# HG changeset patch
# User iuc
# Date 1508840999 14400
# Node ID 3bad335ccea9027a4085f587a94c6638837516cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
diff -r 000000000000 -r 3bad335ccea9 generate_test_data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_test_data.sh Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,195 @@
+#!/usr/bin/env bash
+
+# 1st test
+mkdir multiqc_WDir
+
+mkdir 'multiqc_WDir/cutadapt_0'
+cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt'
+sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt'
+
+mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0'
+cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt'
+mkdir 'multiqc_WDir/fastqc_1/data_0/file_1'
+cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt'
+
+mkdir 'multiqc_WDir/flexbar_2'
+cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt'
+
+mkdir 'multiqc_WDir/sortmerna_3'
+cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt'
+
+mkdir 'multiqc_WDir/trimmomatic_4'
+cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt'
+
+multiqc multiqc_WDir
+
+mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html'
+mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt'
+mv 'multiqc_data/multiqc_cutadapt.txt' 'test-data/cutadapt_stats.tabular'
+mv 'multiqc_data/multiqc_fastqc.txt' 'test-data/fastqc_stats.tabular'
+mv 'multiqc_data/multiqc_flexbar.txt' 'test-data/flexbar_stats.tabular'
+mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/pre_alignment_soft_stats.tabular'
+mv 'multiqc_data/multiqc_sortmerna.txt' 'test-data/sortmerna_stats.tabular'
+mv 'multiqc_data/multiqc_trimmomatic.txt' 'test-data/trimmomatic_stats.tabular'
+
+rm -rf 'multiqc_WDir'
+rm -rf 'multiqc_data/'
+
+# 2nd test
+mkdir multiqc_WDir
+
+mkdir 'multiqc_WDir/bismark_0'
+cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt'
+
+mkdir 'multiqc_WDir/bowtie2_1'
+cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt'
+cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt'
+
+mkdir 'multiqc_WDir/hisat2_3'
+cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt'
+cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt'
+
+mkdir 'multiqc_WDir/kallisto_4'
+cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt'
+cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt'
+
+mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0'
+cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt'
+
+mkdir -p 'multiqc_WDir/star_6/log_0'
+cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out'
+mkdir 'multiqc_WDir/star_6/genecounts_1'
+cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab'
+
+mkdir 'multiqc_WDir/tophat_7'
+cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt'
+
+multiqc multiqc_WDir
+
+mv 'multiqc_report.html' 'test-data/aligner_soft_report.html'
+mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular'
+mv 'multiqc_data/multiqc_bowtie2.txt' 'test-data/bowtie2_stats.tabular'
+mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/aligner_soft_stats.tabular'
+mv 'multiqc_data/multiqc_hisat2.txt' 'test-data/hisat2_stats.tabular'
+mv 'multiqc_data/multiqc_kallisto.txt' 'test-data/kallisto_stats.tabular'
+mv 'multiqc_data/multiqc_star.txt' 'test-data/star_stats.tabular'
+mv 'multiqc_data/multiqc_tophat.txt.txt' 'test-data/tophat_stats.tabular'
+
+rm -rf 'multiqc_WDir'
+rm -rf 'multiqc_data/'
+
+# 3rd test
+mkdir multiqc_WDir
+
+mkdir 'multiqc_WDir/bamtools_0'
+cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools_0/bamtools.txt'
+
+mkdir 'multiqc_WDir/bcftools_1'
+cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools_1/bcftools.txt'
+
+mkdir 'multiqc_WDir/busco_2'
+cp 'test-data/busco.txt' 'multiqc_WDir/busco_2/short_summary_busco.txt'
+
+mkdir 'multiqc_WDir/featureCounts_3'
+cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts_3/featureCounts.summary'
+
+mkdir 'multiqc_WDir/gatk_4'
+cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk_4/gatk_BaseRecalibrator.txt'
+cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk_4/gatk_varianteval.txt'
+
+mkdir 'multiqc_WDir/htseq_5'
+cp 'test-data/htseq.txt' 'multiqc_WDir/htseq_5/htseq.txt'
+
+mkdir 'multiqc_WDir/picard_6'
+cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard_6/picard_collectGcBias.txt'
+cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectInsertSizeMetrics.txt'
+cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard_6/picard_MarkDuplicates.txt'
+cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard_6/picard_CollectBaseDistributionByCycle.txt'
+cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectRnaSeqMetrics.txt'
+cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectAlignmentSummaryMetrics.txt'
+
+mkdir 'multiqc_WDir/prokka_7'
+cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka_7/prokka_1.txt'
+cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka_7/prokka_2.txt'
+
+mkdir -p 'multiqc_WDir/quast_8/file_0'
+cp 'test-data/quast.tsv' 'multiqc_WDir/quast_8/file_0/report.tsv'
+
+#mkdir 'multiqc_WDir/rsem_9'
+#cp 'test-data/rsem.txt' 'multiqc_WDir/rsem_9/rsem.cnt'
+
+mkdir -p 'multiqc_WDir/rseqc_10/read_gc_0'
+cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls'
+
+mkdir 'multiqc_WDir/samblaster_11'
+cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster_11/samblaster.txt'
+
+mkdir -p 'multiqc_WDir/samtools_12/stats_0'
+cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt'
+mkdir 'multiqc_WDir/samtools_12/flagstat_1'
+cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt'
+mkdir 'multiqc_WDir/samtools_12/idxstats_2'
+cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat'
+
+#mkdir 'multiqc_WDir/snpeff_13'
+#cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff_13/snpeff.txt'
+
+mkdir -p 'multiqc_WDir/vcftools_14/tstv_by_qual_0'
+cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual'
+
+multiqc multiqc_WDir
+
+mv 'multiqc_report.html' 'test-data/post_aligner_soft_report.html'
+mv 'multiqc_data/multiqc_bamtools_stats.txt' 'test-data/bamtools_stats.tabular'
+mv 'multiqc_data/multiqc_bcftools_stats.txt' 'test-data/bcftools_stats.tabular'
+mv 'multiqc_data/multiqc_busco.txt' 'test-data/busco_stats.tabular'
+mv 'multiqc_data/multiqc_featureCounts.txt' 'test-data/featureCounts_stats.tabular'
+mv 'multiqc_data/multiqc_gatk_varianteval.txt' 'test-data/gatk_varianteval_stats.tabular'
+mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/post_aligner_soft_stats.tabular'
+mv 'multiqc_data/multiqc_htseq.txt' 'test-data/htseq_stats.tabular'
+mv 'multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt' 'test-data/picard_AlignmentSummaryMetrics_stats.tabular'
+mv 'multiqc_data/multiqc_picard_RnaSeqMetrics.txt' 'test-data/picard_RnaSeqMetrics_stats.tabular'
+mv 'multiqc_data/multiqc_picard_baseContent.txt' 'test-data/picard_baseContent_stats.tabular'
+mv 'multiqc_data/multiqc_picard_dups.txt' 'test-data/picard_dups_stats.tabular'
+mv 'multiqc_data/multiqc_picard_insertSize.txt' 'test-data/picard_insertSize_stats.tabular'
+mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular'
+mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular'
+#mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular'
+mv 'multiqc_data/multiqc_rseqc.txt' 'test-data/rseqc_stats.tabular'
+mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular'
+mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular'
+mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular'
+#mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular'
+
+rm -rf 'multiqc_WDir'
+rm -rf 'multiqc_data/'
+
+# 4th test
+mkdir multiqc_WDir
+
+mkdir 'multiqc_WDir/custom_content_0'
+cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv'
+cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv'
+
+echo "custom_data:" > 'config_file'
+echo " section_0:" >> 'config_file'
+echo " file_format: 'tsv'" >> 'config_file'
+echo " section_name: 'BPC'" >> 'config_file'
+echo " title: 'Base peak chromatogram'" >> 'config_file'
+echo " description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'" >> 'config_file'
+echo " plot_type: 'linegraph'" >> 'config_file'
+echo " pconfig:" >> 'config_file'
+echo " id: 'section_0_linegraph'" >> 'config_file'
+echo " ylab: 'Base Peak Intensity'" >> 'config_file'
+echo " xlab: 'Retention Time'" >> 'config_file'
+echo "sp:" >> 'config_file'
+echo " section_0:" >> 'config_file'
+echo " fn: 'file_0_*'" >> 'config_file'
+
+multiqc multiqc_WDir -c 'config_file'
+
+mv 'multiqc_report.html' 'test-data/report_manual_custom_content.html'
+
+rm 'config_file'
+rm -rf 'multiqc_WDir'
+rm -rf 'multiqc_data/'
diff -r 000000000000 -r 3bad335ccea9 multiqc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/multiqc.xml Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,994 @@
+
+ aggregate results from bioinformatics analyses into a single report
+
+ 1.2
+
+
+
+
+
+
+
+
+ multiqc
+
+ mulitqc --version
+
+&2 ; exit 1; } &&
+
+mkdir multiqc_WDir &&
+
+#set $configfile="F"
+
+#for $i, $repeat in enumerate( $results )
+ #set software_dir = 'multiqc_WDir/' + str($repeat.software_cond.software) + '_' + str($i)
+ mkdir $software_dir &&
+
+ #if str($repeat.software_cond.software) == "bamtools"
+ #set $pattern = "Stats for BAM file(s)"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "bcftools"
+ #set $pattern = "This file was produced by bcftools stats"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "bismark"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set file_prefix = $software_dir + '/' + str($repeat2.type) + '_' + str($j)
+ #if str($repeat2.type) == "align"
+ #for $file in $repeat2.input
+ ln -s '$file' '${file_prefix}_${file.element_identifier}_SE_report.txt' &&
+ #end for
+ #elif str($repeat2.type) == "dedup"
+ #for $file in $repeat2.input
+ ln -s '$file' '${file_prefix}_${file.element_identifier}_deduplication_report.txt' &&
+ #end for
+ #elif str($repeat2.type) == "meth_extract"
+ #for $file in $repeat2.input
+ ln -s '$file' '${file_prefix}_${file.element_identifier}_splitting_report.txt' &&
+ #end for
+ #elif str($repeat2.type) == "m_bias"
+ #for $file in $repeat2.input
+ ln -s '$file' '${file_prefix}_${file.element_identifier}_M-bias.txt' &&
+ #end for
+ #elif str($repeat2.type) == "bam2nuc"
+ #for $file in $repeat2.input
+ ln -s '$file' '${file_prefix}_${file.element_identifier}.nucleotide_stats.txt' &&
+ #end for
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "bowtie2"
+ #set $pattern = "reads; of these:"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "busco"
+ ## Searches for files "short_summary_[samplename].txt"
+ #for $file in $repeat.software_cond.input
+ ln -s '$file' '$software_dir/short_summary_${file.element_identifier}' &&
+ #end for
+ #elif str($repeat.software_cond.software) == "cutadapt"
+ #set $pattern = "This is cutadapt"
+ #for $file in $repeat.software_cond.input
+ #set file_path = $software_dir + '/' + str($file.element_identifier) + '.txt'
+ ln -s '$file' '$file_path' &&
+ ## replace header for old cutadapt release
+ sed -i.old 's/You are running/This is/' '$file_path' &&
+ grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" &&
+ #end for
+ #elif str($repeat.software_cond.software) == "fastqc"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set repeat_dir = $software_dir + '/' + str($repeat2.type) + '_' + str($j)
+ mkdir '$repeat_dir' &&
+ #if str($repeat2.type) == "data"
+ #for $k, $file in enumerate($repeat2.input)
+ #set file_dir = $repeat_dir + '/file_' + str($k)
+ mkdir '$file_dir' &&
+ ln -s '$file' '$file_dir/fastqc_data.txt' &&
+ #end for
+ #elif str($repeat2.type) == "theoretical_gc"
+ #for $file in $repeat2.input
+ ln -s '$file' '$repeat_dir/${file.element_identifier}_fastqc_theoretical_gc' &&
+ #end for
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "featureCounts"
+ #for $file in $repeat.software_cond.input
+ #set file_prefix = $software_dir + '/' + str($file.element_identifier)
+ #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1
+ echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> '$file_prefix.summary' &&
+ cat '$file' >> '${file_prefix}.summary' &&
+ #else
+ ln -s '$file' '${file_prefix}.summary' &&
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "flexbar"
+ #set $pattern = "flexible barcode and adapter removal"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "gatk"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #if str($repeat2.type) == "varianteval"
+ #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "base_recalibrator"
+ #set $pattern = "#:GATKTable:Arguments:Recalibration"
+ @LN_2_FILES@
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "hicup"
+ #for $file in $repeat.software_cond.input
+ ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' &&
+ #end for
+ #elif str($repeat.software_cond.software) == "hisat2"
+ #set $pattern = "HISAT2 summary stats:"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "htseq"
+ #set $pattern = "__too_low_aQual"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "kallisto"
+ #set $pattern = "finding pseudoalignments for the reads"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "picard"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #if str($repeat2.type) == "alignment_metrics"
+ #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "basedistributionbycycle"
+ #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "gcbias"
+ #set $pattern = "picard.analysis.GcBias"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "hsmetrics"
+ #set $pattern = "picard.analysis.directed.HsMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "insertsize"
+ #set $pattern = "picard.analysis.InsertSizeMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "markdups"
+ #set $pattern = "picard.sam.DuplicationMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "oxogmetrics"
+ #set $pattern = "picard.analysis.CollectOxoGMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "pcr_metrics"
+ #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "rnaseqmetrics"
+ #set $pattern = "Collect"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "rrbs_metrics"
+ #set $pattern = "picard.analysis.RrbsSummaryMetrics"
+ @LN_2_FILES@
+ #elif str($repeat2.type) == "wgs_metrics"
+ #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
+ @LN_2_FILES@
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "prokka"
+ #set $pattern = "contigs:"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "quast"
+ #for $k, $file in enumerate($repeat.software_cond.input)
+ #set file_dir = $software_dir + '/file_' + str($k)
+ mkdir '$file_dir' &&
+ ln -s '$file' '$file_dir/report.tsv' &&
+ #end for
+ #elif str($repeat.software_cond.software) == "rsem"
+ #for $file in $repeat.software_cond.input
+ ln -s '$file' '$software_dir/${file.element_identifier}.cnt' &&
+ #end for
+ #elif str($repeat.software_cond.software) == "rseqc"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
+ mkdir '$repeat_dir' &&
+ #if str($repeat2.type.type) == "bam_stat"
+ #set $pattern = "Proper-paired reads map to different chrom:"
+ @LN_3_FILES@
+ #elif str($repeat2.type.type) == "gene_body_coverage"
+ #for $k, $file in enumerate($repeat2.type.input)
+ ln -s '$file' '$repeat_dir/file_${k}.geneBodyCoverage.txt' &&
+ #end for
+ #elif str($repeat2.type.type) == "inner_distance"
+ #for $k, $file in enumerate($repeat2.type.input)
+ ln -s '${file}' '$repeat_dir/file_${k}.inner_distance_freq.txt' &&
+ #end for
+ #elif str($repeat2.type.type) == "junction_annotation"
+ #set $pattern = "Partial Novel Splicing Junctions:"
+ @LN_3_FILES@
+ #elif str($repeat2.type.type) == "read_gc"
+ #for $k, $file in enumerate($repeat2.type.input)
+ ln -s '$file' '$repeat_dir/file_${k}.GC.xls' &&
+ #end for
+ #elif str($repeat2.type.type) == "junction_annotation"
+ #set $pattern = "Group Total_bases Tag_count Tags/Kb"
+ @LN_3_FILES@
+ #elif str($repeat2.type.type) == "read_duplication_pos"
+ #for $k, $file in enumerate($repeat2.type.input)
+ ln -s '$file' '$repeat_dir/file_${k}.pos.DupRate.xls' &&
+ #end for
+ #elif str($repeat2.type.type) == "infer_experiment"
+ #set $pattern = "Fraction of reads explained by"
+ #for $k, $file in enumerate($repeat2.type.input)
+ grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
+ ln -s '$file' '$repeat_dir/$file_${k}_infer_experiment.txt' &&
+ #end for
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "salmon"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
+ mkdir '$repeat_dir' &&
+ #if str($repeat2.type.type) == "meta"
+ #for $k, $file in enumerate($repeat2.type.input)
+ #set file_dir = $repeat_dir + '/file_' + str($k)
+ mkdir '$file_dir' &&
+ ln -s '$file' '$file_dir/meta_info.json' &&
+ #end for
+ #elif str($repeat2.type.type) == "fld"
+ #for $k, $file in enumerate($repeat2.type.input)
+ #set file_dir = $repeat_dir + '/file_' + str($k)
+ mkdir '$file_dir' &&
+ ln -s '$file' '$file_dir/flenDist.txt' &&
+ #end for
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "samblaster"
+ #set $pattern = "samblaster: Version"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "samtools"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
+ mkdir '$repeat_dir' &&
+ #if str($repeat2.type.type) == "stats"
+ #set $pattern = "This file was produced by samtools stats"
+ @LN_3_FILES@
+ #elif str($repeat2.type.type) == "flagstat"
+ #set $pattern = "in total (QC-passed reads + QC-failed reads)"
+ @LN_3_FILES@
+ #elif str($repeat2.type.type) == "idxstats"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '$repeat_dir/${file.element_identifier}_idxstat' &&
+ #end for
+ #elif str($repeat2.type.type) == "rmdup"
+ #set $pattern = "[bam_rmdup"
+ @LN_3_FILES@
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "snpeff"
+ #set $pattern = "SnpEff_version"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "sortmerna"
+ #set $pattern = "Minimal SW score based on E-value"
+ @LN_FILES@
+ #else if str($repeat.software_cond.software) == "star":
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
+ mkdir $repeat_dir &&
+ #if str($repeat2.type.type) == "log"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '${repeat_dir}/{$file.element_identifier}_Log.final.out' &&
+ #end for
+ #elif str($repeat2.type.type) == "genecounts"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '${repeat_dir}/{$file.element_identifier}_ReadsPerGene.out.tab' &&
+ #end for
+ #end if
+ #end for
+ #elif str($repeat.software_cond.software) == "tophat"
+ #for $file in $repeat.software_cond.input
+ ln -s '$file' '$software_dir/${file.element_identifier}align_summary.txt' &&
+ #end for
+ #elif str($repeat.software_cond.software) == "trimmomatic"
+ #set $pattern = "Trimmomatic"
+ @LN_FILES@
+ #elif str($repeat.software_cond.software) == "vcftools"
+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
+ #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j)
+ mkdir $file_dir &&
+ #if str($repeat2.type.type) == "relatedness2"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '${repeat_dir}/{$file.element_identifier}.relatedness2' &&
+ #end for
+ #elif str($repeat2.type) == "tstv_by_count"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.count' &&
+ #end for
+ #elif str($repeat2.type) == "tstv_by_qual"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.qual' &&
+ #end for
+ #elif str($repeat2.type) == "tstv_summary"
+ #for $file in $repeat2.type.input
+ ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.summary' &&
+ #end for
+ #end if
+ #end for
+ #else if str($repeat.software_cond.software) == "custom_content":
+ #set $configfile = "T"
+ #for $j, $file in enumerate( $repeat.software_cond.input )
+ ln -s '$file' '${software_dir}/file_${i}_${j}' &&
+ more $file &&
+ #end for
+ #end if
+#end for
+
+multiqc multiqc_WDir
+
+#if $configfile == "T"
+ -c '$multiqc_config'
+#end if
+ ]]>
+
+
+
+
+
+
+
+
+
+
+ Bamtools
+ Bcftools
+
+
+ Bismark
+
+ Bowtie 2
+ BUSCO
+
+ Cutadapt/Trim Galore!
+
+
+
+ FastQC
+ featureCounts
+ Flexbar
+ GATK (BaseRecalibrator or VariantEval output)
+
+
+ HISAT2
+
+ HTSeq
+
+ Kallisto
+
+
+
+
+ Picard
+
+ Prokka
+
+
+ QUAST
+
+
+ RSeQC (bam_stat, gene_body_coverage, infer_experiment, ...)
