.00 29.00 28.00 0.00 0.00 +LBC 141 21.00 24.00 25.00 30.00 0.00 0.00 +LBC 142 17.00 32.00 35.00 16.00 0.00 0.00 +LBC 143 23.00 23.00 28.00 26.00 0.00 0.00 +LBC 144 20.00 33.00 24.00 23.00 0.00 0.00 +LBC 145 20.00 26.00 24.00 30.00 0.00 0.00 +LBC 146 26.00 15.00 40.00 19.00 0.00 0.00 +LBC 147 23.00 23.00 30.00 24.00 0.00 0.00 +LBC 148 12.00 32.00 33.00 23.00 0.00 0.00 +LBC 149 27.00 24.00 23.00 26.00 0.00 0.00 +LBC 150 12.00 32.00 21.00 35.00 0.00 0.00 +LBC 151 22.00 29.00 34.00 15.00 0.00 0.00 +LBC 152 16.00 21.00 26.00 37.00 0.00 0.00 +LBC 153 24.00 20.00 34.00 22.00 0.00 0.00 +LBC 154 25.00 22.00 28.00 25.00 0.00 0.00 +LBC 155 21.00 28.00 17.00 34.00 0.00 0.00 +LBC 156 16.00 23.00 36.00 25.00 0.00 0.00 +LBC 157 23.00 34.00 20.00 23.00 0.00 0.00 +LBC 158 21.00 33.00 21.00 25.00 0.00 0.00 +LBC 159 19.00 15.00 44.00 22.00 0.00 0.00 +LBC 160 24.00 31.00 22.00 23.00 0.00 0.00 +LBC 161 13.00 28.00 40.00 19.00 0.00 0.00 +LBC 162 33.00 19.00 20.00 28.00 0.00 0.00 +LBC 163 23.00 26.00 31.00 20.00 0.00 0.00 +LBC 164 33.00 19.00 20.00 28.00 0.00 0.00 +LBC 165 13.00 16.00 37.00 34.00 0.00 0.00 +LBC 166 20.00 36.00 30.00 14.00 0.00 0.00 +LBC 167 17.00 28.00 25.00 30.00 0.00 0.00 +LBC 168 16.00 24.00 31.00 29.00 0.00 0.00 +LBC 169 21.00 23.00 21.00 35.00 0.00 0.00 +LBC 170 22.00 24.00 27.00 27.00 0.00 0.00 +LBC 171 23.00 30.00 31.00 16.00 0.00 0.00 +LBC 172 24.00 22.00 30.00 24.00 0.00 0.00 +LBC 173 24.00 17.00 33.00 26.00 0.00 0.00 +LBC 174 21.00 24.00 33.00 22.00 0.00 0.00 +LBC 175 34.00 19.00 34.00 13.00 0.00 0.00 +LBC 176 17.00 37.00 24.00 22.00 0.00 0.00 +LBC 177 24.00 24.00 25.00 27.00 0.00 0.00 +LBC 178 19.00 26.00 30.00 25.00 0.00 0.00 +LBC 179 24.00 20.00 20.00 36.00 0.00 0.00 +LBC 180 22.00 25.00 31.00 22.00 0.00 0.00 +LBC 181 21.00 17.00 38.00 24.00 0.00 0.00 +LBC 182 35.00 21.00 20.00 24.00 0.00 0.00 +LBC 183 28.00 15.00 27.00 30.00 0.00 0.00 +LBC 184 17.00 30.00 29.00 24.00 0.00 0.00 +LBC 185 16.00 32.00 33.00 19.00 0.00 0.00 +LBC 186 21.00 22.00 36.00 21.00 0.00 0.00 +LBC 187 24.00 13.00 41.00 22.00 0.00 0.00 +LBC 188 29.00 19.00 30.00 22.00 0.00 0.00 +LBC 189 19.00 23.00 33.00 25.00 0.00 0.00 +LBC 190 24.00 28.00 25.00 23.00 0.00 0.00 +LBC 191 28.00 21.00 29.00 22.00 0.00 0.00 +LBC 192 37.00 25.00 13.00 25.00 0.00 0.00 +LBC 193 18.00 26.00 25.00 31.00 0.00 0.00 +LBC 194 21.00 34.00 24.00 21.00 0.00 0.00 +LBC 195 16.00 28.00 21.00 35.00 0.00 0.00 +LBC 196 23.00 23.00 27.00 27.00 0.00 0.00 +LBC 197 18.00 20.00 24.00 38.00 0.00 0.00 +LBC 198 15.00 19.00 39.00 27.00 0.00 0.00 +LBC 199 23.00 17.00 27.00 33.00 0.00 0.00 +LBC 200 25.00 27.00 23.00 25.00 0.00 0.00 +LBC 201 26.00 19.00 25.00 30.00 0.00 0.00 +LBC 202 23.00 23.00 21.00 33.00 0.00 0.00 +LBC 203 21.00 19.00 32.00 28.00 0.00 0.00 +LBC 204 26.00 29.00 24.00 21.00 0.00 0.00 +LBC 205 16.00 23.00 21.00 40.00 0.00 0.00 +LBC 206 28.00 25.00 21.00 26.00 0.00 0.00 +LBC 207 22.00 22.00 19.00 