+
+ Samblaster
+ Samtools
+
+ SortMeRNA
+
+
+ STAR
+
+ TopHat2
+ Trimmomatic
+ VCFTools
+
+ Custom Content
+
+
+
+
+
+
+
+
+
+
+ Alignment file
+ Deduplication file
+ Methylation file
+ m_bias file
+ bam2nuc file
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Raw data
+ Theorectical GC
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Variant eval file
+ Base recalibrator file
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Alignment metrics
+ Base distribution by cycle
+ GC bias
+ HS Metrics
+ Insert size
+ Markdups
+ Oxog metrics
+ PCR metrics
+ RNA Seq metrics
+ RRBS metrics
+ WGS metrics
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ bam_stat
+ gene_body_coverage
+ infer_experiment
+ inner_distance
+ junction_annotation
+ junction_saturation
+ read_distribution
+ read_duplication_pos
+ read_gc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ stats
+ flagstat
+ idxstats
+ rmdup
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Log
+ Gene counts
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ relatedness2
+ tstv_by_count
+ tstv_by_qual
+ tstv_summary
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ linegraph
+ bargraph
+ scatter
+ generalstats
+ table
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ saveLog
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ `_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.
+
+**Inputs**
+
+MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
+
+----
+
+The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`EnginesOn `_ and Rennes GenOuest Bio-informatics Core Facility).
+ ]]>
+
+ 10.1093/bioinformatics/btw354
+
+
diff -r 000000000000 -r 3bad335ccea9 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,21 @@
+Galaxy MultiQC wrapper
+========================
+
+Aggregate results from bioinformatics analyses across many samples into a single report
+
+MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+
+
+Prevent displaying MultiQC webpage as gibberish
+-----------------------------------------------
+
+For Galaxy to display MultiQC's HTML output properly, you need to either:
+
+1. Deactivate the sanitize_all_html option in galaxy.ini (sanitize_all_html = False), or
+2. Whitelist the tool in "Manage Display Whitelist" after installing
+
+Support new modules
+-------------------
+
+Currently, the wrapper supports the modules for tools found on the MTS.
+To add new ones, you can look at the patterns at https://github.com/ewels/MultiQC/blob/master/multiqc/utils/search_patterns.yaml
diff -r 000000000000 -r 3bad335ccea9 test-data/aligner_soft_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aligner_soft_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,14 @@
+Sample Cutadapt_percent_trimmed Kallisto_fragment_length Kallisto_percent_aligned Kallisto_pseudoaligned_reads Bismark_aligned_reads Bismark_percent_aligned Bowtie 2_overall_alignment_rate HISAT2_overall_alignment_rate STAR_uniquely_mapped_percent STAR_uniquely_mapped Tophat_overall_aligned_percent Tophat_aligned_not_multimapped_discordant
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.65114569077758 48531088.0
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.50278473550448 59280920.0
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055
+bismark_SE_report 220558.0 69.71079996207212
+bowtie2_1 98.33
+bowtie2_2 98.31
+hisat2_1 96.15
+hisat2_2 96.15
+star_log 89.0 89.0
+tophat_align 99.5 307733.0
diff -r 000000000000 -r 3bad335ccea9 test-data/bamtools.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,16 @@
+**********************************************
+Stats for BAM file(s):
+**********************************************
+
+Total reads: 339957930
+Mapped reads: 316585701 (93.125%)
+Forward strand: 181666967 (53.4381%)
+Reverse strand: 158290963 (46.5619%)
+Failed QC: 0 (0%)
+Duplicates: 0 (0%)
+Paired-end reads: 339957930 (100%)
+'Proper-pairs': 312895116 (92.0394%)
+Both pairs mapped: 314020716 (92.3705%)
+Read 1: 169978965
+Read 2: 169978965
+Singletons: 2564985 (0.754501%)
diff -r 000000000000 -r 3bad335ccea9 test-data/bamtools_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamtools_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample mapped_reads mapped_reads_pct forward_strand_pct read_2 read_1 duplicates both_mapped reverse_strand_pct duplicates_pct reverse_strand forward_strand failed_qc_pct both_mapped_pct failed_qc singletons total_reads singletons_pct paired_end paired_end_pct
+bamtools 316585701.0 93.125 53.4381 169978965.0 169978965.0 0.0 314020716.0 46.5619 0.0 158290963.0 181666967.0 0.0 92.3705 0.0 2564985.0 339957930.0 0.754501 339957930.0 100.0
diff -r 000000000000 -r 3bad335ccea9 test-data/bcftools.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bcftools.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,1177 @@
+# This file was produced by bcftools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-vcfstats.
+# The command line was: bcftools stats Test1.vcf.gz
+#
+# Definition of sets:
+# ID [2]id [3]tab-separated file names
+ID 0 Test1.vcf.gz
+# SN, Summary numbers:
+# SN [2]id [3]key [4]value
+SN 0 number of samples: 1
+SN 0 number of records: 5522770
+SN 0 number of no-ALTs: 0
+SN 0 number of SNPs: 4474244
+SN 0 number of MNPs: 72330
+SN 0 number of indels: 902934
+SN 0 number of others: 73262
+SN 0 number of multiallelic sites: 0
+SN 0 number of multiallelic SNP sites: 0
+# TSTV, transitions/transversions:
+# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
+TSTV 0 2968539 1505704 1.97 2968539 1505704 1.97
+# SiS, Singleton stats:
+# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
+SiS 0 1 4474243 2968539 1505704 902934 0 0 902934
+# AF, Stats by non-reference allele frequency:
+# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
+AF 0 0.000000 4474243 2968539 1505704 902934 0 0 902934
+# QUAL, Stats by quality:
+# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
+QUAL 0 25 0 0 0 2
+QUAL 0 26 0 0 0 14
+QUAL 0 27 330 117 213 52
+QUAL 0 28 0 0 0 36
+QUAL 0 29 698 273 425 136
+QUAL 0 30 0 0 0 70
+QUAL 0 31 0 0 0 70
+QUAL 0 32 1071 538 533 242
+QUAL 0 33 0 0 0 134
+QUAL 0 34 2006 1108 898 483
+QUAL 0 35 0 0 0 169
+QUAL 0 36 0 0 0 114
+QUAL 0 37 3117 1822 1295 717
+QUAL 0 38 0 0 0 203
+QUAL 0 39 4890 2607 2283 794
+QUAL 0 40 475 251 224 194
+QUAL 0 41 0 0 0 100
+QUAL 0 42 9823 5611 4212 1577
+QUAL 0 43 0 0 0 44
+QUAL 0 44 1294 671 623 107
+QUAL 0 45 575 308 267 113
+QUAL 0 46 0 0 0 53
+QUAL 0 47 1220 724 496 137
+QUAL 0 48 755 419 336 160
+QUAL 0 49 0 0 0 78
+QUAL 0 50 2490 1450 1040 280
+QUAL 0 51 389 160 229 161
+QUAL 0 52 0 0 0 103
+QUAL 0 53 1428 759 669 291
+QUAL 0 54 170 93 77 179
+QUAL 0 55 1497 897 600 419
+QUAL 0 56 810 385 425 214
+QUAL 0 57 0 0 0 186
+QUAL 0 58 2427 1436 991 501
+QUAL 0 59 1370 675 695 333
+QUAL 0 60 180 97 83 185
+QUAL 0 61 4117 2446 1671 678
+QUAL 0 62 756 376 380 329
+QUAL 0 63 3582 2107 1475 672
+QUAL 0 64 2047 1062 985 355
+QUAL 0 65 404 190 214 277
+QUAL 0 66 7220 4196 3024 1273
+QUAL 0 67 502 248 254 266
+QUAL 0 68 1707 962 745 230
+QUAL 0 69 2503 1319 1184 492
+QUAL 0 70 0 0 0 231
+QUAL 0 71 3085 1777 1308 644
+QUAL 0 72 142 58 84 298
+QUAL 0 73 1880 1048 832 389
+QUAL 0 74 2127 1225 902 646
+QUAL 0 75 1181 691 490 404
+QUAL 0 76 3685 2138 1547 709
+QUAL 0 77 715 403 312 398
+QUAL 0 78 3041 1780 1261 641
+QUAL 0 79 3287 1867 1420 790
+QUAL 0 80 2149 1253 896 592
+QUAL 0 81 4668 2759 1909 964
+QUAL 0 82 1655 910 745 529
+QUAL 0 83 3422 2034 1388 604
+QUAL 0 84 5891 3393 2498 1272
+QUAL 0 85 3175 1872 1303 701
+QUAL 0 86 1797 1052 745 474
+QUAL 0 87 2673 1550 1123 627
+QUAL 0 88 3927 2334 1593 783
+QUAL 0 89 2503 1498 1005 632
+QUAL 0 90 4171 2440 1731 884
+QUAL 0 91 3268 2019 1249 735
+QUAL 0 92 3328 1950 1378 929
+QUAL 0 93 4280 2602 1678 764
+QUAL 0 94 1197 692 505 640
+QUAL 0 95 7503 4457 3046 1207
+QUAL 0 96 914 533 381 683
+QUAL 0 97 7986 4762 3224 1443
+QUAL 0 98 1750 1062 688 496
+QUAL 0 99 3108 1917 1191 845
+QUAL 0 100 3476 2094 1382 734
+QUAL 0 101 3338 2007 1331 824
+QUAL 0 102 3860 2320 1540 933
+QUAL 0 103 3775 2295 1480 840
+QUAL 0 104 3468 2115 1353 1002
+QUAL 0 105 4727 2877 1850 1006
+QUAL 0 106 4536 2690 1846 976
+QUAL 0 107 3022 1895 1127 874
+QUAL 0 108 5322 3178 2144 1189
+QUAL 0 109 3979 2458 1521 957
+QUAL 0 110 2929 1739 1190 787
+QUAL 0 111 3070 1833 1237 818
+QUAL 0 112 5040 3031 2009 1124
+QUAL 0 113 4212 2576 1636 1001
+QUAL 0 114 3621 2186 1435 968
+QUAL 0 115 5099 2986 2113 1122
+QUAL 0 116 3852 2361 1491 949
+QUAL 0 117 4707 2837 1870 1269
+QUAL 0 118 3947 2396 1551 879
+QUAL 0 119 3287 1983 1304 823
+QUAL 0 120 5247 3143 2104 1090
+QUAL 0 121 2306 1414 892 808
+QUAL 0 122 6622 4048 2574 1269
+QUAL 0 123 1732 1099 633 749
+QUAL 0 124 6548 3882 2666 1262
+QUAL 0 125 2220 1308 912 753
+QUAL 0 126 6761 4055 2706 1409
+QUAL 0 127 5667 3398 2269 1053
+QUAL 0 128 1392 861 531 654
+QUAL 0 129 6512 3880 2632 1259
+QUAL 0 130 2571 1566 1005 825
+QUAL 0 131 4866 2920 1946 1007
+QUAL 0 132 5050 3107 1943 1046
+QUAL 0 133 4195 2459 1736 965
+QUAL 0 134 3776 2315 1461 932
+QUAL 0 135 3828 2338 1490 954
+QUAL 0 136 4106 2495 1611 868
+QUAL 0 137 4609 2828 1781 978
+QUAL 0 138 2879 1792 1087 854
+QUAL 0 139 4686 2851 1835 1092
+QUAL 0 140 3988 2391 1597 997
+QUAL 0 141 2942 1816 1126 802
+QUAL 0 142 3706 2258 1448 928
+QUAL 0 143 4544 2714 1830 1124
+QUAL 0 144 3151 1878 1273 748
+QUAL 0 145 3459 2069 1390 928
+QUAL 0 146 3747 2282 1465 1003
+QUAL 0 147 3272 2000 1272 813
+QUAL 0 148 2796 1665 1131 834
+QUAL 0 149 3762 2273 1489 924
+QUAL 0 150 3795 2321 1474 1055
+QUAL 0 151 2732 1640 1092 766
+QUAL 0 152 2689 1609 1080 787
+QUAL 0 153 3350 2045 1305 896
+QUAL 0 154 2595 1570 1025 753
+QUAL 0 155 3515 2153 1362 915
+QUAL 0 156 3004 1793 1211 800
+QUAL 0 157 2671 1632 1039 725
+QUAL 0 158 3084 1857 1227 864
+QUAL 0 159 3513 2137 1376 925
+QUAL 0 160 3039 1802 1237 854
+QUAL 0 161 3335 2030 1305 818
+QUAL 0 162 2925 1718 1207 802
+QUAL 0 163 3013 1836 1177 765
+QUAL 0 164 3555 2166 1389 865
+QUAL 0 165 2997 1811 1186 868
+QUAL 0 166 3144 1887 1257 841
+QUAL 0 167 3052 1783 1269 797
+QUAL 0 168 3072 1850 1222 809
+QUAL 0 169 3642 2254 1388 1000
+QUAL 0 170 3396 2080 1316 886
+QUAL 0 171 3205 1900 1305 843
+QUAL 0 172 2939 1765 1174 808
+QUAL 0 173 3385 2026 1359 920
+QUAL 0 174 2737 1659 1078 756
+QUAL 0 175 3371 2011 1360 910
+QUAL 0 176 3390 2034 1356 914
+QUAL 0 177 3485 2103 1382 963
+QUAL 0 178 3053 1875 1178 845
+QUAL 0 179 3009 1865 1144 823
+QUAL 0 180 3840 2256 1584 989
+QUAL 0 181 3110 1885 1225 885
+QUAL 0 182 3929 2359 1570 969
+QUAL 0 183 3321 1996 1325 927
+QUAL 0 184 3421 2128 1293 967
+QUAL 0 185 3535 2127 1408 1027
+QUAL 0 186 3167 1964 1203 953
+QUAL 0 187 3520 2100 1420 968
+QUAL 0 188 3673 2153 1520 1072
+QUAL 0 189 3178 1924 1254 1014
+QUAL 0 190 3494 2117 1377 973
+QUAL 0 191 3692 2306 1386 1067
+QUAL 0 192 3427 2140 1287 1045
+QUAL 0 193 3637 2246 1391 1093
+QUAL 0 194 3285 2037 1248 1031
+QUAL 0 195 3618 2208 1410 1059
+QUAL 0 196 3818 2297 1521 1181
+QUAL 0 197 3471 2109 1362 1101
+QUAL 0 198 3328 1998 1330 1120
+QUAL 0 199 3947 2483 1464 1286
+QUAL 0 200 3755 2267 1488 1205
+QUAL 0 201 3501 2114 1387 1193
+QUAL 0 202 3823 2346 1477 1325
+QUAL 0 203 3523 2147 1376 1263
+QUAL 0 204 4091 2533 1558 1419
+QUAL 0 205 3760 2309 1451 1342
+QUAL 0 206 3537 2182 1355 1316
+QUAL 0 207 4248 2633 1615 1457
+QUAL 0 208 3900 2351 1549 1566
+QUAL 0 209 4094 2582 1512 1663
+QUAL 0 210 3770 2386 1384 1467
+QUAL 0 211 4167 2586 1581 1750
+QUAL 0 212 4021 2494 1527 1756
+QUAL 0 213 4136 2536 1600 1760
+QUAL 0 214 4161 2579 1582 1823
+QUAL 0 215 4229 2620 1609 1906
+QUAL 0 216 4546 2809 1737 2015
+QUAL 0 217 4317 2693 1624 2084
+QUAL 0 218 4719 2969 1750 2214
+QUAL 0 219 4321 2705 1616 1997
+QUAL 0 220 4733 2965 1768 2398
+QUAL 0 221 4658 2919 1739 2300
+QUAL 0 222 5127 3193 1934 2734
+QUAL 0 223 4680 2974 1706 2468
+QUAL 0 224 4964 3089 1875 2679
+QUAL 0 225 5306 3294 2012 2930
+QUAL 0 226 5598 3584 2014 3066
+QUAL 0 227 4927 3099 1828 2916
+QUAL 0 228 5765 3657 2108 3459
+QUAL 0 229 5454 3415 2039 3391
+QUAL 0 230 6173 3964 2209 3846
+QUAL 0 231 6208 3946 2262 3928
+QUAL 0 232 6191 3944 2247 3925
+QUAL 0 233 6870 4392 2478 4324
+QUAL 0 234 6429 4138 2291 4239
+QUAL 0 235 7404 4770 2634 4744
+QUAL 0 236 6979 4537 2442 4492
+QUAL 0 237 8025 5154 2871 5163
+QUAL 0 238 7823 5057 2766 5031
+QUAL 0 239 8695 5633 3062 5578
+QUAL 0 240 9342 6082 3260 5915
+QUAL 0 241 8878 5700 3178 5623
+QUAL 0 242 10636 6929 3707 6573
+QUAL 0 243 9884 6543 3341 5864
+QUAL 0 244 11179 7403 3776 6915
+QUAL 0 245 12194 8018 4176 6606
+QUAL 0 246 12694 8423 4271 7049
+QUAL 0 247 13832 9107 4725 7147
+QUAL 0 248 15033 10019 5014 7726
+QUAL 0 249 16340 10981 5359 8435
+QUAL 0 250 15983 10606 5377 7025
+QUAL 0 251 18827 12625 6202 8959
+QUAL 0 252 18985 12763 6222 7352
+QUAL 0 253 23285 15668 7617 9338
+QUAL 0 254 22641 15257 7384 7839
+QUAL 0 255 26397 17951 8446 9732
+QUAL 0 256 27497 18642 8855 8767
+QUAL 0 257 31232 21346 9886 9710
+QUAL 0 258 32336 21819 10517 9634
+QUAL 0 259 37257 25423 11834 9932
+QUAL 0 260 39314 26646 12668 10972
+QUAL 0 261 43915 29773 14142 9577
+QUAL 0 262 47601 32214 15387 11366
+QUAL 0 263 49953 33764 16189 10165
+QUAL 0 264 58772 39736 19036 11729
+QUAL 0 265 57526 39175 18351 10498
+QUAL 0 266 63691 43209 20482 11543
+QUAL 0 267 70262 47572 22690 11472
+QUAL 0 268 70319 47454 22865 11939
+QUAL 0 269 75576 51140 24436 11553
+QUAL 0 270 85702 58010 27692 12340
+QUAL 0 271 81004 54716 26288 11922
+QUAL 0 272 86215 58196 28019 12002
+QUAL 0 273 97568 66002 31566 13014
+QUAL 0 274 87081 58937 28144 11351
+QUAL 0 275 93430 63075 30355 12262
+QUAL 0 276 92973 62849 30124 12156
+QUAL 0 277 91424 61649 29775 11788
+QUAL 0 278 86626 58166 28460 11229
+QUAL 0 279 83656 56067 27589 10917
+QUAL 0 280 84709 56967 27742 11398
+QUAL 0 281 75864 50950 24914 10084
+QUAL 0 282 68929 46480 22449 9574
+QUAL 0 283 64791 43594 21197 9747
+QUAL 0 284 58085 38946 19139 8586
+QUAL 0 285 54168 36401 17767 8383
+QUAL 0 286 43577 29332 14245 7721
+QUAL 0 287 39894 26909 12985 7220
+QUAL 0 288 35137 23682 11455 6763
+QUAL 0 289 31305 21324 9981 6272
+QUAL 0 290 24049 16134 7915 5541
+QUAL 0 291 23199 15615 7584 5330
+QUAL 0 292 20562 13813 6749 5093
+QUAL 0 293 19040 12855 6185 4968
+QUAL 0 294 16504 11102 5402 4224
+QUAL 0 295 16717 11235 5482 4456
+QUAL 0 296 16778 11208 5570 4300
+QUAL 0 297 16919 11450 5469 4270
+QUAL 0 298 18030 12205 5825 4222
+QUAL 0 299 19111 12862 6249 4485
+QUAL 0 300 20921 14221 6700 4708
+QUAL 0 301 22989 15387 7602 4511
+QUAL 0 302 25105 17180 7925 5078
+QUAL 0 303 27790 18837 8953 4970
+QUAL 0 304 29714 20073 9641 4946
+QUAL 0 305 32569 21949 10620 5188
+QUAL 0 306 35625 24264 11361 5272
+QUAL 0 307 38822 26449 12373 5606
+QUAL 0 308 42847 29108 13739 6084
+QUAL 0 309 45378 30695 14683 5902
+QUAL 0 310 48380 32640 15740 6156
+QUAL 0 311 49339 33306 16033 5770
+QUAL 0 312 55058 37479 17579 6323
+QUAL 0 313 55811 37800 18011 6264
+QUAL 0 314 56259 38020 18239 6255
+QUAL 0 315 56060 38049 18011 6169
+QUAL 0 316 57791 39014 18777 6194
+QUAL 0 317 55214 37201 18013 5648
+QUAL 0 318 55033 37054 17979 5633
+QUAL 0 319 50648 34177 16471 5211
+QUAL 0 320 48084 32355 15729 5109
+QUAL 0 321 43805 29749 14056 4699
+QUAL 0 322 38379 25723 12656 4206
+QUAL 0 323 34047 22933 11114 3851
+QUAL 0 324 28776 19284 9492 3431
+QUAL 0 325 23696 15884 7812 2896
+QUAL 0 326 18492 12386 6106 2551
+QUAL 0 327 14482 9751 4731 2011
+QUAL 0 328 11451 7706 3745 1718
+QUAL 0 329 8817 5911 2906 1384
+QUAL 0 330 6416 4309 2107 1116
+QUAL 0 331 4389 2951 1438 867
+QUAL 0 332 3157 2118 1039 610
+QUAL 0 333 2174 1471 703 431
+QUAL 0 334 1606 1040 566 326
+QUAL 0 335 1195 772 423 227
+QUAL 0 336 983 597 386 168
+QUAL 0 337 768 486 282 139
+QUAL 0 338 672 430 242 92
+QUAL 0 339 678 429 249 84
+QUAL 0 340 590 397 193 72
+QUAL 0 341 548 346 202 66
+QUAL 0 342 536 325 211 62
+QUAL 0 343 518 323 195 47
+QUAL 0 344 534 340 194 48
+QUAL 0 345 533 348 185 50
+QUAL 0 346 494 311 183 42
+QUAL 0 347 489 292 197 55
+QUAL 0 348 544 343 201 42
+QUAL 0 349 464 288 176 49
+QUAL 0 350 504 317 187 50
+QUAL 0 351 511 319 192 56
+QUAL 0 352 505 332 173 41
+QUAL 0 353 481 297 184 48
+QUAL 0 354 500 318 182 42
+QUAL 0 355 459 285 174 44
+QUAL 0 356 436 277 159 44
+QUAL 0 357 469 302 167 35
+QUAL 0 358 429 277 152 44
+QUAL 0 359 432 255 177 24
+QUAL 0 360 354 244 110 34
+QUAL 0 361 372 236 136 35
+QUAL 0 362 353 228 125 34
+QUAL 0 363 360 225 135 36
+QUAL 0 364 316 217 99 26
+QUAL 0 365 337 219 118 25
+QUAL 0 366 283 181 102 33
+QUAL 0 367 298 188 110 26
+QUAL 0 368 303 185 118 30
+QUAL 0 369 277 171 106 27
+QUAL 0 370 313 194 119 24
+QUAL 0 371 245 154 91 27
+QUAL 0 372 246 150 96 24
+QUAL 0 373 267 169 98 20
+QUAL 0 374 252 159 93 11
+QUAL 0 375 244 147 97 24
+QUAL 0 376 270 169 101 17
+QUAL 0 377 246 157 89 22
+QUAL 0 378 226 150 76 19
+QUAL 0 379 245 153 92 27
+QUAL 0 380 238 149 89 19
+QUAL 0 381 203 126 77 24
+QUAL 0 382 216 138 78 21
+QUAL 0 383 220 137 83 14
+QUAL 0 384 199 132 67 12
+QUAL 0 385 163 104 59 18
+QUAL 0 386 176 103 73 15
+QUAL 0 387 146 96 50 14
+QUAL 0 388 147 101 46 23
+QUAL 0 389 125 81 44 14
+QUAL 0 390 137 89 48 15
+QUAL 0 391 123 78 45 17
+QUAL 0 392 124 69 55 12
+QUAL 0 393 120 86 34 14
+QUAL 0 394 98 69 29 5
+QUAL 0 395 87 58 29 6
+QUAL 0 396 102 74 28 12
+QUAL 0 397 83 52 31 12
+QUAL 0 398 92 50 42 6
+QUAL 0 399 75 51 24 9
+QUAL 0 400 85 54 31 13
+QUAL 0 401 86 55 31 11
+QUAL 0 402 69 41 28 6
+QUAL 0 403 67 33 34 2
+QUAL 0 404 53 31 22 9
+QUAL 0 405 56 35 21 6
+QUAL 0 406 57 34 23 6
+QUAL 0 407 51 33 18 8
+QUAL 0 408 55 33 22 1
+QUAL 0 409 48 34 14 4
+QUAL 0 410 42 24 18 7
+QUAL 0 411 45 22 23 6
+QUAL 0 412 56 26 30 5
+QUAL 0 413 41 26 15 4
+QUAL 0 414 59 36 23 5
+QUAL 0 415 40 21 19 6
+QUAL 0 416 27 15 12 1
+QUAL 0 417 37 24 13 2
+QUAL 0 418 25 17 8 2
+QUAL 0 419 24 15 9 3
+QUAL 0 420 26 15 11 1
+QUAL 0 421 21 9 12 1
+QUAL 0 422 24 16 8 1
+QUAL 0 423 25 18 7 3
+QUAL 0 424 16 11 5 0
+QUAL 0 425 9 5 4 2
+QUAL 0 426 18 14 4 2
+QUAL 0 427 15 10 5 1
+QUAL 0 428 12 9 3 1
+QUAL 0 429 12 9 3 2
+QUAL 0 430 11 6 5 2
+QUAL 0 431 12 4 8 0
+QUAL 0 432 10 5 5 1
+QUAL 0 433 10 6 4 0
+QUAL 0 434 12 8 4 0
+QUAL 0 435 8 4 4 3
+QUAL 0 436 4 1 3 3
+QUAL 0 437 13 6 7 0
+QUAL 0 438 9 6 3 0
+QUAL 0 439 5 3 2 1
+QUAL 0 440 5 4 1 0
+QUAL 0 441 6 4 2 3
+QUAL 0 442 2 0 2 0
+QUAL 0 443 3 3 0 1
+QUAL 0 444 5 1 4 4
+QUAL 0 445 4 3 1 0
+QUAL 0 446 5 3 2 0
+QUAL 0 447 4 2 2 0
+QUAL 0 448 6 2 4 0
+QUAL 0 449 1 1 0 2
+QUAL 0 450 1 1 0 1
+QUAL 0 451 4 1 3 0
+QUAL 0 452 0 0 0 1
+QUAL 0 453 4 4 0 3
+QUAL 0 455 2 0 2 0
+QUAL 0 456 4 2 2 1
+QUAL 0 458 0 0 0 1
+QUAL 0 459 1 0 1 0
+QUAL 0 460 4 3 1 0
+QUAL 0 462 2 1 1 0
+QUAL 0 463 2 1 1 0
+QUAL 0 464 1 1 0 0
+QUAL 0 465 4 2 2 0
+QUAL 0 466 2 1 1 0
+QUAL 0 467 0 0 0 1
+QUAL 0 468 2 1 1 0
+QUAL 0 469 0 0 0 1
+QUAL 0 470 1 0 1 0
+QUAL 0 471 2 1 1 1
+QUAL 0 472 2 0 2 2
+QUAL 0 473 1 1 0 0
+QUAL 0 474 1 0 1 0
+QUAL 0 476 1 1 0 0
+QUAL 0 477 0 0 0 1
+QUAL 0 478 0 0 0 1
+QUAL 0 479 2 1 1 0
+QUAL 0 480 1 0 1 0
+QUAL 0 481 1 1 0 1
+QUAL 0 482 1 1 0 0
+QUAL 0 484 3 2 1 2
+QUAL 0 485 1 1 0 0
+QUAL 0 486 2 1 1 0
+QUAL 0 489 0 0 0 1
+QUAL 0 490 0 0 0 1
+QUAL 0 491 1 0 1 0
+QUAL 0 492 2 1 1 1
+QUAL 0 494 2 1 1 0
+QUAL 0 496 1 0 1 0
+QUAL 0 497 1 0 1 0
+QUAL 0 499 2 2 0 0
+QUAL 0 500 0 0 0 2
+QUAL 0 501 2 0 2 1
+QUAL 0 502 0 0 0 1
+QUAL 0 503 0 0 0 2
+QUAL 0 504 0 0 0 1
+QUAL 0 506 1 0 1 0
+QUAL 0 508 1 1 0 0
+QUAL 0 509 1 1 0 0
+QUAL 0 510 1 1 0 0
+QUAL 0 512 2 1 1 0
+QUAL 0 517 0 0 0 1
+QUAL 0 518 0 0 0 1
+QUAL 0 519 1 0 1 0
+QUAL 0 520 1 1 0 0
+QUAL 0 521 2 1 1 2
+QUAL 0 524 2 1 1 0
+QUAL 0 526 2 0 2 0
+QUAL 0 527 2 1 1 0
+QUAL 0 533 1 1 0 0
+QUAL 0 537 0 0 0 1
+QUAL 0 550 1 1 0 0
+QUAL 0 554 1 1 0 0
+QUAL 0 558 1 1 0 0
+QUAL 0 560 1 0 1 1
+QUAL 0 562 1 1 0 0
+QUAL 0 565 1 0 1 0
+QUAL 0 567 1 0 1 1
+QUAL 0 575 1 1 0 0
+QUAL 0 577 1 0 1 0
+QUAL 0 578 2 0 2 0
+QUAL 0 579 1 1 0 0
+QUAL 0 580 2 0 2 0
+QUAL 0 583 1 0 1 0
+QUAL 0 585 1 0 1 0
+QUAL 0 588 1 1 0 0
+QUAL 0 594 2 0 2 0
+QUAL 0 595 0 0 0 1
+QUAL 0 598 0 0 0 2
+QUAL 0 604 1 1 0 0
+QUAL 0 608 1 0 1 0
+QUAL 0 612 0 0 0 1
+QUAL 0 624 1 0 1 0
+QUAL 0 627 1 0 1 0
+QUAL 0 664 0 0 0 1
+QUAL 0 684 0 0 0 1
+# IDD, InDel distribution:
+# IDD [2]id [3]length (deletions negative) [4]count
+IDD 0 -60 2761
+IDD 0 -59 60
+IDD 0 -58 89
+IDD 0 -57 65
+IDD 0 -56 141
+IDD 0 -55 85
+IDD 0 -54 150
+IDD 0 -53 68
+IDD 0 -52 146
+IDD 0 -51 96
+IDD 0 -50 196
+IDD 0 -49 143
+IDD 0 -48 251
+IDD 0 -47 109
+IDD 0 -46 167
+IDD 0 -45 126
+IDD 0 -44 219
+IDD 0 -43 116
+IDD 0 -42 274
+IDD 0 -41 151
+IDD 0 -40 452
+IDD 0 -39 204
+IDD 0 -38 324
+IDD 0 -37 228
+IDD 0 -36 476
+IDD 0 -35 269
+IDD 0 -34 417
+IDD 0 -33 275
+IDD 0 -32 682
+IDD 0 -31 332
+IDD 0 -30 748
+IDD 0 -29 374
+IDD 0 -28 983
+IDD 0 -27 513
+IDD 0 -26 914
+IDD 0 -25 632
+IDD 0 -24 1487
+IDD 0 -23 627
+IDD 0 -22 1253
+IDD 0 -21 778
+IDD 0 -20 2355
+IDD 0 -19 935
+IDD 0 -18 2258
+IDD 0 -17 1134
+IDD 0 -16 3574
+IDD 0 -15 2161
+IDD 0 -14 3343
+IDD 0 -13 1954
+IDD 0 -12 7196
+IDD 0 -11 2464
+IDD 0 -10 6677
+IDD 0 -9 4123
+IDD 0 -8 12639
+IDD 0 -7 4880
+IDD 0 -6 15111
+IDD 0 -5 13607
+IDD 0 -4 50873
+IDD 0 -3 31879
+IDD 0 -2 84831
+IDD 0 -1 211446
+IDD 0 1 204974
+IDD 0 2 71798
+IDD 0 3 24987
+IDD 0 4 41760
+IDD 0 5 10916
+IDD 0 6 12286
+IDD 0 7 3696
+IDD 0 8 10221
+IDD 0 9 3013
+IDD 0 10 5210
+IDD 0 11 1711
+IDD 0 12 5375
+IDD 0 13 1275
+IDD 0 14 2243
+IDD 0 15 1482
+IDD 0 16 2442
+IDD 0 17 731
+IDD 0 18 1359
+IDD 0 19 598
+IDD 0 20 1581
+IDD 0 21 552
+IDD 0 22 716
+IDD 0 23 418
+IDD 0 24 1022
+IDD 0 25 430
+IDD 0 26 503
+IDD 0 27 310
+IDD 0 28 550
+IDD 0 29 230
+IDD 0 30 407
+IDD 0 31 200
+IDD 0 32 361
+IDD 0 33 154
+IDD 0 34 253
+IDD 0 35 164
+IDD 0 36 250
+IDD 0 37 118
+IDD 0 38 168
+IDD 0 39 123
+IDD 0 40 190
+IDD 0 41 106
+IDD 0 42 128
+IDD 0 43 122
+IDD 0 44 128
+IDD 0 45 99
+IDD 0 46 116
+IDD 0 47 82
+IDD 0 48 133
+IDD 0 49 88
+IDD 0 50 98
+IDD 0 51 81
+IDD 0 52 96
+IDD 0 53 70
+IDD 0 54 73
+IDD 0 55 74
+IDD 0 56 78
+IDD 0 57 92
+IDD 0 58 96
+IDD 0 59 79
+IDD 0 60 5497
+# ST, Substitution types:
+# ST [2]id [3]type [4]count
+ST 0 A>C 190164
+ST 0 A>G 721395
+ST 0 A>T 166827
+ST 0 C>A 196831
+ST 0 C>G 197211
+ST 0 C>T 762114
+ST 0 G>A 763594
+ST 0 G>C 197866
+ST 0 G>T 201005
+ST 0 T>A 166222
+ST 0 T>C 721436
+ST 0 T>G 189578
+# DP, Depth distribution
+# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)
+DP 0 1 0 0.000000 4 0.000072
+DP 0 2 0 0.000000 1655 0.029967
+DP 0 3 0 0.000000 2091 0.037861
+DP 0 4 0 0.000000 2126 0.038495
+DP 0 5 0 0.000000 2259 0.040903
+DP 0 6 0 0.000000 2114 0.038278
+DP 0 7 0 0.000000 2132 0.038604
+DP 0 8 0 0.000000 2030 0.036757
+DP 0 9 0 0.000000 2118 0.038350
+DP 0 10 0 0.000000 2085 0.037753
+DP 0 11 0 0.000000 2033 0.036811
+DP 0 12 0 0.000000 2014 0.036467
+DP 0 13 0 0.000000 1995 0.036123
+DP 0 14 0 0.000000 1981 0.035870
+DP 0 15 0 0.000000 2018 0.036540
+DP 0 16 0 0.000000 2015 0.036485
+DP 0 17 0 0.000000 2070 0.037481
+DP 0 18 0 0.000000 1976 0.035779
+DP 0 19 0 0.000000 1962 0.035526
+DP 0 20 0 0.000000 1961 0.035508
+DP 0 21 0 0.000000 1925 0.034856
+DP 0 22 0 0.000000 1902 0.034439
+DP 0 23 0 0.000000 2069 0.037463
+DP 0 24 0 0.000000 2021 0.036594
+DP 0 25 0 0.000000 2005 0.036304
+DP 0 26 0 0.000000 2072 0.037517
+DP 0 27 0 0.000000 2029 0.036739
+DP 0 28 0 0.000000 1986 0.035960
+DP 0 29 0 0.000000 2063 0.037354
+DP 0 30 0 0.000000 2083 0.037717
+DP 0 31 0 0.000000 2097 0.037970
+DP 0 32 0 0.000000 2062 0.037336
+DP 0 33 0 0.000000 2050 0.037119
+DP 0 34 0 0.000000 2047 0.037065
+DP 0 35 0 0.000000 2069 0.037463
+DP 0 36 0 0.000000 2097 0.037970
+DP 0 37 0 0.000000 2047 0.037065
+DP 0 38 0 0.000000 2123 0.038441
+DP 0 39 0 0.000000 2097 0.037970
+DP 0 40 0 0.000000 2052 0.037155
+DP 0 41 0 0.000000 2123 0.038441
+DP 0 42 0 0.000000 2107 0.038151
+DP 0 43 0 0.000000 2106 0.038133
+DP 0 44 0 0.000000 2134 0.038640
+DP 0 45 0 0.000000 2198 0.039799
+DP 0 46 0 0.000000 2085 0.037753
+DP 0 47 0 0.000000 2220 0.040197
+DP 0 48 0 0.000000 2187 0.039600
+DP 0 49 0 0.000000 2262 0.040958
+DP 0 50 0 0.000000 2217 0.040143
+DP 0 51 0 0.000000 2280 0.041284
+DP 0 52 0 0.000000 2278 0.041247
+DP 0 53 0 0.000000 2362 0.042768
+DP 0 54 0 0.000000 2307 0.041773
+DP 0 55 0 0.000000 2317 0.041954
+DP 0 56 0 0.000000 2359 0.042714
+DP 0 57 0 0.000000 2423 0.043873
+DP 0 58 0 0.000000 2346 0.042479
+DP 0 59 0 0.000000 2399 0.043438
+DP 0 60 0 0.000000 2421 0.043837
+DP 0 61 0 0.000000 2478 0.044869
+DP 0 62 0 0.000000 2449 0.044344
+DP 0 63 0 0.000000 2485 0.044996
+DP 0 64 0 0.000000 2586 0.046824
+DP 0 65 0 0.000000 2556 0.046281
+DP 0 66 0 0.000000 2628 0.047585
+DP 0 67 0 0.000000 2146 0.038857
+DP 0 68 0 0.000000 2174 0.039364
+DP 0 69 0 0.000000 2149 0.038912
+DP 0 70 0 0.000000 2209 0.039998
+DP 0 71 0 0.000000 2208 0.039980
+DP 0 72 0 0.000000 2232 0.040415
+DP 0 73 0 0.000000 2263 0.040976
+DP 0 74 0 0.000000 2309 0.041809
+DP 0 75 0 0.000000 2357 0.042678
+DP 0 76 0 0.000000 2334 0.042261
+DP 0 77 0 0.000000 2419 0.043800
+DP 0 78 0 0.000000 2363 0.042787
+DP 0 79 0 0.000000 2425 0.043909
+DP 0 80 0 0.000000 2561 0.046372
+DP 0 81 0 0.000000 2473 0.044778
+DP 0 82 0 0.000000 2574 0.046607
+DP 0 83 0 0.000000 2520 0.045629
+DP 0 84 0 0.000000 2628 0.047585
+DP 0 85 0 0.000000 2620 0.047440
+DP 0 86 0 0.000000 2542 0.046028
+DP 0 87 0 0.000000 2637 0.047748
+DP 0 88 0 0.000000 2722 0.049287
+DP 0 89 0 0.000000 2793 0.050572
+DP 0 90 0 0.000000 2772 0.050192
+DP 0 91 0 0.000000 2936 0.053162
+DP 0 92 0 0.000000 2938 0.053198
+DP 0 93 0 0.000000 3030 0.054864
+DP 0 94 0 0.000000 3013 0.054556
+DP 0 95 0 0.000000 3186 0.057688
+DP 0 96 0 0.000000 3222 0.058340
+DP 0 97 0 0.000000 3346 0.060586
+DP 0 98 0 0.000000 3364 0.060911
+DP 0 99 0 0.000000 3508 0.063519
+DP 0 100 0 0.000000 3051 0.055244
+DP 0 101 0 0.000000 3079 0.055751
+DP 0 102 0 0.000000 3152 0.057073
+DP 0 103 0 0.000000 3274 0.059282
+DP 0 104 0 0.000000 3413 0.061799
+DP 0 105 0 0.000000 3516 0.063664
+DP 0 106 0 0.000000 3599 0.065167
+DP 0 107 0 0.000000 3755 0.067991
+DP 0 108 0 0.000000 3784 0.068516
+DP 0 109 0 0.000000 4059 0.073496
+DP 0 110 0 0.000000 4161 0.075343
+DP 0 111 0 0.000000 4169 0.075487
+DP 0 112 0 0.000000 4331 0.078421
+DP 0 113 0 0.000000 4481 0.081137
+DP 0 114 0 0.000000 4730 0.085645
+DP 0 115 0 0.000000 4812 0.087130
+DP 0 116 0 0.000000 4893 0.088597
+DP 0 117 0 0.000000 5201 0.094174
+DP 0 118 0 0.000000 5163 0.093486
+DP 0 119 0 0.000000 5441 0.098519
+DP 0 120 0 0.000000 5466 0.098972
+DP 0 121 0 0.000000 5615 0.101670
+DP 0 122 0 0.000000 5715 0.103481
+DP 0 123 0 0.000000 5622 0.101797
+DP 0 124 0 0.000000 5809 0.105183
+DP 0 125 0 0.000000 5909 0.106993
+DP 0 126 0 0.000000 6031 0.109202
+DP 0 127 0 0.000000 5938 0.107519
+DP 0 128 0 0.000000 6364 0.115232
+DP 0 129 0 0.000000 6360 0.115160
+DP 0 130 0 0.000000 6337 0.114743
+DP 0 131 0 0.000000 6466 0.117079
+DP 0 132 0 0.000000 6417 0.116192
+DP 0 133 0 0.000000 6370 0.115341
+DP 0 134 0 0.000000 5913 0.107066
+DP 0 135 0 0.000000 5925 0.107283
+DP 0 136 0 0.000000 5875 0.106378
+DP 0 137 0 0.000000 5826 0.105491
+DP 0 138 0 0.000000 5878 0.106432
+DP 0 139 0 0.000000 5896 0.106758
+DP 0 140 0 0.000000 5948 0.107700
+DP 0 141 0 0.000000 5828 0.105527
+DP 0 142 0 0.000000 5818 0.105346
+DP 0 143 0 0.000000 5884 0.106541
+DP 0 144 0 0.000000 5917 0.107138
+DP 0 145 0 0.000000 5704 0.103282
+DP 0 146 0 0.000000 5716 0.103499
+DP 0 147 0 0.000000 5647 0.102249
+DP 0 148 0 0.000000 5604 0.101471
+DP 0 149 0 0.000000 5564 0.100747
+DP 0 150 0 0.000000 5460 0.098863
+DP 0 151 0 0.000000 5408 0.097922
+DP 0 152 0 0.000000 5345 0.096781
+DP 0 153 0 0.000000 5558 0.100638
+DP 0 154 0 0.000000 5520 0.099950
+DP 0 155 0 0.000000 5471 0.099063
+DP 0 156 0 0.000000 5520 0.099950
+DP 0 157 0 0.000000 5419 0.098121
+DP 0 158 0 0.000000 5363 0.097107
+DP 0 159 0 0.000000 5545 0.100403
+DP 0 160 0 0.000000 5617 0.101706
+DP 0 161 0 0.000000 5468 0.099008
+DP 0 162 0 0.000000 5549 0.100475
+DP 0 163 0 0.000000 5800 0.105020
+DP 0 164 0 0.000000 5643 0.102177
+DP 0 165 0 0.000000 5647 0.102249
+DP 0 166 0 0.000000 5934 0.107446
+DP 0 167 0 0.000000 5648 0.102268
+DP 0 168 0 0.000000 5689 0.103010
+DP 0 169 0 0.000000 5801 0.105038
+DP 0 170 0 0.000000 5746 0.104042
+DP 0 171 0 0.000000 6010 0.108822
+DP 0 172 0 0.000000 6004 0.108714
+DP 0 173 0 0.000000 6278 0.113675
+DP 0 174 0 0.000000 6318 0.114399
+DP 0 175 0 0.000000 6293 0.113946
+DP 0 176 0 0.000000 6652 0.120447
+DP 0 177 0 0.000000 6587 0.119270
+DP 0 178 0 0.000000 6757 0.122348
+DP 0 179 0 0.000000 7102 0.128595
+DP 0 180 0 0.000000 7319 0.132524
+DP 0 181 0 0.000000 7421 0.134371
+DP 0 182 0 0.000000 7483 0.135494
+DP 0 183 0 0.000000 7869 0.142483
+DP 0 184 0 0.000000 8043 0.145633
+DP 0 185 0 0.000000 8261 0.149581
+DP 0 186 0 0.000000 8269 0.149726
+DP 0 187 0 0.000000 8604 0.155791
+DP 0 188 0 0.000000 9081 0.164428
+DP 0 189 0 0.000000 9347 0.169245
+DP 0 190 0 0.000000 9356 0.169408
+DP 0 191 0 0.000000 9715 0.175908
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diff -r 000000000000 -r 3bad335ccea9 test-data/bcftools_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bcftools_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample substitution_type_G>T number_of_samples substitution_type_G>C substitution_type_G>A tstv tv_1st_ALT number_of_others number_of_multiallelic_SNP_sites number_of_no-ALTs ts_1st_ALT number_of_MNPs ts number_of_multiallelic_sites number_of_SNPs number_of_indels substitution_type_C>A substitution_type_C>G substitution_type_A>T substitution_type_A>C number_of_records substitution_type_A>G substitution_type_C>T substitution_type_T>A substitution_type_T>C tstv_1st_ALT substitution_type_T>G tv
+Test1 201005.0 1.0 197866.0 763594.0 1.97 1505704.0 73262.0 0.0 0.0 2968539.0 72330.0 2968539.0 0.0 4474244.0 902934.0 196831.0 197211.0 166827.0 190164.0 5522770.0 721395.0 762114.0 166222.0 721436.0 1.97 189578.0 1505704.0
diff -r 000000000000 -r 3bad335ccea9 test-data/bismark.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bismark.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,39 @@
+Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0)
+Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!)
+Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet
+
+Final Alignment report
+======================
+Sequences analysed in total: 316390
+Number of alignments with a unique best hit from the different alignments: 220558
+Mapping efficiency: 69.7%
+Sequences with no alignments under any condition: 93928
+Sequences did not map uniquely: 1904
+Sequences which were discarded because genomic sequence could not be extracted: 0
+
+Number of sequences with unique best (first) alignment came from the bowtie output:
+CT/CT: 108352 ((converted) top strand)
+CT/GA: 112206 ((converted) bottom strand)
+GA/CT: 0 (complementary to (converted) top strand)
+GA/GA: 0 (complementary to (converted) bottom strand)
+
+Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
+
+Final Cytosine Methylation Report
+=================================
+Total number of C's analysed: 5291918
+
+Total methylated C's in CpG context: 465068
+Total methylated C's in CHG context: 1358074
+Total methylated C's in CHH context: 3449120
+Total methylated C's in Unknown context: 1499
+
+Total unmethylated C's in CpG context: 6399
+Total unmethylated C's in CHG context: 2988
+Total unmethylated C's in CHH context: 10269
+Total unmethylated C's in Unknown context: 454
+
+C methylated in CpG context: 98.6%
+C methylated in CHG context: 99.8%
+C methylated in CHH context: 99.7%
+C methylated in Unknown context (CN or CHN): 76.8%
diff -r 000000000000 -r 3bad335ccea9 test-data/bismark_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bismark_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample aligned_reads ambig_reads discarded_reads meth_chg meth_chh meth_cpg no_alignments percent_aligned percent_chg_meth percent_chh_meth percent_cpg_meth strand_ctob strand_ctot strand_ob strand_ot total_c total_reads unmeth_chg unmeth_chh unmeth_cpg
+bismark_SE_report 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.7107999621 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0
diff -r 000000000000 -r 3bad335ccea9 test-data/bowtie2_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2_1.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,6 @@
+21040602 reads; of these:
+ 21040602 (100.00%) were unpaired; of these:
+ 351563 (1.67%) aligned 0 times
+ 13299463 (63.21%) aligned exactly 1 time
+ 7389576 (35.12%) aligned >1 times
+98.33% overall alignment rate
diff -r 000000000000 -r 3bad335ccea9 test-data/bowtie2_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2_2.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,6 @@
+16199126 reads; of these:
+ 16199126 (100.00%) were unpaired; of these:
+ 274008 (1.69%) aligned 0 times
+ 10087714 (62.27%) aligned exactly 1 time
+ 5837404 (36.04%) aligned >1 times
+98.31% overall alignment rate
diff -r 000000000000 -r 3bad335ccea9 test-data/bowtie2_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,3 @@
+Sample overall_alignment_rate unpaired_total unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi total_reads
+bowtie2_1 98.33 21040602 13299463 351563 7389576 21040602
+bowtie2_2 98.31 16199126 10087714 274008 5837404 16199126
diff -r 000000000000 -r 3bad335ccea9 test-data/busco.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/busco.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,15 @@
+# BUSCO version is: 2.0
+# The lineage dataset is: fungi_odb9 (Creation date: 2016-02-13, number of species: 85, number of BUSCOs: 290)
+# To reproduce this run: python /home/remi/opt/busco/BUSCO.py -i /assemblies/BUSCO_v2_test.scf.fasta -o BUSCO_v2_test -l fungi_odb9/ -m genome -c 4 -sp aspergillus_nidulans
+#
+# Summarized benchmarking in BUSCO notation for file /assemblies/BUSCO_v2_test.scf.fasta
+# BUSCO was run in mode: genome
+
+ C:88.6%[S:87.9%,D:0.7%],F:1.7%,M:9.7%,n:290
+
+ 257 Complete BUSCOs (C)
+ 255 Complete and single-copy BUSCOs (S)
+ 2 Complete and duplicated BUSCOs (D)
+ 5 Fragmented BUSCOs (F)
+ 28 Missing BUSCOs (M)
+ 290 Total BUSCO groups searched
\ No newline at end of file
diff -r 000000000000 -r 3bad335ccea9 test-data/busco_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/busco_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample fragmented complete missing complete_single_copy total lineage_dataset complete_duplicated
+short 5.0 257.0 28.0 255.0 290.0 fungi_odb9 2.0
diff -r 000000000000 -r 3bad335ccea9 test-data/cc_ko15.bpc.embedded.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cc_ko15.bpc.embedded.tab Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,1289 @@
+# file_format: 'tsv'
+# section_name: 'BPC'
+# title: 'Base peak chromatogram'
+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+# id: 'bpc_lineplot'
+# title: 'Base peak chromatogram'
+# ylab: 'Base Peak Intensity'
+# xlab: 'Retention Time'
+Retention Time Base Peak Intensity
+2502.98928676082 43888
+2504.55428676082 43960
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diff -r 000000000000 -r 3bad335ccea9 test-data/cc_ko15.bpc.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cc_ko15.bpc.tab Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,1278 @@
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diff -r 000000000000 -r 3bad335ccea9 test-data/cc_wt15.bpc.embedded.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cc_wt15.bpc.embedded.tab Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,1289 @@
+# file_format: 'tsv'
+# section_name: 'BPC'
+# title: 'Base peak chromatogram'
+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
+# plot_type: 'linegraph'
+# pconfig:
+# id: 'bpc_lineplot'
+# title: 'Base peak chromatogram'
+# ylab: 'Base Peak Intensity'
+# xlab: 'Retention Time'
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diff -r 000000000000 -r 3bad335ccea9 test-data/cc_wt15.bpc.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cc_wt15.bpc.tab Tue Oct 24 06:29:59 2017 -0400
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diff -r 000000000000 -r 3bad335ccea9 test-data/cutadapt.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cutadapt.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,129 @@
+You are running cutadapt 1.6 with Python 2.7.3
+Command line parameters: --format=fastq --anywhere=fakadaptater=CACG --error-rate=0.1 --times=1 --overlap=3 --output=/omaha-beach/cloud_26/files/000/dataset_82.dat /omaha-beach/cloud_26/files/000/dataset_33.dat
+Maximum error rate: 10.00%
+ No. of adapters: 1
+ Processed reads: 316390
+ Processed bases: 31955390 bp (32.0 Mbp)
+ Trimmed reads: 68795 (21.7%)
+ Trimmed bases: 3443775 bp (3.4 Mbp) (10.78% of total)
+ Too short reads: 0 (0.0% of processed reads)
+ Too long reads: 0 (0.0% of processed reads)
+ Total time: 5.28 s
+ Time per read: 0.017 ms
+
+=== Adapter 'fakadaptater' ===
+
+Sequence: CACG; Length: 4; Trimmed: 68795 times.
+2162 times, it overlapped the 5' end of a read
+66633 times, it overlapped the 3' end or was within the read
+
+No. of allowed errors:
+0-4 bp: 0
+
+Overview of removed sequences (5')
+length count expect max.err error counts
+3 357 4943.6 0 357
+4 1805 1235.9 0 1805
+
+
+Overview of removed sequences (3' or within)
+length count expect max.err error counts
+3 4175 4943.6 0 4175
+4 520 1235.9 0 520
+5 442 1235.9 0 442
+6 522 1235.9 0 522
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+
diff -r 000000000000 -r 3bad335ccea9 test-data/cutadapt_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cutadapt_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample r_trimmed bp_trimmed bp_processed too_short r_processed too_long percent_trimmed
+dataset_33 68795 3443775 31955390 0 316390 0 10.7768204362
diff -r 000000000000 -r 3bad335ccea9 test-data/fastqc_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_1.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2181 @@
+##FastQC 0.11.4
+>>Basic Statistics pass
+#Measure Value
+Filename poulet5_1
+File type Conventional base calls
+Encoding Sanger / Illumina 1.9
+Total Sequences 267849
+Sequences flagged as poor quality 0
+Sequence length 101
+%GC 48
+>>END_MODULE
+>>Per base sequence quality warn
+#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
+1 20.91988023102569 21.0 21.0 21.0 21.0 21.0
+2 20.71684045861661 21.0 20.0 22.0 19.0 23.0
+3 20.351574954545285 21.0 20.0 21.0 18.0 22.0
+4 22.531542025544244 23.0 22.0 24.0 20.0 24.0
+5 24.673566076408722 25.0 24.0 26.0 24.0 26.0
+6 25.813099918237516 26.0 25.0 27.0 25.0 27.0
+7 27.587864804423386 28.0 27.0 29.0 26.0 29.0
+8 27.598941941168345 28.0 27.0 29.0 26.0 29.0
+9 27.07115949658203 28.0 26.0 28.0 26.0 28.0
+10-11 27.129873548155864 28.0 26.0 28.0 25.5 28.0
+12-13 27.009298149330405 27.5 26.0 28.0 25.5 28.0
+14-15 27.123565889736383 28.0 26.5 28.0 26.0 28.0
+16-17 27.086309823818645 28.0 26.0 28.0 26.0 28.0
+18-19 27.07924614241606 28.0 26.0 28.0 25.5 28.0
+20-21 27.082520375286073 28.0 26.0 28.0 26.0 28.0
+22-23 27.054301117420636 28.0 26.0 28.0 25.0 28.0
+24-25 27.06350966402712 28.0 26.0 28.0 25.0 28.0
+26-27 27.082996389756914 28.0 26.0 28.0 26.0 28.0
+28-29 27.065495857740743 28.0 26.0 28.0 25.5 28.0
+30-31 27.09608772106672 28.0 26.0 28.0 26.0 28.0
+32-33 27.087097581099798 28.0 26.0 28.0 26.0 28.0
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+38-39 27.06521958267531 28.0 26.0 28.0 26.0 28.0
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+42-43 27.065725464720796 28.0 26.0 28.0 25.5 28.0
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+46-47 27.048083061725073 28.0 26.0 28.0 25.5 28.0
+48-49 27.04642354460909 28.0 26.0 28.0 25.5 28.0
+50-51 27.062865644448927 28.0 26.0 28.0 25.5 28.0
+52-53 27.01859629866081 28.0 26.0 28.0 25.0 28.0
+54-55 26.994157155710866 27.5 26.0 28.0 25.0 28.0
+56-57 27.110127347871376 28.0 27.0 28.0 26.0 28.0
+58-59 26.995846540401494 27.5 26.0 28.0 25.0 28.0
+60-61 27.00461640700544 27.5 26.0 28.0 25.0 28.0
+62-63 26.981614641085088 27.5 26.5 28.0 25.5 28.5
+64-65 26.98900313236189 28.0 26.0 28.0 25.0 28.0
+66-67 27.001189102815392 28.0 26.0 28.0 25.0 28.0
+68-69 26.917739099268616 27.5 26.0 28.0 25.0 28.5
+70-71 26.98481793846533 28.0 27.0 28.0 25.0 29.0
+72-73 26.89518908041471 27.5 26.5 28.0 25.0 28.5
+74-75 26.93677034448514 28.0 27.0 28.0 25.0 29.0
+76-77 26.87640237596556 28.0 26.5 28.0 25.0 29.0
+78-79 26.906094478605482 28.0 27.0 28.0 25.0 29.0
+80-81 26.80463992772047 28.0 26.5 28.0 25.0 29.0
+82-83 26.717012197170796 28.0 26.5 28.0 25.0 29.0
+84-85 26.46960974280285 27.5 26.5 28.0 25.0 29.0
+86-87 26.442842795754324 27.5 26.5 28.0 25.0 29.0
+88-89 26.34282375517549 28.0 26.0 28.0 25.0 29.0
+90-91 26.03493946215965 28.0 26.0 28.0 24.5 29.0
+92-93 25.833215729758187 28.0 26.0 28.0 24.0 29.0
+94-95 25.503102494315826 27.5 26.0 28.0 22.5 29.0
+96-97 24.52807178671565 27.0 25.5 27.5 21.0 28.0
+98-99 23.202399486277717 26.0 24.5 26.5 10.0 27.0
+100-101 23.72906749698524 27.0 26.0 28.0 2.0 29.0
+>>END_MODULE
+>>Per tile sequence quality pass
+#Tile Base Mean
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+2206 62-63 4.947442650511391E-4
+2206 64-65 0.036486579881575665
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+2206 68-69 -0.02092568690058627
+2206 70-71 0.05680793926853411
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+2206 76-77 0.04604664887257215
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+2206 88-89 0.030613831733997898
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+2207 9 0.01220423945600757
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+2207 14-15 -0.0698321324850042
+2207 16-17 -0.06805529875060401
+2207 18-19 -0.06982873984200211
+2207 20-21 -0.05114010392984625
+2207 22-23 -0.0240395825760622
+2207 24-25 0.009494346948930144
+2207 26-27 -0.08921026545140265
+2207 28-29 -0.06835850107044195
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+2207 38-39 -0.02692069177714984
+2207 40-41 -9.279482380222248E-4
+2207 42-43 -0.062360612005317506
+2207 44-45 -0.055384311937707764
+2207 46-47 -0.049846025365699376
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+2207 54-55 -0.048645405157309085
+2207 56-57 -0.06858832002135173
+2207 58-59 0.001033679471046156
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+2207 86-87 -0.16396227704018784
+2207 88-89 -0.15996606758497833
+2207 90-91 0.03965137240097505
+2207 92-93 0.06471362198210784
+2207 94-95 -0.0052651695579477575
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+2207 100-101 -0.317504603542055
+2208 1 0.028306679484682462
+2208 2 0.05956479768100209
+2208 3 0.07532731887178556
+2208 4 -0.02467557745944049
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+2208 6 -0.008436489536933323
+2208 7 -0.02119498434333522
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+2208 12-13 -0.05989000824499513
+2208 14-15 -0.042708422097859966
+2208 16-17 -0.03322339870416613
+2208 18-19 -0.07296078961051222
+2208 20-21 -0.03914427362052919
+2208 22-23 -0.12332051282937684
+2208 24-25 -0.05509122893912277
+2208 26-27 -0.014280158775751062
+2208 28-29 -0.0692564084680285
+2208 30-31 -0.04417808765723663
+2208 32-33 -0.040125896134991734
+2208 34-35 -0.031030129337018764
+2208 36-37 -0.039894194979503084
+2208 38-39 -0.10138856210019753
+2208 40-41 -0.014309424992845265
+2208 42-43 -0.024890245605966754
+2208 44-45 -0.08135774450486366
+2208 46-47 -0.14277890970991436
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+2208 52-53 0.02111813520589223
+2208 54-55 -0.030096976070211667
+2208 56-57 -0.027114030457372706
+2208 58-59 0.03207683534458283
+2208 60-61 -0.016849241164688777
+2208 62-63 -0.018792724619515866
+2208 64-65 0.006814181525321317
+2208 66-67 -0.027201602076967646
+2208 68-69 0.0011893644965859096
+2208 70-71 -0.021593659438860158
+2208 72-73 -0.0341979110595112
+2208 74-75 0.019465473246153664
+2208 76-77 -0.046394473677136006
+2208 78-79 0.019336702164924446
+2208 80-81 -0.08162520439996968
+2208 82-83 -0.12279121951477734
+2208 84-85 -0.20884928087605914
+2208 86-87 -0.3596062041577319
+2208 88-89 -0.08637910286264372
+2208 90-91 -0.993780535933837
+2208 92-93 -0.26723742984468046
+2208 94-95 -0.4391510258693856
+2208 96-97 -0.5338388591234597
+2208 98-99 -0.5674666924173444
+2208 100-101 -0.677027788148628
+>>END_MODULE
+>>Per sequence quality scores warn
+#Quality Count
+2 91.0
+3 0.0
+4 0.0
+5 0.0
+6 1.0
+7 4.0
+8 1.0
+9 4.0
+10 19.0
+11 20.0
+12 36.0
+13 57.0
+14 112.0
+15 185.0
+16 315.0
+17 488.0
+18 667.0
+19 878.0
+20 1127.0
+21 1933.0
+22 2846.0
+23 4426.0
+24 7254.0
+25 15604.0
+26 147526.0
+27 84255.0
+>>END_MODULE
+>>Per base sequence content fail
+#Base G A T C
+1 24.561095571182623 12.690042536664064 10.404490437653351 52.344371454499964
+2 18.339437518900574 21.261606352833127 40.84540170021169 19.55355442805461
+3 24.3623968130108 22.75060764115756 24.606199993279546 28.28079555255209
+4 24.70272429615194 30.13376939992309 20.251335640603475 24.912170663321497
+5 26.912278605776415 30.437785609748815 22.448552910606015 20.201382873868763
+6 21.71820690015643 32.44626636649754 23.826857669806493 22.008669063539532
+7 20.05719640543739 18.11617739845958 38.19876124234177 23.62786495376126
+8 20.67097506430862 21.73762082367304 30.101661757184083 27.489742354834252
+9 21.03797288770912 20.6063864341476 32.13340352213374 26.22223715600954
+10-11 24.92953119108154 29.215714824397327 22.228755754174927 23.6259982303462
+12-13 23.055154210021318 24.05403790941911 27.701242117760376 25.189565762799187
+14-15 23.740988392713806 25.209166358657303 26.766200359157583 24.283644889471308
+16-17 24.568320210267725 25.528936079656823 25.649339739928095 24.253403970147357
+18-19 24.04209087956274 25.55880365429776 25.791957408838563 24.607148057300943
+20-21 23.93419426617236 25.75256954478083 26.05945887421644 24.253777314830373
+22-23 24.163987918566058 25.89910733286292 25.740809187265963 24.196095561305064
+24-25 23.988702589892068 25.91833458403802 25.975642992880317 24.117319833189597
+26-27 23.946327968370237 26.093246568029 25.94857550336197 24.01184996023879
+28-29 23.988889262233574 25.78393049815381 25.775716915127557 24.451463324485065
+30-31 23.98944927925809 25.67715391881247 26.00980403137589 24.32359277055356
+32-33 23.93998110875904 26.05105861884868 26.071779248755828 23.93718102363645
+34-35 24.114706420408513 25.96780275453707 25.658300012320375 24.25919081273404
+36-37 23.890886282943 25.775530242786047 25.919454618087055 24.414128856183893
+38-39 23.981422368573337 25.796064200351694 26.301572901149527 23.920940529925446
+40-41 23.981422368573337 25.791397391814048 26.08111286583112 24.146067373781495
+42-43 23.894806402114625 25.829665221822744 26.05553875504482 24.219989621017813
+44-45 23.729228035198936 26.04489843157899 26.20394326654197 24.02193026668011
+46-47 24.046010998734364 25.874839928467157 25.88977371578763 24.189375357010853
+48-49 24.049744445564478 25.742302565998003 25.94857550336197 24.259377485075547
+50-51 23.948381364126803 26.056285444410843 26.02343111230581 23.97190207915654
+52-53 23.98758255584303 26.181169240878255 25.754062923512876 24.07718527976584
+54-55 24.002329670821993 25.763956557612683 26.049005223092113 24.184708548473207
+56-57 24.145694029098486 25.93812185223764 26.200956509077876 23.715227609585998
+58-59 24.10443944162569 26.029031282550992 25.90638755418165 23.96014172164167