37.00 0.00 0.00 +LBC 208 12.00 32.00 32.00 24.00 0.00 0.00 +LBC 209 18.00 20.00 15.00 47.00 0.00 0.00 +LBC 210 18.00 15.00 45.00 22.00 0.00 0.00 +LBC 211 28.00 14.00 28.00 30.00 0.00 0.00 +LBC 212 23.00 27.00 22.00 28.00 0.00 0.00 +LBC 213 22.00 12.00 34.00 32.00 0.00 0.00 +LBC 214 16.00 24.00 26.00 34.00 0.00 0.00 +LBC 215 28.00 22.00 25.00 25.00 0.00 0.00 +LBC 216 18.00 17.00 26.00 39.00 0.00 0.00 +LBC 217 27.00 30.00 16.00 27.00 0.00 0.00 +LBC 218 18.00 24.00 24.00 34.00 0.00 0.00 +LBC 219 19.00 18.00 24.00 39.00 0.00 0.00 +LBC 220 28.00 23.00 24.00 25.00 0.00 0.00 +LBC 221 20.00 24.00 20.00 36.00 0.00 0.00 +LBC 222 22.00 21.00 19.00 38.00 0.00 0.00 +LBC 223 19.00 22.00 33.00 26.00 0.00 0.00 +LBC 224 19.00 20.00 27.00 34.00 0.00 0.00 +LBC 225 14.00 32.00 34.00 20.00 0.00 0.00 +LBC 226 20.00 20.00 29.00 31.00 0.00 0.00 +LBC 227 17.00 22.00 26.00 35.00 0.00 0.00 +LBC 228 34.00 20.00 25.00 21.00 0.00 0.00 +LBC 229 22.00 27.00 16.00 35.00 0.00 0.00 +LBC 230 23.00 33.00 15.00 29.00 0.00 0.00 +LBC 231 20.00 27.00 31.00 22.00 0.00 0.00 +LBC 232 25.00 23.00 11.00 41.00 0.00 0.00 +LBC 233 22.00 25.00 27.00 26.00 0.00 0.00 +LBC 234 14.00 27.00 23.00 36.00 0.00 0.00 +LBC 235 17.00 11.00 32.00 40.00 0.00 0.00 +LBC 236 29.00 20.00 24.00 27.00 0.00 0.00 +LBC 237 16.00 19.00 23.00 42.00 0.00 0.00 +LBC 238 22.00 25.00 29.00 24.00 0.00 0.00 +LBC 239 18.00 8.00 17.00 57.00 0.00 0.00 +LBC 240 27.00 26.00 14.00 33.00 0.00 0.00 +LBC 241 21.00 22.00 17.00 40.00 0.00 0.00 +LBC 242 26.00 28.00 10.00 36.00 0.00 0.00 +LBC 243 25.00 15.00 24.00 36.00 0.00 0.00 +LBC 244 15.00 24.00 16.00 45.00 0.00 0.00 +LBC 245 24.00 23.00 19.00 34.00 0.00 0.00 +LBC 246 18.00 25.00 29.00 28.00 0.00 0.00 +LBC 247 30.00 13.00 14.00 43.00 0.00 0.00 +LBC 248 22.00 17.00 26.00 35.00 0.00 0.00 +LBC 249 25.00 22.00 22.00 31.00 0.00 0.00 +LBC 250 25.00 20.00 20.00 35.00 0.00 0.00 +LBC 251 13.00 17.00 40.00 30.00 0.00 0.00 # 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 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count RL 251 200 +# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count +FRL 251 100 +# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count +LRL 251 100 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions ID 1 1 0 ID 2 1 0 @@ -1129,10 +1642,22 @@ IC 241 1 0 0 0 IC 247 1 0 0 0 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. -COV [1-1] 1 1 -COV [7-7] 7 1 +COV [2-2] 2 1 +COV [3-3] 3 3 +COV [4-4] 4 1 +COV [5-5] 5 5 +COV [9-9] 9 3 +COV [10-10] 10 2 +COV [11-11] 11 3 +COV [12-12] 12 2 +COV [13-13] 13 1 +COV [14-14] 14 1 +COV [15-15] 15 1 COV [18-18] 18 1 +COV [20-20] 20 6 +COV [21-21] 21 6 +COV [23-23] 23 3 COV [24-24] 24 1 -COV [25-25] 25 249 +COV [25-25] 25 211 # 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 0.0 100.000 0.000 0.000 0.000 0.000 0.000 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/samtools_stats_out1__gcc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out1__gcc.tab Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,252 @@ +# ACGT content per cycle. 