+60-61 23.907500121337023 25.956415741705214 26.048818550750607 24.087265586207156
+62-63 23.989262606916583 25.956975758729733 26.25397145406554 23.799790180288145
+64-65 24.19852230174464 25.83377201333587 25.889960388129136 24.077745296790358
+66-67 23.939421091734523 25.92654816706428 26.010737393083417 24.123293348117784
+68-69 23.959021687592635 25.83750546016599 26.237170943330014 23.966301908911365
+70-71 23.97992898984129 26.19087620263656 25.813424728111734 24.015770079410416
+72-73 23.799976852629655 26.096606670176108 26.129087657598127 23.974328819596117
+74-75 24.05739801156622 26.019324320792688 26.18191593024428 23.741361737396815
+76-77 24.116013126799054 25.837318787824483 26.0995934276402 23.947074657736263
+78-79 24.028463798632814 26.152981717310876 25.835452064409424 23.98310241964689
+80-81 24.037984088049612 25.988336712102715 26.165115419508755 23.808563780338922
+82-83 24.09286575645233 25.723635331847422 26.134501155501795 24.048997756198457
+84-85 23.749388648081567 25.817531519624865 26.270771964801064 24.162307867492505
+86-87 23.906566759629495 26.199276458004324 26.24613121572229 23.648025566643895
+88-89 24.194788854914524 25.881373460419866 25.988710056785724 23.935127627879886
+90-91 24.30641891513502 25.716915127553207 25.838438821873517 24.13822713543825
+92-93 23.89331302338258 26.09231320632147 26.2431444582582 23.771229312037754
+94-95 24.343006694070166 25.78803728966694 25.850945868754412 24.018010147508484
+96-97 24.293351851229612 25.853745953877 25.936815145847103 23.916087049046293
+98-99 24.295965264010693 25.91702787764748 26.050311929482657 23.73669492885917
+100-101 24.65138940223783 25.744542634096078 25.755742974586425 23.848324989079668
+>>END_MODULE
+>>Per sequence GC content pass
+#GC Content Count
+0 0.0
+1 0.0
+2 0.0
+3 0.0
+4 0.0
+5 0.0
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10 0.0
+11 0.0
+12 0.0
+13 0.0
+14 0.5
+15 2.0
+16 5.0
+17 7.5
+18 10.5
+19 15.5
+20 20.0
+21 28.5
+22 42.5
+23 63.0
+24 126.5
+25 228.0
+26 385.0
+27 545.0
+28 720.0
+29 1080.5
+30 1474.5
+31 1743.5
+32 2015.0
+33 2324.0
+34 2747.0
+35 3375.5
+36 3996.5
+37 4590.5
+38 5365.0
+39 6219.5
+40 7284.0
+41 8648.0
+42 9680.5
+43 10325.5
+44 10906.0
+45 11123.5
+46 11325.5
+47 12122.5
+48 12960.5
+49 13030.0
+50 12518.5
+51 11744.0
+52 10781.0
+53 10248.5
+54 10433.5
+55 9922.0
+56 8785.5
+57 7997.0
+58 6901.0
+59 5796.0
+60 4967.0
+61 4072.5
+62 3639.5
+63 3267.0
+64 2561.5
+65 2002.5
+66 1561.5
+67 1355.5
+68 1222.0
+69 1019.0
+70 803.0
+71 568.5
+72 371.5
+73 235.0
+74 164.5
+75 110.5
+76 70.5
+77 56.0
+78 39.5
+79 27.0
+80 18.0
+81 17.0
+82 15.5
+83 12.5
+84 6.5
+85 1.5
+86 0.0
+87 0.0
+88 0.0
+89 0.0
+90 0.0
+91 0.0
+92 0.0
+93 0.0
+94 0.0
+95 0.0
+96 0.0
+97 0.0
+98 0.0
+99 0.0
+100 0.0
+>>END_MODULE
+>>Per base N content pass
+#Base N-Count
+1 0.029867574640935753
+2 0.0
+3 0.003733446830116969
+4 0.0
+5 3.733446830116969E-4
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10-11 0.0
+12-13 0.0
+14-15 0.0
+16-17 0.0
+18-19 0.0
+20-21 0.0
+22-23 0.0
+24-25 0.0
+26-27 0.0
+28-29 0.0
+30-31 0.0
+32-33 0.0
+34-35 0.0
+36-37 0.0
+38-39 0.0
+40-41 0.0
+42-43 0.0
+44-45 0.0
+46-47 0.0
+48-49 0.0
+50-51 0.0
+52-53 0.0
+54-55 0.0
+56-57 0.0
+58-59 0.0
+60-61 0.0
+62-63 0.0
+64-65 0.0
+66-67 0.0
+68-69 0.0
+70-71 0.0
+72-73 0.0
+74-75 0.0
+76-77 0.0
+78-79 0.0
+80-81 0.0
+82-83 0.0
+84-85 0.0
+86-87 0.0
+88-89 0.0
+90-91 0.0
+92-93 0.0
+94-95 0.0
+96-97 0.0
+98-99 0.0
+100-101 0.0
+>>END_MODULE
+>>Sequence Length Distribution pass
+#Length Count
+101 267849.0
+>>END_MODULE
+>>Sequence Duplication Levels warn
+#Total Deduplicated Percentage 63.69408840068983
+#Duplication Level Percentage of deduplicated Percentage of total
+1 81.5623716290639 51.950409087115126
+2 9.995611185249079 12.733226849043577
+3 3.1947144335386772 6.104532706343167
+4 1.4905270052149588 3.797510353351082
+5 0.8725392208870194 2.778779513412342
+6 0.55360835935223 2.115694786796508
+7 0.38537193434967776 1.718213983752925
+8 0.314619574221819 1.603152557845755
+9 0.2033036957962869 1.1654319215012086
+>10 1.4223398099582591 15.850860027094066
+>50 0.0049931523680946535 0.18218821374420768
+>100 0.0 0.0
+>500 0.0 0.0
+>1k 0.0 0.0
+>5k 0.0 0.0
+>10k+ 0.0 0.0
+>>END_MODULE
+>>Overrepresented sequences pass
+>>END_MODULE
+>>Adapter Content pass
+#Position Illumina Universal Adapter Illumina Small RNA Adapter Nextera Transposase Sequence SOLID Small RNA Adapter
+1 0.0 0.0 0.0 0.0
+2 0.0 0.0 0.0 0.0
+3 0.0 0.0 0.0 0.0
+4 0.0 0.0 0.0 0.0
+5 0.0 0.0 0.0 0.0
+6 0.0 0.0 0.0 0.0
+7 0.0 0.0 0.0 0.0
+8 0.0 0.0 0.0 0.0
+9 0.0 0.0 0.0 0.0
+10-11 0.0 0.0 0.0 0.0
+12-13 0.0 0.0 0.0 0.0
+14-15 0.0 0.0 0.0 0.0
+16-17 0.0 0.0 0.0 0.0
+18-19 0.0 0.0 0.0 0.0
+20-21 0.0 0.0 0.0 0.0
+22-23 0.0 0.0 0.0 0.0
+24-25 0.0 0.0 0.0 0.0
+26-27 0.0 0.0 0.0 0.0
+28-29 0.0 0.0 0.0 0.0
+30-31 0.0 0.0 0.0 0.0
+32-33 0.0 0.0 0.0 0.0
+34-35 0.0 0.0 0.0 0.0
+36-37 0.0 0.0 0.0 0.0
+38-39 0.0 0.0 0.0 0.0
+40-41 0.0 0.0 0.0 0.0
+42-43 0.0 0.0 0.0 0.0
+44-45 0.0 0.0 0.0 0.0
+46-47 0.0 0.0 0.0 0.0
+48-49 0.0 0.0 0.0 0.0
+50-51 0.0 0.0 0.0 0.0
+52-53 0.0 0.0 0.0 0.0
+54-55 0.0 0.0 0.0 0.0
+56-57 0.0 0.0 0.0 0.0
+58-59 0.0 0.0 0.0 0.0
+60-61 0.0 0.0 0.0 0.0
+62-63 0.0 0.0 0.0 0.0
+64-65 0.0 0.0 0.0 0.0
+66-67 0.0 0.0 0.0 0.0
+68-69 0.0 0.0 0.0 0.0
+70-71 0.0 0.0 0.0 0.0
+72-73 0.0 0.0 0.0 0.0
+74-75 0.0 0.0 0.0 0.0
+76-77 0.0 0.0 0.0 0.0
+78-79 0.0 0.0 0.0 0.0
+80-81 0.0 0.0 0.0 0.0
+82-83 0.0 0.0 0.0 0.0
+84-85 0.0 0.0 0.0 0.0
+86-87 0.0 0.0 0.0 0.0
+88-89 0.0 0.0 0.0 0.0
+>>END_MODULE
+>>Kmer Content warn
+#Sequence Count PValue Obs/Exp Max Max Obs/Exp Position
+TTAGTGG 50 0.0016122013 38.00672 3
+CCGGGAA 65 0.0058204937 29.246862 1
+CTCGCCA 65 0.0058204937 29.246862 1
+CCCGCTT 70 0.008357804 27.157803 1
+AACAATT 125 0.006013185 19.00336 2
+CTGGGAT 205 3.3062082E-4 16.228443 1
+AGTTCAA 195 0.0044498937 14.615241 5
+GAGTAGT 125 0.0014974214 13.29987 30-31
+AAGTTCA 220 0.009890434 12.954418 4
+CTGAAAT 275 0.003044474 12.097567 1
+CCCAGCT 405 3.2130985E-5 11.734852 1
+AGGGTGT 145 0.0045575905 11.465405 66-67
+CTGAATT 335 0.001024679 11.349529 1
+CTTGAAT 295 0.0051441877 11.277392 1
+GAATGTC 425 6.555659E-4 10.058724 4
+GGTAGTA 190 0.002949709 9.999902 52-53
+CTCTGCC 390 0.0036302158 9.748955 1
+CTCCTTT 535 5.356131E-4 8.883393 1
+CTTTGCT 500 0.0028739348 8.5547085 1
+>>END_MODULE
diff -r 000000000000 -r 3bad335ccea9 test-data/fastqc_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_2.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2170 @@
+##FastQC 0.11.4
+>>Basic Statistics pass
+#Measure Value
+Filename poulet5_2
+File type Conventional base calls
+Encoding Sanger / Illumina 1.9
+Total Sequences 267849
+Sequences flagged as poor quality 0
+Sequence length 101
+%GC 48
+>>END_MODULE
+>>Per base sequence quality warn
+#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
+1 20.590586487162543 21.0 21.0 21.0 20.0 21.0
+2 20.458478471078855 21.0 19.0 22.0 19.0 22.0
+3 20.178608096352797 21.0 20.0 21.0 18.0 22.0
+4 22.495204387546714 23.0 22.0 24.0 20.0 24.0
+5 24.59397272343746 25.0 24.0 26.0 24.0 26.0
+6 25.77560491172265 26.0 25.0 27.0 25.0 27.0
+7 26.651378201897337 27.0 26.0 28.0 26.0 28.0
+8 27.54968284369178 28.0 27.0 29.0 26.0 29.0
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+>>END_MODULE
+>>Per sequence quality scores warn
+#Quality Count
+2 308.0
+3 0.0
+4 0.0
+5 2.0
+6 2.0
+7 5.0
+8 11.0
+9 19.0
+10 24.0
+11 37.0
+12 67.0
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+21 2574.0
+22 3707.0
+23 5673.0
+24 9154.0
+25 18567.0
+26 152994.0
+27 69334.0
+>>END_MODULE
+>>Per base sequence content fail
+#Base G A T C
+1 24.259742395586485 12.979270544437881 10.183447832489852 52.57753922748578
+2 18.617901052497956 21.439745518763136 40.641206097693015 19.30114733104589
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+6 21.71820690015643 32.48808097099485 23.803336954776757 21.990375174071957
+7 20.013888422208034 18.00865412975221 38.0975848332456 23.879872614794156
+8 20.609746536294704 21.85895784565184 29.885495185720313 27.645800432333147
+9 20.915142486998274 20.74116386471482 31.829127605479208 26.5145660428077
+10-11 24.97414588070144 29.204327811565474 22.19142128587376 23.630105021859332
+12-13 22.91160317940332 24.228949893410093 27.574118253194897 25.285328673991692
+14-15 23.741361737396815 25.36261102337511 26.722705703586726 24.17332153564135
+16-17 24.579147206075064 25.610138548211864 25.582884386352013 24.22782985936106
+18-19 24.019316853899024 25.60957853118735 25.727182106336034 24.643922508577596
+20-21 23.88827287016192 25.856546038999582 26.02679121445292 24.228389876385574
+22-23 23.961261755690707 26.122927470328435 25.75256954478083 24.163241229200032
+24-25 23.863818793424656 26.03985827835833 25.928974907503854 24.167348020713163
+26-27 23.84141811244395 26.16418205780122 26.033138074064116 23.961261755690707
+28-29 23.890326265918485 25.823318362211545 25.908814294621223 24.37754107724875
+30-31 23.84515155927407 25.788223962008445 25.969856150293637 24.39676832842385
+32-33 23.917393755436834 26.149621615163767 26.046018465628023 23.88696616377138
+34-35 24.097159220306963 26.049191895433623 25.611445254602405 24.24220362965701
+36-37 23.718027694708585 25.954922362973164 25.862706226269278 24.464343716048965
+38-39 23.9228072533405 25.979376439710432 26.10724699364194 23.990569313307127
+40-41 23.882672699916743 25.983296558882056 26.044338414554467 24.08969232664673
+42-43 23.787283133407257 26.000097069617585 25.91497448189092 24.297645315084246
+44-45 23.768055882232154 26.142154721503534 26.11620726603422 23.973582130230092
+46-47 23.956034930128542 26.0038305164477 25.79867761313277 24.241456940290984
+48-49 23.8716590317679 25.95436234594865 25.834892047384905 24.339086574898545
+50-51 23.940727798125064 26.11900735115681 25.965562686439004 23.974702164279126
+52-53 23.85952532957002 26.227277309230203 25.698807910427146 24.214389450772636
+54-55 23.936621006611936 25.95342898424112 25.899480677545935 24.210469331601015
+56-57 24.102199373527622 25.939801903311192 26.084286295636723 23.873712427524463
+58-59 24.02267695604613 26.216823658105877 25.769370055516355 23.991129330331642
+60-61 23.884726095673308 26.040978312407365 25.961455894925873 24.112839696993454
+62-63 23.794563354725984 26.08801974246684 26.275252100997204 23.842164801809975
+64-65 23.963688496130285 26.01055072074191 25.83302532396985 24.19273545915796
+66-67 23.792323286627916 25.963135945999426 25.901534073302496 24.343006694070166
+68-69 23.88509944035632 26.06225895933903 26.086713036076297 23.965928564228353
+70-71 23.78392303126015 26.232877479475373 25.739315808533913 24.243883680730562
+72-73 23.80445698882579 26.11751397242476 25.980869818442482 24.097159220306963
+74-75 23.956781619494567 26.278238858461293 26.054418720995788 23.710560801048352
+76-77 23.885659457380836 26.073085955146368 25.85971946880519 24.181535118667608
+78-79 23.94035445344205 26.194236304783665 25.794384149278137 24.071025092496146
+80-81 23.81640401868217 26.158021870531527 26.12890098525662 23.896673125529684
+82-83 23.995467587087475 25.704269391092353 26.116256017860845 24.18400700395933
+84-85 23.760588988571918 25.9592158268278 26.086339691393285 24.193855493206993
+86-87 23.802261352966323 26.35799715137475 26.019186219075337 23.82055527658359
+88-89 24.123840280759396 26.200414418786984 25.7484739308182 23.927271369635424
+90-91 24.09603918625793 25.911801052085316 25.786170566251883 24.20598919540487
+92-93 23.827497890578915 26.454007153364245 25.948866139498072 23.769628816558768
+94-95 24.156707697247327 25.997670329178007 25.765076591661717 24.080545381912945
+96-97 24.214576123114142 26.079246142416064 25.670433714518254 24.03574401995154
+98-99 24.170334778177256 26.024551146354852 25.918147911696515 23.88696616377138
+100-101 24.662260557858183 25.864978902953588 25.310294611851685 24.162465927336545
+>>END_MODULE
+>>Per sequence GC content pass
+#GC Content Count
+0 0.0
+1 0.0
+2 0.0
+3 0.0
+4 0.0
+5 0.0
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10 0.0
+11 0.0
+12 0.0
+13 0.0
+14 0.5
+15 2.5
+16 5.0
+17 6.0
+18 9.5
+19 18.0
+20 26.0
+21 35.5
+22 46.0
+23 71.0
+24 130.0
+25 233.5
+26 389.5
+27 542.5
+28 724.5
+29 1063.0
+30 1433.0
+31 1683.5
+32 1996.0
+33 2367.5
+34 2840.5
+35 3318.0
+36 3924.5
+37 4721.0
+38 5510.0
+39 6259.0
+40 7364.0
+41 8736.0
+42 9608.5
+43 10256.0
+44 10928.5
+45 11153.5
+46 11271.5
+47 12042.0
+48 12804.5
+49 12874.0
+50 12482.5
+51 11758.0
+52 10827.0
+53 10433.0
+54 10615.0
+55 9955.0
+56 8760.0
+57 7986.5
+58 6982.5
+59 5802.5
+60 4913.5
+61 4177.5
+62 3751.5
+63 3282.0
+64 2533.0
+65 1954.0
+66 1513.0
+67 1247.5
+68 1102.0
+69 957.0
+70 777.0
+71 535.5
+72 361.5
+73 253.0
+74 157.0
+75 99.0
+76 60.0
+77 46.5
+78 37.0
+79 21.5
+80 13.5
+81 16.5
+82 19.5
+83 14.0
+84 6.5
+85 3.0
+86 0.5
+87 0.0
+88 0.0
+89 0.0
+90 0.0
+91 0.0
+92 0.0
+93 0.0
+94 0.0
+95 0.0
+96 0.0
+97 0.0
+98 0.0
+99 0.0
+100 0.0
+>>END_MODULE
+>>Per base N content pass
+#Base N-Count
+1 0.11461681768459094
+2 0.003733446830116969
+3 0.0
+4 0.0
+5 0.0
+6 0.0
+7 0.0
+8 0.0
+9 0.0
+10-11 0.0
+12-13 0.0
+14-15 0.0
+16-17 0.0
+18-19 0.0
+20-21 0.0
+22-23 0.0
+24-25 0.0
+26-27 0.0
+28-29 0.0
+30-31 0.0
+32-33 0.0
+34-35 0.0
+36-37 0.0
+38-39 0.0
+40-41 0.0
+42-43 0.0
+44-45 0.0
+46-47 0.0
+48-49 0.0
+50-51 0.0
+52-53 0.0
+54-55 0.0
+56-57 0.0
+58-59 0.0
+60-61 0.0
+62-63 0.0
+64-65 0.0
+66-67 0.0
+68-69 0.0
+70-71 0.0
+72-73 0.0
+74-75 0.0
+76-77 0.0
+78-79 0.0
+80-81 0.0
+82-83 1.8667234150584845E-4
+84-85 0.0
+86-87 1.8667234150584845E-4
+88-89 0.0014933787320467876
+90-91 0.0
+92-93 0.0011200340490350907
+94-95 0.0
+96-97 0.0
+98-99 0.0
+100-101 0.01456044263745618
+>>END_MODULE
+>>Sequence Length Distribution pass
+#Length Count
+101 267849.0
+>>END_MODULE
+>>Sequence Duplication Levels warn
+#Total Deduplicated Percentage 63.826611251945884
+#Duplication Level Percentage of deduplicated Percentage of total
+1 81.66283073871745 52.122617512935754
+2 9.894108596885154 12.630148461958491
+3 3.18062640137576 6.090258145748586
+4 1.5566170090070461 3.974143548082379
+5 0.8538567368205473 2.7249391002950074
+6 0.5533319107768025 2.119038045746843
+7 0.3960736941041749 1.7696029190496514
+8 0.2698969625036296 1.3781286803040145
+9 0.23212846037984958 1.3334375701059644
+>10 1.3969694370078172 15.730893862039416
+>50 0.0035600524217624095 0.12679215373389083
+>100 0.0 0.0
+>500 0.0 0.0
+>1k 0.0 0.0
+>5k 0.0 0.0
+>10k+ 0.0 0.0
+>>END_MODULE
+>>Overrepresented sequences pass
+>>END_MODULE
+>>Adapter Content pass
+#Position Illumina Universal Adapter Illumina Small RNA Adapter Nextera Transposase Sequence SOLID Small RNA Adapter
+1 0.0 0.0 0.0 0.0
+2 0.0 0.0 0.0 0.0
+3 0.0 0.0 0.0 0.0
+4 0.0 0.0 0.0 0.0
+5 0.0 0.0 0.0 0.0
+6 0.0 0.0 0.0 0.0
+7 0.0 0.0 0.0 0.0
+8 0.0 0.0 0.0 0.0
+9 0.0 0.0 0.0 0.0
+10-11 0.0 0.0 0.0 0.0
+12-13 0.0 0.0 0.0 0.0
+14-15 0.0 0.0 0.0 0.0
+16-17 0.0 0.0 0.0 0.0
+18-19 0.0 0.0 0.0 0.0
+20-21 0.0 0.0 0.0 0.0
+22-23 0.0 0.0 0.0 0.0
+24-25 0.0 0.0 0.0 0.0
+26-27 0.0 0.0 0.0 0.0
+28-29 0.0 0.0 0.0 0.0
+30-31 0.0 0.0 0.0 0.0
+32-33 0.0 0.0 0.0 0.0
+34-35 0.0 0.0 0.0 0.0
+36-37 0.0 0.0 0.0 0.0
+38-39 0.0 0.0 0.0 0.0
+40-41 0.0 0.0 0.0 0.0
+42-43 0.0 0.0 0.0 0.0
+44-45 0.0 0.0 0.0 0.0
+46-47 0.0 0.0 0.0 0.0
+48-49 0.0 0.0 0.0 0.0
+50-51 0.0 0.0 0.0 0.0
+52-53 0.0 0.0 0.0 0.0
+54-55 0.0 0.0 0.0 0.0
+56-57 0.0 0.0 0.0 0.0
+58-59 0.0 0.0 0.0 0.0
+60-61 0.0 0.0 0.0 0.0
+62-63 0.0 0.0 0.0 0.0
+64-65 0.0 0.0 0.0 0.0
+66-67 0.0 0.0 0.0 0.0
+68-69 0.0 0.0 0.0 0.0
+70-71 0.0 0.0 0.0 0.0
+72-73 0.0 0.0 0.0 0.0
+74-75 0.0 0.0 0.0 0.0
+76-77 0.0 0.0 0.0 0.0
+78-79 0.0 0.0 0.0 0.0
+80-81 0.0 0.0 0.0 0.0
+82-83 0.0 0.0 0.0 0.0
+84-85 0.0 0.0 0.0 0.0
+86-87 0.0 0.0 0.0 0.0
+88-89 0.0 0.0 0.0 0.0
+>>END_MODULE
+>>Kmer Content warn
+#Sequence Count PValue Obs/Exp Max Max Obs/Exp Position
+TACGAGG 60 0.0039460836 31.665857 9
+CCCAGAT 105 6.861368E-5 27.157375 1
+AATCAAC 70 0.008381328 27.142164 5
+CTTGTAT 120 0.004739449 19.802252 1
+TCGCTCA 130 0.007549489 18.268764 2
+CCCCACT 195 0.0044338168 14.623201 1
+TTCAACA 295 0.005166332 11.270898 2
+CTTGAAG 305 0.006593838 10.90747 1
+>>END_MODULE
diff -r 000000000000 -r 3bad335ccea9 test-data/fastqc_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,3 @@
+Sample adapter_content Sequences flagged as poor quality sequence_duplication_levels avg_sequence_length Encoding kmer_content per_base_sequence_quality sequence_length_distribution Sequence length File type basic_statistics per_sequence_gc_content Total Sequences per_base_n_content per_base_sequence_content overrepresented_sequences %GC total_deduplicated_percentage Filename per_tile_sequence_quality per_sequence_quality_scores
+poulet5_1 pass 0.0 warn 101.0 Sanger / Illumina 1.9 warn warn pass 101.0 Conventional base calls pass pass 267849.0 pass fail pass 48.0 63.6940884007 poulet5_1 pass warn
+poulet5_2 pass 0.0 warn 101.0 Sanger / Illumina 1.9 warn warn pass 101.0 Conventional base calls pass pass 267849.0 pass fail pass 48.0 63.8266112519 poulet5_2 pass warn
diff -r 000000000000 -r 3bad335ccea9 test-data/featureCounts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featureCounts.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,12 @@
+Status 70: TopHat on data 1, data 4, and data 3: accepted_hits 75: TopHat on data 1, data 6, and data 5: accepted_hits 80: TopHat on data 1, data 8, and data 7: accepted_hits 85: TopHat on data 1, data 10, and data 9: accepted_hits 90: TopHat on data 1, data 12, and data 11: accepted_hits 95: TopHat on data 1, data 14, and data 13: accepted_hits
+Assigned 321797 445012 394981 437485 388170 453929
+Unassigned_Ambiguity 2333 3424 3121 3692 2782 3554
+Unassigned_MultiMapping 19123 25293 22580 19907 21164 23533
+Unassigned_NoFeatures 111117 165786 129664 146327 132063 160805
+Unassigned_Unmapped 0 0 0 0 0 0
+Unassigned_MappingQuality 0 0 0 0 0 0
+Unassigned_FragmentLength 0 0 0 0 0 0
+Unassigned_Chimera 0 0 0 0 0 0
+Unassigned_Secondary 0 0 0 0 0 0
+Unassigned_Nonjunction 0 0 0 0 0 0
+Unassigned_Duplicate 0 0 0 0 0 0
diff -r 000000000000 -r 3bad335ccea9 test-data/featureCounts_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/featureCounts_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,7 @@
+Sample Unassigned_Ambiguity Unassigned_MappingQuality percent_assigned Unassigned_Nonjunction Unassigned_Duplicate Unassigned_Chimera Unassigned_Unmapped Assigned Unassigned_MultiMapping Unassigned_Secondary Unassigned_NoFeatures Unassigned_FragmentLength Total
+70: TopHat on data 1, data 4, and data 3: accepted_hits 2333 0 70.8226775535 0 0 0 0 321797 19123 0 111117 0 454370
+75: TopHat on data 1, data 6, and data 5: accepted_hits 3424 0 69.585858033 0 0 0 0 445012 25293 0 165786 0 639515
+80: TopHat on data 1, data 8, and data 7: accepted_hits 3121 0 71.7695776839 0 0 0 0 394981 22580 0 129664 0 550346
+85: TopHat on data 1, data 10, and data 9: accepted_hits 3692 0 72.0245435134 0 0 0 0 437485 19907 0 146327 0 607411
+90: TopHat on data 1, data 12, and data 11: accepted_hits 2782 0 71.3313082644 0 0 0 0 388170 21164 0 132063 0 544179
+95: TopHat on data 1, data 14, and data 13: accepted_hits 3554 0 70.7251710368 0 0 0 0 453929 23533 0 160805 0 641821
diff -r 000000000000 -r 3bad335ccea9 test-data/flexbar.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flexbar.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,71 @@
+
+ ________ __
+ / ____/ /__ _ __/ /_ ____ ______
+ / /_ / / _ \| |/ / __ \/ __ `/ ___/
+ / __/ / / __/> /_/ / /_/ / /
+ /_/ /_/\___/_/|_/_.___/\__._/_/
+
+Flexbar - flexible barcode and adapter removal, version 3.0
+Developed with SeqAn, the library for sequence analysis
+
+Available on github.com/seqan/flexbar
+
+
+Local time: Mon Jun 5 13:20:34 2017
+
+Number of threads: 1
+Bundled fragments: 256
+
+Target name: result_right
+File type: fasta
+Reads file: reads.fasta
+Adapter file: adapters.fasta
+
+max-uncalled: 0
+min-read-length: 10
+
+adapter-trim-end: RIGHT
+adapter-min-overlap: 4
+adapter-error-rate: 0.1
+adapter-match: 1
+adapter-mismatch: -1
+adapter-gap: -6
+
+Adapter: Sequence:
+ad1 CGTCTT
+
+
+Processing reads ...done.
+
+Elapsed time: < 1 sec
+
+
+Adapter removal statistics
+==========================
+Adapter: Overlap removal: Full length:
+ad1 11 10
+
+Min, max, mean and median overlap: 5 / 6 / 5 / 6
+
+
+Output file statistics
+======================
+Read file: result_right.fasta
+ written reads 10
+ short reads 3
+
+
+Filtering statistics
+====================
+Processed reads 13
+ skipped due to uncalled bases 0
+ short prior to adapter removal 0
+ finally skipped short reads 3
+Discarded reads overall 3
+Remaining reads 10 (76%)
+
+Processed bases 422
+Remaining bases 231 (54% of input)
+
+
+Flexbar completed adapter removal.
diff -r 000000000000 -r 3bad335ccea9 test-data/flexbar_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flexbar_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample removed_bases_pct remaining_reads short_prior_to_adapter_removal remaining_bases skipped_due_to_uncalled_bases processed_reads processed_bases removed_bases discarded_reads_overall finally_skipped_short_reads
+result_right 45.2606635071 10 0 231 0 13 422 191 3 3
diff -r 000000000000 -r 3bad335ccea9 test-data/gatk_BaseRecalibrator.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk_BaseRecalibrator.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,3040 @@
+#:GATKReport.v1.1:5
+#:GATKTable:2:17:%s:%s:;
+#:GATKTable:Arguments:Recalibration argument collection values used in this run
+Argument Value
+binary_tag_name null
+covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate
+default_platform null
+deletions_default_quality 45
+force_platform null
+indels_context_size 3
+insertions_default_quality 45
+low_quality_tail 2
+maximum_cycle_value 500
+mismatches_context_size 2
+mismatches_default_quality -1
+no_standard_covs false
+quantizing_levels 16
+recalibration_report null
+run_without_dbsnp false
+solid_nocall_strategy THROW_EXCEPTION
+solid_recal_mode SET_Q_ZERO
+
+#:GATKTable:3:94:%s:%s:%s:;
+#:GATKTable:Quantized:Quality quantization map
+QualityScore Count QuantizedScore
+ 0 0 93
+ 1 0 93
+ 2 0 93
+ 3 0 93
+ 4 0 93
+ 5 0 93
+ 6 0 93
+ 7 0 93
+ 8 0 93
+ 9 0 93
+ 10 0 93
+ 11 0 93
+ 12 0 93
+ 13 6755595 13
+ 14 19683376 14
+ 15 0 93
+ 16 0 93
+ 17 0 93
+ 18 7903490 18
+ 19 0 93
+ 20 0 93
+ 21 0 93
+ 22 0 93
+ 23 898722 23
+ 24 2706118 24
+ 25 0 93
+ 26 0 93
+ 27 70849987 27
+ 28 736517063 28
+ 29 0 93
+ 30 0 93
+ 31 0 93
+ 32 0 93
+ 33 0 93
+ 34 0 93
+ 35 0 93
+ 36 0 93
+ 37 0 93
+ 38 0 93
+ 39 0 93
+ 40 0 93
+ 41 0 93
+ 42 845314351 42
+ 43 0 43
+ 44 845314351 44
+ 45 0 93
+ 46 0 93
+ 47 0 93
+ 48 0 93
+ 49 0 93
+ 50 0 93
+ 51 0 93
+ 52 0 93
+ 53 0 93
+ 54 0 93
+ 55 0 93
+ 56 0 93
+ 57 0 93
+ 58 0 93
+ 59 0 93
+ 60 0 93
+ 61 0 93
+ 62 0 93
+ 63 0 93
+ 64 0 93
+ 65 0 93
+ 66 0 93
+ 67 0 93
+ 68 0 93
+ 69 0 93
+ 70 0 93
+ 71 0 93
+ 72 0 93
+ 73 0 93
+ 74 0 93
+ 75 0 93
+ 76 0 93
+ 77 0 93
+ 78 0 93
+ 79 0 93
+ 80 0 93
+ 81 0 93
+ 82 0 93
+ 83 0 93
+ 84 0 93
+ 85 0 93
+ 86 0 93
+ 87 0 93
+ 88 0 93
+ 89 0 93
+ 90 0 93
+ 91 0 93
+ 92 0 93
+ 93 0 93
+
+#:GATKTable:6:12:%s:%s:%.4f:%.4f:%d:%.2f:;
+#:GATKTable:RecalTable0:
+ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 M 25.0000 27.7511 204609258 637006.75
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 I 44.0000 45.0000 204609258 8181.44
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 D 42.0000 45.0000 204609258 13857.53
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 M 25.0000 28.0824 216735396 678622.29
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 I 44.0000 45.0000 216735396 8787.41
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 D 42.0000 45.0000 216735396 14494.80
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 M 25.0000 27.6759 201238597 633483.85
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 I 44.0000 45.0000 201238597 8179.63
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 D 42.0000 45.0000 201238597 13164.04
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 M 26.0000 28.1954 222731100 613617.33
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 I 44.0000 45.0000 222731100 8548.18
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 D 42.0000 45.0000 222731100 14363.33
+
+#:GATKTable:6:28:%s:%s:%s:%.4f:%d:%.2f:;
+#:GATKTable:RecalTable1:
+ReadGroup QualityScore EventType EmpiricalQuality Observations Errors
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 M 14.0000 6726044 298061.40
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 M 18.0000 2002697 32870.45
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 M 24.0000 921965 3770.98
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 M 27.0000 23489123 43436.18
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 M 28.0000 171469429 258867.74
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 I 44.0000 204609258 8181.44
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 D 42.0000 204609258 13857.53
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 14 M 14.0000 6491358 287373.59
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 21 M 18.0000 1962027 32953.63
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 27 M 23.0000 898722 4231.61
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 32 M 27.0000 24094367 51915.49
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 36 M 28.0000 183288922 302147.96
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 45 I 44.0000 216735396 8787.41
+NB501183:321:HYF5WBGX2:2:PAV10-50254229 45 D 42.0000 216735396 14494.80
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 14 M 13.0000 6755595 302926.37
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 21 M 18.0000 2009522 33519.75
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 27 M 24.0000 894901 3495.30
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 32 M 27.0000 23266497 41966.53
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 36 M 28.0000 168312082 251575.90
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 45 I 44.0000 201238597 8179.63
+NB501183:321:HYF5WBGX2:3:PAV10-50254229 45 D 42.0000 201238597 13164.04
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 14 M 14.0000 6465974 271643.23
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 21 M 18.0000 1929244 29634.03
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 27 M 24.0000 889252 3268.05
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 32 M 28.0000 24602264 40880.18
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 36 M 28.0000 188844366 268191.83
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 I 44.0000 222731100 8548.18
+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 D 42.0000 222731100 14363.33
+
+#:GATKTable:8:2868:%s:%s:%s:%s:%s:%.4f:%d:%.2f:;
+#:GATKTable:RecalTable2:
+ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 AA Context M 13.0000 420096 21343.35
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 CA Context M 14.0000 861623 34351.22
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 GA Context M 15.0000 636582 21519.56
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 TA Context M 10.0000 292116 29206.84
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 AC Context M 12.0000 255178 18004.97
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 CC Context M 12.0000 487522 31940.26
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 GC Context M 10.0000 375521 35131.14
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 TC Context M 15.0000 382319 12255.32
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 AG Context M 16.0000 382747 8796.28
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 CG Context M 9.0000 167755 19503.02
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 GG Context M 15.0000 407944 14484.14
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 TG Context M 17.0000 432341 9495.98
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 AT Context M 14.0000 307242 12435.60
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 CT Context M 18.0000 492645 8321.29
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 GT Context M 16.0000 343249 9437.94
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 14 TT Context M 15.0000 380502 11345.84
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 AA Context M 19.0000 357619 4780.98
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 CA Context M 21.0000 186228 1505.30
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 GA Context M 21.0000 296171 2134.35
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 TA Context M 16.0000 170108 4355.06
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 AC Context M 13.0000 50594 2465.34
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 CC Context M 17.0000 67014 1287.30
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 GC Context M 13.0000 61672 3383.43
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 TC Context M 17.0000 67920 1443.19
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 AG Context M 20.0000 149508 1477.03
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 CG Context M 14.0000 20207 1009.85
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 GG Context M 17.0000 86834 1716.49
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 TG Context M 20.0000 124593 1335.92
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 AT Context M 16.0000 92398 2597.38
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 CT Context M 22.0000 58193 343.72
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 GT Context M 19.0000 76171 1041.99
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 21 TT Context M 16.0000 70108 1910.11
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 AA Context M 25.0000 6587 43.96
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 CA Context M 25.0000 39252 145.16
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 GA Context M 26.0000 11177 43.00
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 TA Context M 25.0000 5522 46.38
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 AC Context M 24.0000 68192 320.43
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 CC Context M 23.0000 195774 1043.97
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 GC Context M 23.0000 115421 649.38
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 TC Context M 26.0000 107700 249.54
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 AG Context M 27.0000 42306 91.35
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 CG Context M 21.0000 38128 382.27
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 GG Context M 26.0000 66527 204.54
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 TG Context M 27.0000 58527 127.09
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 AT Context M 25.0000 21389 94.60
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 CT Context M 27.0000 67502 136.34
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 GT Context M 26.0000 28957 94.41
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 27 TT Context M 27.0000 42621 92.26
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 AA Context M 27.0000 1259737 2394.29
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 CA Context M 27.0000 1844022 3394.37
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 GA Context M 28.0000 1335402 2041.75
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 TA Context M 26.0000 1318671 3186.68
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 AC Context M 27.0000 1030413 2324.68
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 CC Context M 26.0000 1970205 4658.98
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 GC Context M 27.0000 1248175 2766.52
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 TC Context M 28.0000 1556790 2564.21
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 AG Context M 28.0000 1026038 1869.07
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 CG Context M 21.0000 407488 3192.36
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 GG Context M 27.0000 1068091 2278.54
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 TG Context M 28.0000 1251289 2280.17
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 AT Context M 27.0000 1227615 2625.32
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 CT Context M 29.0000 1674965 2247.65
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 GT Context M 27.0000 1107504 2071.54
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 32 TT Context M 28.0000 1517371 2483.66
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 AA Context M 29.0000 13418282 17152.68
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 CA Context M 29.0000 12483397 16432.54
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 GA Context M 29.0000 10434129 13050.18
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 TA Context M 28.0000 7940797 14281.52
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 AC Context M 28.0000 8806876 14589.52
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 CC Context M 28.0000 10235451 17523.47
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 GC Context M 29.0000 9548944 12309.10
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 TC Context M 29.0000 10311734 13105.78
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 AG Context M 29.0000 13186363 17001.12
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 CG Context M 23.0000 3818821 20171.84
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 GG Context M 28.0000 11561899 20574.85
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 TG Context M 29.0000 13413468 17525.14
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 AT Context M 28.0000 10944647 18316.60
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 CT Context M 29.0000 12337017 13992.42
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 GT Context M 28.0000 9016048 15722.49
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 36 TT Context M 30.0000 13491008 15191.97
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AAA Context I 37.0000 5169154 1102.21
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AAA Context D 35.0000 5169154 1782.18
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CAA Context I 45.0000 3474609 126.73