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 [%] +1 21.94 30.10 34.18 13.78 2.04 0.00 +2 30.00 16.00 11.00 43.00 0.00 0.00 +3 33.00 25.00 9.00 33.00 0.00 0.00 +4 17.00 29.00 13.00 41.00 0.00 0.00 +5 37.00 22.00 12.00 29.00 0.00 0.00 +6 36.00 26.00 17.00 21.00 0.00 0.00 +7 29.50 13.50 31.50 25.50 0.00 0.00 +8 50.50 14.50 19.50 15.50 0.00 0.00 +9 17.00 33.00 18.00 32.00 0.00 0.00 +10 37.00 14.00 21.00 28.00 0.00 0.00 +11 20.50 14.50 29.50 35.50 0.00 0.00 +12 30.00 24.00 22.00 24.00 0.00 0.00 +13 27.00 15.00 21.00 37.00 0.00 0.00 +14 24.24 22.22 26.26 27.27 1.01 0.00 +15 25.50 20.50 24.50 29.50 0.00 0.00 +16 31.00 15.00 20.00 34.00 0.00 0.00 +17 28.00 25.00 14.00 33.00 0.00 0.00 +18 30.50 28.50 19.50 21.50 0.00 0.00 +19 29.00 26.00 21.00 24.00 0.00 0.00 +20 22.50 23.50 17.50 36.50 0.00 0.00 +21 35.50 17.50 19.50 27.50 0.00 0.00 +22 37.50 28.50 15.50 18.50 0.00 0.00 +23 31.31 19.19 13.13 36.36 1.01 0.00 +24 37.00 12.00 22.00 29.00 0.00 0.00 +25 35.50 22.50 17.50 24.50 0.00 0.00 +26 33.50 18.50 15.50 32.50 0.00 0.00 +27 34.50 14.50 25.50 25.50 0.00 0.00 +28 31.00 14.00 24.00 31.00 0.00 0.00 +29 30.00 27.00 24.00 19.00 0.00 0.00 +30 31.00 20.00 14.00 35.00 0.00 0.00 +31 33.50 29.50 13.50 23.50 0.00 0.00 +32 42.50 20.50 19.50 17.50 0.00 0.00 +33 25.50 23.50 14.50 36.50 0.00 0.00 +34 39.50 16.50 20.50 23.50 0.00 0.00 +35 32.50 23.50 21.50 22.50 0.00 0.00 +36 42.00 25.00 16.00 17.00 0.00 0.00 +37 38.00 17.00 19.00 26.00 0.00 0.00 +38 24.00 26.00 25.00 25.00 0.00 0.00 +39 22.50 41.50 18.50 17.50 0.00 0.00 +40 32.00 16.00 21.00 31.00 0.00 0.00 +41 33.00 28.00 19.00 20.00 0.00 0.00 +42 30.50 25.50 19.50 24.50 0.00 0.00 +43 35.00 29.00 15.00 21.00 0.00 0.00 +44 20.00 27.00 22.00 31.00 0.00 0.00 +45 40.50 21.50 21.50 16.50 0.00 0.00 +46 26.50 20.50 22.50 30.50 0.00 0.00 +47 38.50 29.50 16.50 15.50 0.00 0.00 +48 27.50 24.50 17.50 30.50 0.00 0.00 +49 28.50 32.50 10.50 28.50 0.00 0.00 +50 46.50 20.50 9.50 23.50 0.00 0.00 +51 34.50 28.50 13.50 23.50 0.00 0.00 +52 41.50 23.50 20.50 14.50 0.00 0.00 +53 20.00 28.00 26.00 26.00 0.00 0.00 +54 31.50 18.50 24.50 25.50 0.00 0.00 +55 30.50 22.50 16.50 30.50 0.00 0.00 +56 33.50 22.50 13.50 30.50 0.00 0.00 +57 23.00 24.00 23.00 30.00 0.00 0.00 +58 25.00 37.00 19.00 19.00 0.00 0.00 +59 34.00 23.00 24.00 19.00 0.00 0.00 +60 29.00 28.00 17.00 26.00 0.00 0.00 +61 25.50 23.50 24.50 26.50 0.00 0.00 +62 31.50 22.50 16.50 29.50 0.00 0.00 +63 27.50 28.50 25.50 18.50 0.00 0.00 +64 33.50 21.50 25.50 19.50 0.00 0.00 +65 35.50 19.50 18.50 26.50 0.00 0.00 +66 34.00 25.00 15.00 26.00 0.00 0.00 +67 37.00 23.00 19.00 21.00 0.00 0.00 +68 36.50 29.50 13.50 20.50 0.00 0.00 +69 38.50 19.50 20.50 21.50 0.00 0.00 +70 38.50 16.50 18.50 26.50 0.00 0.00 +71 25.50 38.50 21.50 14.50 0.00 0.00 +72 29.00 29.00 25.00 17.00 0.00 0.00 +73 32.50 20.50 21.50 25.50 0.00 0.00 +74 28.50 32.50 12.50 26.50 0.00 0.00 +75 41.50 12.50 18.50 27.50 0.00 0.00 +76 24.50 29.50 23.50 22.50 0.00 0.00 +77 36.00 21.00 18.00 25.00 0.00 0.00 +78 27.00 34.00 22.00 17.00 0.00 0.00 +79 21.50 26.50 25.50 26.50 0.00 0.00 +80 34.00 19.00 28.00 19.00 0.00 0.00 +81 17.00 26.00 26.00 31.00 0.00 0.00 +82 31.00 30.00 23.00 16.00 0.00 0.00 +83 31.50 26.50 12.50 29.50 0.00 0.00 +84 19.00 41.00 21.00 19.00 0.00 0.00 +85 37.50 24.50 16.50 21.50 0.00 0.00 +86 15.00 48.00 15.00 22.00 0.00 0.00 +87 41.00 16.00 18.00 25.00 0.00 0.00 +88 23.50 27.50 27.50 21.50 0.00 0.00 +89 26.50 27.50 26.50 19.50 0.00 0.00 +90 18.50 23.50 24.50 33.50 0.00 0.00 +91 27.00 32.00 22.00 19.00 0.00 0.00 +92 23.50 17.50 27.50 31.50 0.00 0.00 +93 25.50 37.50 15.50 21.50 0.00 0.00 +94 27.00 17.00 24.00 32.00 0.00 0.00 +95 26.77 37.88 14.65 20.71 1.01 0.00 +96 29.50 25.50 16.50 28.50 0.00 0.00 +97 29.00 31.00 21.00 19.00 0.00 0.00 +98 18.18 33.33 22.22 26.26 1.01 0.00 +99 24.50 33.50 24.50 17.50 0.00 0.00 +100 24.50 16.50 24.50 34.50 0.00 0.00 +101 25.00 40.00 19.00 16.00 0.00 0.00 +102 17.50 17.50 32.50 32.50 0.00 0.00 +103 31.00 26.00 16.00 27.00 0.00 0.00 +104 26.50 29.50 20.50 23.50 0.00 0.00 +105 34.00 33.00 21.00 12.00 0.00 0.00 +106 23.00 31.00 26.00 20.00 0.00 0.00 +107 17.68 35.86 23.74 22.73 1.01 0.00 +108 24.75 30.81 23.74 20.71 1.01 0.00 +109 17.00 31.00 22.00 30.00 0.00 0.00 +110 16.16 35.35 24.24 24.24 1.01 0.00 +111 24.24 32.32 23.23 20.20 1.01 0.00 +112 37.37 28.28 16.16 18.18 1.01 0.00 +113 19.70 22.73 32.83 24.75 1.01 0.00 +114 17.00 31.00 35.00 17.00 0.00 0.00 +115 29.50 24.50 23.50 22.50 0.00 0.00 +116 22.00 30.00 34.00 14.00 0.00 0.00 +117 27.00 23.00 19.00 31.00 0.00 0.00 +118 25.50 14.50 34.50 25.50 0.00 0.00 +119 22.50 34.50 20.50 22.50 0.00 0.00 +120 17.50 24.50 26.50 31.50 0.00 0.00 +121 27.78 33.84 22.73 15.66 1.01 0.00 +122 17.00 23.00 25.00 35.00 0.00 0.00 +123 23.50 46.50 11.50 18.50 0.00 0.00 +124 9.00 32.00 34.00 25.00 0.00 0.00 +125 24.00 27.00 19.00 30.00 0.00 0.00 +126 26.00 17.00 28.00 29.00 0.00 0.00 +127 26.50 16.50 21.50 35.50 0.00 0.00 +128 18.00 34.00 31.00 17.00 0.00 0.00 +129 25.50 25.50 27.50 21.50 0.00 0.00 +130 25.00 20.00 22.00 33.00 0.00 0.00 +131 17.50 39.50 24.50 18.50 0.00 0.00 +132 21.00 28.00 23.00 28.00 0.00 0.00 +133 13.50 31.50 35.50 19.50 0.00 0.00 +134 24.50 19.50 30.50 25.50 0.00 0.00 +135 16.50 23.50 30.50 29.50 0.00 0.00 +136 28.00 32.00 15.00 25.00 0.00 0.00 +137 22.50 21.50 30.50 25.50 0.00 0.00 +138 14.50 34.50 24.50 26.50 0.00 0.00 +139 20.50 29.50 24.50 25.50 0.00 0.00 +140 17.00 23.00 30.00 30.00 0.00 0.00 +141 20.50 23.50 25.50 30.50 0.00 0.00 +142 18.00 29.00 38.00 15.00 0.00 0.00 +143 22.00 24.00 27.00 27.00 0.00 0.00 +144 21.50 30.50 26.50 21.50 0.00 0.00 +145 22.00 21.00 29.00 28.00 0.00 0.00 +146 25.00 16.00 39.00 20.00 0.00 