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CAA Context D 43.0000 3474609 230.13
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GAA Context I 45.0000 3890072 126.57
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GAA Context D 43.0000 3890072 233.77
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TAA Context I 44.0000 2784758 134.68
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TAA Context D 42.0000 2784758 223.48
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ACA Context I 45.0000 3727915 120.35
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ACA Context D 44.0000 3727915 183.34
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CCA Context I 46.0000 4286756 96.77
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CCA Context D 43.0000 4286756 253.19
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GCA Context I 46.0000 3395879 74.07
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GCA Context D 45.0000 3395879 110.49
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TCA Context I 46.0000 3763506 85.65
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TCA Context D 45.0000 3763506 131.37
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AGA Context I 45.0000 4107008 108.21
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AGA Context D 44.0000 4107008 167.06
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CGA Context I 46.0000 901750 12.66
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CGA Context D 45.0000 901750 23.69
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GGA Context I 46.0000 3675755 82.32
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GGA Context D 42.0000 3675755 254.12
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TGA Context I 46.0000 3738278 90.14
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TGA Context D 45.0000 3738278 139.29
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ATA Context I 45.0000 2720537 80.44
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ATA Context D 44.0000 2720537 130.09
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CTA Context I 45.0000 2058161 62.05
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CTA Context D 44.0000 2058161 113.49
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GTA Context I 45.0000 2076579 59.86
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GTA Context D 44.0000 2076579 96.91
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TTA Context I 44.0000 2790982 134.87
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TTA Context D 41.0000 2790982 291.85
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AAC Context I 43.0000 2591392 146.74
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AAC Context D 42.0000 2591392 220.59
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CAC Context I 45.0000 3210567 94.36
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CAC Context D 44.0000 3210567 139.89
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GAC Context I 44.0000 2237212 88.52
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GAC Context D 45.0000 2237212 86.96
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TAC Context I 45.0000 2025119 78.23
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TAC Context D 44.0000 2025119 82.18
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ACC Context I 45.0000 2511932 81.09
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ACC Context D 44.0000 2511932 118.13
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CCC Context I 42.0000 3318736 229.51
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CCC Context D 40.0000 3318736 447.77
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GCC Context I 45.0000 3271643 98.63
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GCC Context D 43.0000 3271643 171.90
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TCC Context I 45.0000 3598353 103.72
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TCC Context D 43.0000 3598353 195.83
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AGC Context I 46.0000 3355426 74.62
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AGC Context D 45.0000 3355426 100.99
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CGC Context I 45.0000 1143337 36.98
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CGC Context D 45.0000 1143337 48.02
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GGC Context I 45.0000 3297014 99.60
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GGC Context D 43.0000 3297014 209.79
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TGC Context I 45.0000 3308997 85.21
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TGC Context D 44.0000 3308997 125.65
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ATC Context I 45.0000 2591554 66.60
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ATC Context D 45.0000 2591554 88.33
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CTC Context I 43.0000 3635166 202.38
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CTC Context D 44.0000 3635166 168.14
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GTC Context I 45.0000 2274374 56.96
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GTC Context D 45.0000 2274374 86.40
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TTC Context I 44.0000 3785476 148.62
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TTC Context D 42.0000 3785476 278.40
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AAG Context I 44.0000 3952662 180.61
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AAG Context D 42.0000 3952662 316.38
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CAG Context I 46.0000 4934857 123.03
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CAG Context D 46.0000 4934857 128.26
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GAG Context I 46.0000 3721594 94.67
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GAG Context D 45.0000 3721594 137.10
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TAG Context I 45.0000 2047842 75.73
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TAG Context D 45.0000 2047842 75.93
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ACG Context I 45.0000 915888 18.22
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ACG Context D 45.0000 915888 26.26
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CCG Context I 46.0000 1375351 28.36
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CCG Context D 43.0000 1375351 98.33
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GCG Context I 46.0000 1198755 14.66
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GCG Context D 44.0000 1198755 59.54
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TCG Context I 45.0000 912253 16.52
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TCG Context D 45.0000 912253 31.42
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AGG Context I 45.0000 3893217 133.49
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 AGG Context D 44.0000 3893217 173.45
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CGG Context I 45.0000 1381165 29.57
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CGG Context D 43.0000 1381165 88.20
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GGG Context I 42.0000 3349622 256.66
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GGG Context D 39.0000 3349622 493.80
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TGG Context I 46.0000 4286676 107.18
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TGG Context D 43.0000 4286676 241.74
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ATG Context I 45.0000 3527512 100.02
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 ATG Context D 45.0000 3527512 124.17
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CTG Context I 46.0000 4867020 118.53
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 CTG Context D 44.0000 4867020 195.48
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GTG Context I 45.0000 3347436 96.80
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 GTG Context D 44.0000 3347436 164.60
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TTG Context I 44.0000 3446223 138.46
+NB501183:321:HYF5WBGX2:4:PAV10-50254229 45 TTG Context D 42.0000 3446223 273.89
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+
diff -r 000000000000 -r 3bad335ccea9 test-data/gatk_varianteval.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk_varianteval.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,1323 @@
+#:GATKReport.v1.1:2
+#:GATKTable:31:657:%s:%s:%s:%s:%s:%s:%d:%d:%d:%d:%.8f:%.8f:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f:;
+#:GATKTable:CountVariants:Counts different classes of variants in the sample
+CountVariants CompRod EvalRod JexlExpression Novelty Sample nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp insertionDeletionRatio
+CountVariants none eval none all 00O 2675075632 19199310 15505537 3693773 0.00138081 724.00000000 3693773 0 0 0 0 0 0 8703816 1003518 6801721 2690255 17 0 3.75e-04 2665.00 0.37 0.00e+00 0.00 0.00
+CountVariants none eval none all 00V 2675075632 19199310 14841647 4357663 0.00162899 613.00000000 4357663 0 0 0 0 0 0 7100254 1361571 7741393 2996092 13 0 5.09e-04 1964.00 0.45 0.00e+00 0.00 0.00
+CountVariants none eval none all 01K 2675075632 19199310 12298798 6900512 0.00257956 387.00000000 6900512 0 0 0 0 0 0 2615821 3642513 9682977 3257999 830 0 1.36e-03 734.00 1.12 0.00e+00 0.00 0.00
+CountVariants none eval none all 03J 2675075632 19199310 10752303 8447007 0.00315767 316.00000000 8447007 0 0 0 0 0 0 57172 4985840 10695131 3461167 2228 0 1.86e-03 536.00 1.44 0.00e+00 0.00 0.00
+CountVariants none eval none all 04I 2675075632 19199310 15818704 3380606 0.00126374 791.00000000 3380606 0 0 0 0 0 0 9391683 823349 6427021 2557257 3 0 3.08e-04 3249.00 0.32 0.00e+00 0.00 0.00
+CountVariants none eval none all 04T 2675075632 19199310 10437209 8762101 0.00327546 305.00000000 8762101 0 0 0 0 0 0 56906 5562564 10380303 3199537 2292 0 2.08e-03 480.00 1.74 0.00e+00 0.00 0.00
+CountVariants none eval none all 04Z 2675075632 19199310 14053302 5146008 0.00192369 519.00000000 5146008 0 0 0 0 0 0 5384926 1858628 8668376 3287380 409 0 6.95e-04 1439.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none all 07D 2675075632 19199310 10462495 8736815 0.00326601 306.00000000 8736815 0 0 0 0 0 0 53834 5494779 10408661 3242036 1729 0 2.05e-03 486.00 1.69 0.00e+00 0.00 0.00
+CountVariants none eval none all 0A2 2675075632 19199310 11075482 8123828 0.00303686 329.00000000 8123828 0 0 0 0 0 0 593075 4706940 10482407 3416888 671 0 1.76e-03 568.00 1.38 0.00e+00 0.00 0.00
+CountVariants none eval none all 0A4 2675075632 19199310 16635695 2563615 0.00095833 1043.00000000 2563615 0 0 0 0 0 0 11598771 528294 5036924 2035321 3 0 1.97e-04 5063.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none all 0A9 2675075632 19199310 15828174 3371136 0.00126020 793.00000000 3371136 0 0 0 0 0 0 9540540 878455 6287634 2492681 9 0 3.28e-04 3045.00 0.35 0.00e+00 0.00 0.00
+CountVariants none eval none all 0B4 2675075632 19199310 15492095 3707215 0.00138584 721.00000000 3707215 0 0 0 0 0 0 8525168 917119 6966927 2790096 18 0 3.43e-04 2916.00 0.33 0.00e+00 0.00 0.00
+CountVariants none eval none all 0B6 2675075632 19199310 17003740 2195570 0.00082075 1218.00000000 2195570 0 0 0 0 0 0 12434084 309487 4569656 1886083 3 0 1.16e-04 8643.00 0.16 0.00e+00 0.00 0.00
+CountVariants none eval none all 0C6 2675075632 19199310 14685242 4514068 0.00168745 592.00000000 4514068 0 0 0 0 0 0 6817910 1476642 7867332 3037426 4 0 5.52e-04 1811.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none all 0D3 2675075632 19199310 13776508 5422802 0.00202716 493.00000000 5422802 0 0 0 0 0 0 4795178 2022745 8981330 3400057 3 0 7.56e-04 1322.00 0.59 0.00e+00 0.00 0.00
+CountVariants none eval none all 0F6 2675075632 19199310 11325423 7873887 0.00294343 339.00000000 7873887 0 0 0 0 0 0 825710 4390363 10499713 3483524 2080 0 1.64e-03 609.00 1.26 0.00e+00 0.00 0.00
+CountVariants none eval none all 0G9 2675075632 19199310 15147943 4051367 0.00151449 660.00000000 4051367 0 0 0 0 0 0 7870745 1214001 7277198 2837366 91 0 4.54e-04 2203.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none all 0I5 2675075632 19199310 15187803 4011507 0.00149959 666.00000000 4011507 0 0 0 0 0 0 7971845 1209640 7215958 2801867 37 0 4.52e-04 2211.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none all 10S 2675075632 19199310 11816810 7382500 0.00275974 362.00000000 7382500 0 0 0 0 0 0 1793579 4035060 10023231 3347440 276 0 1.51e-03 662.00 1.21 0.00e+00 0.00 0.00
+CountVariants none eval none all 12O 2675075632 19199310 11549452 7649858 0.00285968 349.00000000 7649858 0 0 0 0 0 0 1254007 4211697 10295445 3438161 227 0 1.57e-03 635.00 1.22 0.00e+00 0.00 0.00
+CountVariants none eval none all 14I 2675075632 19199310 14705422 4493888 0.00167991 595.00000000 4493888 0 0 0 0 0 0 7030813 1597643 7674609 2896245 95 0 5.97e-04 1674.00 0.55 0.00e+00 0.00 0.00
+CountVariants none eval none all 14L 2675075632 19199310 13982713 5216597 0.00195007 512.00000000 5216597 0 0 0 0 0 0 5395682 1973107 8587031 3243490 121 0 7.38e-04 1355.00 0.61 0.00e+00 0.00 0.00
+CountVariants none eval none all 17C 2675075632 19199310 14242500 4956810 0.00185296 539.00000000 4956810 0 0 0 0 0 0 6181930 1973304 8060570 2983506 146 0 7.38e-04 1355.00 0.66 0.00e+00 0.00 0.00
+CountVariants none eval none all 17K 2675075632 19199310 14386818 4812492 0.00179901 555.00000000 4812492 0 0 0 0 0 0 6305617 1784488 8081201 3028004 372 0 6.67e-04 1499.00 0.59 0.00e+00 0.00 0.00
+CountVariants none eval none all 17L 2675075632 19199310 14376607 4822703 0.00180283 554.00000000 4822703 0 0 0 0 0 0 6020356 1598766 8356251 3223937 59 0 5.98e-04 1673.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none all 18Z 2675075632 19199310 13841517 5357793 0.00200286 499.00000000 5357793 0 0 0 0 0 0 5243825 2183290 8597692 3174503 144 0 8.16e-04 1225.00 0.69 0.00e+00 0.00 0.00
+CountVariants none eval none all 19A 2675075632 19199310 14887729 4311581 0.00161176 620.00000000 4311581 0 0 0 0 0 0 7224033 1336538 7663696 2975043 73 0 5.00e-04 2001.00 0.45 0.00e+00 0.00 0.00
+CountVariants none eval none all 19T 2675075632 19199310 14732169 4467141 0.00166991 598.00000000 4467141 0 0 0 0 0 0 6915855 1452719 7816314 3014422 96 0 5.43e-04 1841.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none all 1A3 2675075632 19199310 14751984 4447326 0.00166250 601.00000000 4447326 0 0 0 0 0 0 7297452 1676618 7454532 2770708 186 0 6.27e-04 1595.00 0.61 0.00e+00 0.00 0.00
+CountVariants none eval none all 1A6 2675075632 19199310 14586645 4612665 0.00172431 579.00000000 4612665 0 0 0 0 0 0 6424696 1485423 8161949 3127242 0 0 5.55e-04 1800.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none all 1B0 2675075632 19199310 15644051 3555259 0.00132903 752.00000000 3555259 0 0 0 0 0 0 8969809 895627 6674242 2659632 28 0 3.35e-04 2986.00 0.34 0.00e+00 0.00 0.00
+CountVariants none eval none all 1B1 2675075632 19199310 17926297 1273013 0.00047588 2101.00000000 1273013 0 0 0 0 0 0 15140802 94988 2785495 1178025 0 0 3.55e-05 28162.00 0.08 0.00e+00 0.00 0.00
+CountVariants none eval none all 1C0 2675075632 19199310 14620103 4579207 0.00171180 584.00000000 4579207 0 0 0 0 0 0 6570029 1457827 8050074 3121380 66 0 5.45e-04 1834.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none all 1C2 2675075632 19199310 14195757 5003553 0.00187043 534.00000000 5003553 0 0 0 0 0 0 5840356 1868326 8355401 3135227 59 0 6.98e-04 1431.00 0.60 0.00e+00 0.00 0.00
+CountVariants none eval none all 1C5 2675075632 19199310 15244815 3954495 0.00147827 676.00000000 3954495 0 0 0 0 0 0 8094725 1195694 7150090 2758801 20 0 4.47e-04 2237.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none all 1E2 2675075632 19199310 14216607 4982703 0.00186264 536.00000000 4982703 0 0 0 0 0 0 5710995 1749105 8505612 3233598 165 0 6.54e-04 1529.00 0.54 0.00e+00 0.00 0.00
+CountVariants none eval none all 1E3 2675075632 19199310 11074977 8124333 0.00303705 329.00000000 8124333 0 0 0 0 0 0 611006 4759103 10463971 3365230 3859 0 1.78e-03 562.00 1.41 0.00e+00 0.00 0.00
+CountVariants none eval none all 1E5 2675075632 19199310 14296338 4902972 0.00183283 545.00000000 4902972 0 0 0 0 0 0 6065004 1765053 8231334 3137919 26 0 6.60e-04 1515.00 0.56 0.00e+00 0.00 0.00
+CountVariants none eval none all 1E6 2675075632 19199310 16294677 2904633 0.00108581 920.00000000 2904633 0 0 0 0 0 0 10583607 587400 5711070 2317233 19 0 2.20e-04 4554.00 0.25 0.00e+00 0.00 0.00
+CountVariants none eval none all 1F2 2675075632 19199310 13505314 5693996 0.00212854 469.00000000 5693996 0 0 0 0 0 0 4321937 2301668 9183377 3392328 23 0 8.60e-04 1162.00 0.68 0.00e+00 0.00 0.00
+CountVariants none eval none all 1F9 2675075632 19199310 15508283 3691027 0.00137978 724.00000000 3691027 0 0 0 0 0 0 8428208 817540 7080075 2873487 64 0 3.06e-04 3272.00 0.28 0.00e+00 0.00 0.00
+CountVariants none eval none all 20F 2675075632 19199310 13333612 5865698 0.00219272 456.00000000 5865698 0 0 0 0 0 0 4050860 2457785 9282752 3407913 205 0 9.19e-04 1088.00 0.72 0.00e+00 0.00 0.00