0.00 +147 26.50 22.50 30.50 20.50 0.00 0.00 +148 12.50 28.50 36.50 22.50 0.00 0.00 +149 26.50 23.50 23.50 26.50 0.00 0.00 +150 14.00 29.00 24.00 33.00 0.00 0.00 +151 19.50 30.50 32.50 17.50 0.00 0.00 +152 18.50 17.50 29.50 34.50 0.00 0.00 +153 22.50 22.50 31.50 23.50 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b/test-data/samtools_stats_out1__mpc.tab Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,255 @@ +# Mismatches per cycle and quality. +# Columns correspond to qualities, rows to cycles. 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1 1 3 2 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 2 0 0 0 3 0 0 0 +249 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 2 0 5 0 0 0 0 0 0 2 0 0 0 0 0 0 0 +250 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 2 0 0 0 2 0 0 0 +251 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 3 0 0 0 +252 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 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/samtools_stats_out1__sn.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_out1__sn.tab Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,39 @@ +# Summary Numbers. +raw total sequences: 200 +filtered sequences: 0 +sequences: 200 +is sorted: 1 +1st fragments: 100 +last fragments: 100 +reads mapped: 25 +reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +reads unmapped: 175 +reads properly paired: 0 # proper-pair bit set +reads paired: 200 # paired-end technology bit set +reads duplicated: 0 # PCR or optical duplicate bit set +reads MQ0: 6 # mapped and MQ=0 +reads QC failed: 0 +non-primary alignments: 0 +total length: 50200 # ignores clipping +total first fragment length: 25100 # ignores clipping +total last fragment length: 25100 # ignores clipping +bases mapped: 6275 # ignores clipping +bases mapped (cigar): 6275 # more accurate +bases trimmed: 0 +bases duplicated: 0 +mismatches: 591 # from NM fields +error rate: 9.418327e-02 # mismatches / bases mapped (cigar) +average length: 251 +average first fragment length: 251 +average last fragment length: 251 +maximum length: 251 +maximum first fragment length: 251 +maximum last fragment length: 251 +average quality: 34.7 +insert size average: 0.0 +insert size standard deviation: 0.0 +inward oriented pairs: 0 +outward oriented pairs: 0 +pairs with other orientation: 0 +pairs on different chromosomes: 0 +percentage of properly paired reads (%): 0.0 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/samtools_stats_ref.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_ref.fa.fai Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,1 @@ +chrM 16569 6 70 71 diff -r 24c5d43cb545 -r 95a7ddf617e7 test-data/test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Thu Sep 27 09:05:10 2018 -0400 @@ -0,0 +1,3 @@ +>alpha +tggggtgtcatagtaatccggttgggagtccgaggctaagaatattcatttagaggtcgg +catattatccagaactttgcagccatatctccaagacatg