+CountVariants none eval none all 20S 2675075632 19199310 16400770 2798540 0.00104615 955.00000000 2798540 0 0 0 0 0 0 10770437 503015 5630333 2295525 0 0 1.88e-04 5318.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none all 21N 2675075632 19199310 14062191 5137119 0.00192036 520.00000000 5137119 0 0 0 0 0 0 5443416 1874461 8618775 3262658 37 0 7.01e-04 1427.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none all 22H 2675075632 19199310 11659062 7540248 0.00281870 354.00000000 7540248 0 0 0 0 0 0 1600250 4233780 10058812 3306468 1439 0 1.58e-03 631.00 1.28 0.00e+00 0.00 0.00
+CountVariants none eval none all 24B 2675075632 19199310 14460497 4738813 0.00177147 564.00000000 4738813 0 0 0 0 0 0 6419303 1689158 8041194 3049655 99 0 6.31e-04 1583.00 0.55 0.00e+00 0.00 0.00
+CountVariants none eval none all 24V 2675075632 19199310 14543510 4655800 0.00174044 574.00000000 4655800 0 0 0 0 0 0 6586326 1616420 7957184 3039380 173 0 6.04e-04 1654.00 0.53 0.00e+00 0.00 0.00
+CountVariants none eval none all 25L 2675075632 19199310 16668989 2530321 0.00094589 1057.00000000 2530321 0 0 0 0 0 0 11622104 462772 5046885 2067549 14 0 1.73e-04 5780.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none all 25P 2675075632 19199310 10551524 8647786 0.00323273 309.00000000 8647786 0 0 0 0 0 0 160714 5490386 10390810 3157400 5881 0 2.05e-03 487.00 1.74 0.00e+00 0.00 0.00
+CountVariants none eval none all 26P 2675075632 19199310 12321565 6877745 0.00257105 388.00000000 6877745 0 0 0 0 0 0 2470755 3490036 9850810 3387709 222 0 1.30e-03 766.00 1.03 0.00e+00 0.00 0.00
+CountVariants none eval none all 28B 2675075632 19199310 14801741 4397569 0.00164390 608.00000000 4397569 0 0 0 0 0 0 7071647 1391599 7730094 3005970 114 0 5.20e-04 1922.00 0.46 0.00e+00 0.00 0.00
+CountVariants none eval none all 28J 2675075632 19199310 15226166 3973144 0.00148525 673.00000000 3973144 0 0 0 0 0 0 7941355 1098510 7284811 2874634 9 0 4.11e-04 2435.00 0.38 0.00e+00 0.00 0.00
+CountVariants none eval none all 29B 2675075632 19199310 14632464 4566846 0.00170718 585.00000000 4566846 0 0 0 0 0 0 6669976 1506203 7962488 3060643 27 0 5.63e-04 1776.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none all 29V 2675075632 19199310 16223857 2975453 0.00111229 899.00000000 2975453 0 0 0 0 0 0 10403315 616553 5820542 2358900 28 0 2.30e-04 4338.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none all 29Z 2675075632 19199310 13413294 5786016 0.00216294 462.00000000 5786016 0 0 0 0 0 0 4252148 2418350 9161146 3367666 107 0 9.04e-04 1106.00 0.72 0.00e+00 0.00 0.00
+CountVariants none eval none all 2A2 2675075632 19199310 15530231 3669079 0.00137158 729.00000000 3669079 0 0 0 0 0 0 8667981 940005 6862250 2729074 3 0 3.51e-04 2845.00 0.34 0.00e+00 0.00 0.00
+CountVariants none eval none all 2A5 2675075632 19199310 16790148 2409162 0.00090060 1110.00000000 2409162 0 0 0 0 0 0 11871953 380841 4918195 2028321 4 0 1.42e-04 7024.00 0.19 0.00e+00 0.00 0.00
+CountVariants none eval none all 2A7 2675075632 19199310 13535114 5664196 0.00211740 472.00000000 5664196 0 0 0 0 0 0 4384577 2283041 9150537 3381155 29 0 8.53e-04 1171.00 0.68 0.00e+00 0.00 0.00
+CountVariants none eval none all 2A8 2675075632 19199310 16384746 2814564 0.00105214 950.00000000 2814564 0 0 0 0 0 0 10726988 503184 5657758 2311380 5 0 1.88e-04 5316.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none all 2C3 2675075632 19199310 15735035 3464275 0.00129502 772.00000000 3464275 0 0 0 0 0 0 9353027 964797 6382008 2499478 39 0 3.61e-04 2772.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none all 2C4 2675075632 19199310 14175534 5023776 0.00187799 532.00000000 5023776 0 0 0 0 0 0 6068015 2059567 8107519 2964209 27 0 7.70e-04 1298.00 0.69 0.00e+00 0.00 0.00
+CountVariants none eval none all 2C8 2675075632 19199310 16672858 2526452 0.00094444 1058.00000000 2526452 0 0 0 0 0 0 11546210 405977 5126648 2120475 8 0 1.52e-04 6589.00 0.19 0.00e+00 0.00 0.00
+CountVariants none eval none all 2C9 2675075632 19199310 15810956 3388354 0.00126664 789.00000000 3388354 0 0 0 0 0 0 9386600 812811 6424356 2575543 44 0 3.04e-04 3291.00 0.32 0.00e+00 0.00 0.00
+CountVariants none eval none all 2D5 2675075632 19199310 16875168 2324142 0.00086881 1150.00000000 2324142 0 0 0 0 0 0 12090863 350143 4784305 1973999 16 0 1.31e-04 7639.00 0.18 0.00e+00 0.00 0.00
+CountVariants none eval none all 2F0 2675075632 19199310 16057296 3142014 0.00117455 851.00000000 3142014 0 0 0 0 0 0 9927249 650186 6130047 2491828 16 0 2.43e-04 4114.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none all 2F2 2675075632 19199310 14634170 4565140 0.00170655 585.00000000 4565140 0 0 0 0 0 0 6629397 1465016 8004773 3100124 7 0 5.48e-04 1825.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none all 2F9 2675075632 19199310 14718930 4480380 0.00167486 597.00000000 4480380 0 0 0 0 0 0 6899300 1449942 7819630 3030438 32 0 5.42e-04 1844.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none all 2G2 2675075632 19199310 13619070 5580240 0.00208601 479.00000000 5580240 0 0 0 0 0 0 4631199 2274745 8987871 3305495 179 0 8.50e-04 1175.00 0.69 0.00e+00 0.00 0.00
+CountVariants none eval none all 30C 2675075632 19199310 12293127 6906183 0.00258168 387.00000000 6906183 0 0 0 0 0 0 2648560 3606251 9644567 3299932 813 0 1.35e-03 741.00 1.09 0.00e+00 0.00 0.00
+CountVariants none eval none all 30L 2675075632 19199310 12175962 7023348 0.00262548 380.00000000 7023348 0 0 0 0 0 0 2171072 3534490 10004890 3488858 1194 0 1.32e-03 756.00 1.01 0.00e+00 0.00 0.00
+CountVariants none eval none all 31S 2675075632 19199310 13063627 6135683 0.00229365 435.00000000 6135683 0 0 0 0 0 0 3795303 2811315 9268324 3324368 1080 0 1.05e-03 951.00 0.85 0.00e+00 0.00 0.00
+CountVariants none eval none all 32S 2675075632 19199310 15482306 3717004 0.00138949 719.00000000 3717004 0 0 0 0 0 0 8549202 950108 6933104 2766896 41 0 3.55e-04 2815.00 0.34 0.00e+00 0.00 0.00
+CountVariants none eval none all 33T 2675075632 19199310 10525310 8674000 0.00324253 308.00000000 8674000 0 0 0 0 0 0 50977 5353806 10474333 3320194 4083 0 2.00e-03 499.00 1.61 0.00e+00 0.00 0.00
+CountVariants none eval none all 33V 2675075632 19199310 11227243 7972067 0.00298013 335.00000000 7972067 0 0 0 0 0 0 691236 4525320 10536007 3446747 3657 0 1.69e-03 591.00 1.31 0.00e+00 0.00 0.00
+CountVariants none eval none all 34N 2675075632 19199310 16449631 2749679 0.00102789 972.00000000 2749679 0 0 0 0 0 0 10957555 504463 5492076 2245216 1 0 1.89e-04 5302.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none all 34P 2675075632 19199310 13964819 5234491 0.00195676 511.00000000 5234491 0 0 0 0 0 0 5318429 1996108 8646390 3238383 126 0 7.46e-04 1340.00 0.62 0.00e+00 0.00 0.00
+CountVariants none eval none all 35N 2675075632 19199310 11788457 7410853 0.00277033 360.00000000 7410853 0 0 0 0 0 0 1585818 3937867 10202639 3472986 532 0 1.47e-03 679.00 1.13 0.00e+00 0.00 0.00
+CountVariants none eval none all 35V 2675075632 19199310 10451754 8747556 0.00327002 305.00000000 8747556 0 0 0 0 0 0 51945 5587881 10399809 3159675 3184 0 2.09e-03 478.00 1.77 0.00e+00 0.00 0.00
+CountVariants none eval none all 36T 2675075632 19199310 16042481 3156829 0.00118009 847.00000000 3156829 0 0 0 0 0 0 10320586 942036 5721895 2214793 178 0 3.52e-04 2839.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none all 36Z 2675075632 19199310 16026792 3172518 0.00118595 843.00000000 3172518 0 0 0 0 0 0 9868016 671116 6158776 2501402 4 0 2.51e-04 3986.00 0.27 0.00e+00 0.00 0.00
+CountVariants none eval none all 37N 2675075632 19199310 10561121 8638189 0.00322914 309.00000000 8638189 0 0 0 0 0 0 165521 5426547 10395600 3211642 6324 0 2.03e-03 492.00 1.69 0.00e+00 0.00 0.00
+CountVariants none eval none all 37V 2675075632 19199310 15208837 3990473 0.00149172 670.00000000 3990473 0 0 0 0 0 0 7885661 1102987 7323176 2887486 25 0 4.12e-04 2425.00 0.38 0.00e+00 0.00 0.00
+CountVariants none eval none all 3A9 2675075632 19199310 15389066 3810244 0.00142435 702.00000000 3810244 0 0 0 0 0 0 8508367 1122910 6880699 2687334 45 0 4.20e-04 2382.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none all 3B9 2675075632 19199310 16065072 3134238 0.00117164 853.00000000 3134238 0 0 0 0 0 0 9936946 628813 6128126 2505425 11 0 2.35e-04 4254.00 0.25 0.00e+00 0.00 0.00
+CountVariants none eval none all 3D9 2675075632 19199310 15176090 4023220 0.00150396 664.00000000 4023220 0 0 0 0 0 0 7752589 1096230 7423501 2926990 14 0 4.10e-04 2440.00 0.37 0.00e+00 0.00 0.00
+CountVariants none eval none all 3E2 2675075632 19199310 13325802 5873508 0.00219564 455.00000000 5873508 0 0 0 0 0 0 4166673 2549617 9159129 3323891 147 0 9.53e-04 1049.00 0.77 0.00e+00 0.00 0.00
+CountVariants none eval none all 3E4 2675075632 19199310 15179135 4020175 0.00150283 665.00000000 4020175 0 0 0 0 0 0 7985140 1196547 7193995 2823628 110 0 4.47e-04 2235.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none all 3F4 2675075632 19199310 14810533 4388777 0.00164062 609.00000000 4388777 0 0 0 0 0 0 7156297 1465908 7654236 2922869 93 0 5.48e-04 1824.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none all 40L 2675075632 19199310 14770130 4429180 0.00165572 603.00000000 4429180 0 0 0 0 0 0 7024668 1476091 7745462 2953089 18 0 5.52e-04 1812.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none all 42L 2675075632 19199310 11453572 7745738 0.00289552 345.00000000 7745738 0 0 0 0 0 0 1315520 4360872 10138052 3384866 2377 0 1.63e-03 613.00 1.29 0.00e+00 0.00 0.00
+CountVariants none eval none all 42T 2675075632 19199310 10621247 8578063 0.00320666 311.00000000 8578063 0 0 0 0 0 0 198743 5322077 10422504 3255986 6673 0 1.99e-03 502.00 1.63 0.00e+00 0.00 0.00
+CountVariants none eval none all 43F 2675075632 19199310 16565749 2633561 0.00098448 1015.00000000 2633561 0 0 0 0 0 0 11208481 440374 5357268 2193187 2 0 1.65e-04 6074.00 0.20 0.00e+00 0.00 0.00
+CountVariants none eval none all 43H 2675075632 19199310 14442978 4756332 0.00177802 562.00000000 4756332 0 0 0 0 0 0 6356611 1643209 8086367 3113123 112 0 6.14e-04 1627.00 0.53 0.00e+00 0.00 0.00
+CountVariants none eval none all 43J 2675075632 19199310 14357871 4841439 0.00180983 552.00000000 4841439 0 0 0 0 0 0 6116170 1717560 8241701 3123879 91 0 6.42e-04 1557.00 0.55 0.00e+00 0.00 0.00
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+CountVariants none eval none novel 01K 2675075632 19199310 12298798 6900512 0.00257956 387.00000000 6900512 0 0 0 0 0 0 2615821 3642513 9682977 3257999 830 0 1.36e-03 734.00 1.12 0.00e+00 0.00 0.00
+CountVariants none eval none novel 03J 2675075632 19199310 10752303 8447007 0.00315767 316.00000000 8447007 0 0 0 0 0 0 57172 4985840 10695131 3461167 2228 0 1.86e-03 536.00 1.44 0.00e+00 0.00 0.00
+CountVariants none eval none novel 04I 2675075632 19199310 15818704 3380606 0.00126374 791.00000000 3380606 0 0 0 0 0 0 9391683 823349 6427021 2557257 3 0 3.08e-04 3249.00 0.32 0.00e+00 0.00 0.00
+CountVariants none eval none novel 04T 2675075632 19199310 10437209 8762101 0.00327546 305.00000000 8762101 0 0 0 0 0 0 56906 5562564 10380303 3199537 2292 0 2.08e-03 480.00 1.74 0.00e+00 0.00 0.00
+CountVariants none eval none novel 04Z 2675075632 19199310 14053302 5146008 0.00192369 519.00000000 5146008 0 0 0 0 0 0 5384926 1858628 8668376 3287380 409 0 6.95e-04 1439.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none novel 07D 2675075632 19199310 10462495 8736815 0.00326601 306.00000000 8736815 0 0 0 0 0 0 53834 5494779 10408661 3242036 1729 0 2.05e-03 486.00 1.69 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0A2 2675075632 19199310 11075482 8123828 0.00303686 329.00000000 8123828 0 0 0 0 0 0 593075 4706940 10482407 3416888 671 0 1.76e-03 568.00 1.38 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0A4 2675075632 19199310 16635695 2563615 0.00095833 1043.00000000 2563615 0 0 0 0 0 0 11598771 528294 5036924 2035321 3 0 1.97e-04 5063.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0A9 2675075632 19199310 15828174 3371136 0.00126020 793.00000000 3371136 0 0 0 0 0 0 9540540 878455 6287634 2492681 9 0 3.28e-04 3045.00 0.35 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0B4 2675075632 19199310 15492095 3707215 0.00138584 721.00000000 3707215 0 0 0 0 0 0 8525168 917119 6966927 2790096 18 0 3.43e-04 2916.00 0.33 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0B6 2675075632 19199310 17003740 2195570 0.00082075 1218.00000000 2195570 0 0 0 0 0 0 12434084 309487 4569656 1886083 3 0 1.16e-04 8643.00 0.16 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0C6 2675075632 19199310 14685242 4514068 0.00168745 592.00000000 4514068 0 0 0 0 0 0 6817910 1476642 7867332 3037426 4 0 5.52e-04 1811.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none novel 0D3 2675075632 19199310 13776508 5422802 0.00202716 493.00000000 5422802 0 0 0 0 0 0 4795178 2022745 8981330 3400057 3 0 7.56e-04 1322.00 0.59 0.00e+00 0.00 0.00
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+CountVariants none eval none novel 0I5 2675075632 19199310 15187803 4011507 0.00149959 666.00000000 4011507 0 0 0 0 0 0 7971845 1209640 7215958 2801867 37 0 4.52e-04 2211.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none novel 10S 2675075632 19199310 11816810 7382500 0.00275974 362.00000000 7382500 0 0 0 0 0 0 1793579 4035060 10023231 3347440 276 0 1.51e-03 662.00 1.21 0.00e+00 0.00 0.00
+CountVariants none eval none novel 12O 2675075632 19199310 11549452 7649858 0.00285968 349.00000000 7649858 0 0 0 0 0 0 1254007 4211697 10295445 3438161 227 0 1.57e-03 635.00 1.22 0.00e+00 0.00 0.00
+CountVariants none eval none novel 14I 2675075632 19199310 14705422 4493888 0.00167991 595.00000000 4493888 0 0 0 0 0 0 7030813 1597643 7674609 2896245 95 0 5.97e-04 1674.00 0.55 0.00e+00 0.00 0.00
+CountVariants none eval none novel 14L 2675075632 19199310 13982713 5216597 0.00195007 512.00000000 5216597 0 0 0 0 0 0 5395682 1973107 8587031 3243490 121 0 7.38e-04 1355.00 0.61 0.00e+00 0.00 0.00
+CountVariants none eval none novel 17C 2675075632 19199310 14242500 4956810 0.00185296 539.00000000 4956810 0 0 0 0 0 0 6181930 1973304 8060570 2983506 146 0 7.38e-04 1355.00 0.66 0.00e+00 0.00 0.00
+CountVariants none eval none novel 17K 2675075632 19199310 14386818 4812492 0.00179901 555.00000000 4812492 0 0 0 0 0 0 6305617 1784488 8081201 3028004 372 0 6.67e-04 1499.00 0.59 0.00e+00 0.00 0.00
+CountVariants none eval none novel 17L 2675075632 19199310 14376607 4822703 0.00180283 554.00000000 4822703 0 0 0 0 0 0 6020356 1598766 8356251 3223937 59 0 5.98e-04 1673.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none novel 18Z 2675075632 19199310 13841517 5357793 0.00200286 499.00000000 5357793 0 0 0 0 0 0 5243825 2183290 8597692 3174503 144 0 8.16e-04 1225.00 0.69 0.00e+00 0.00 0.00
+CountVariants none eval none novel 19A 2675075632 19199310 14887729 4311581 0.00161176 620.00000000 4311581 0 0 0 0 0 0 7224033 1336538 7663696 2975043 73 0 5.00e-04 2001.00 0.45 0.00e+00 0.00 0.00
+CountVariants none eval none novel 19T 2675075632 19199310 14732169 4467141 0.00166991 598.00000000 4467141 0 0 0 0 0 0 6915855 1452719 7816314 3014422 96 0 5.43e-04 1841.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1A3 2675075632 19199310 14751984 4447326 0.00166250 601.00000000 4447326 0 0 0 0 0 0 7297452 1676618 7454532 2770708 186 0 6.27e-04 1595.00 0.61 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1A6 2675075632 19199310 14586645 4612665 0.00172431 579.00000000 4612665 0 0 0 0 0 0 6424696 1485423 8161949 3127242 0 0 5.55e-04 1800.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1B0 2675075632 19199310 15644051 3555259 0.00132903 752.00000000 3555259 0 0 0 0 0 0 8969809 895627 6674242 2659632 28 0 3.35e-04 2986.00 0.34 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1B1 2675075632 19199310 17926297 1273013 0.00047588 2101.00000000 1273013 0 0 0 0 0 0 15140802 94988 2785495 1178025 0 0 3.55e-05 28162.00 0.08 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1C0 2675075632 19199310 14620103 4579207 0.00171180 584.00000000 4579207 0 0 0 0 0 0 6570029 1457827 8050074 3121380 66 0 5.45e-04 1834.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1C2 2675075632 19199310 14195757 5003553 0.00187043 534.00000000 5003553 0 0 0 0 0 0 5840356 1868326 8355401 3135227 59 0 6.98e-04 1431.00 0.60 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1C5 2675075632 19199310 15244815 3954495 0.00147827 676.00000000 3954495 0 0 0 0 0 0 8094725 1195694 7150090 2758801 20 0 4.47e-04 2237.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1E2 2675075632 19199310 14216607 4982703 0.00186264 536.00000000 4982703 0 0 0 0 0 0 5710995 1749105 8505612 3233598 165 0 6.54e-04 1529.00 0.54 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1E3 2675075632 19199310 11074977 8124333 0.00303705 329.00000000 8124333 0 0 0 0 0 0 611006 4759103 10463971 3365230 3859 0 1.78e-03 562.00 1.41 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1E5 2675075632 19199310 14296338 4902972 0.00183283 545.00000000 4902972 0 0 0 0 0 0 6065004 1765053 8231334 3137919 26 0 6.60e-04 1515.00 0.56 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1E6 2675075632 19199310 16294677 2904633 0.00108581 920.00000000 2904633 0 0 0 0 0 0 10583607 587400 5711070 2317233 19 0 2.20e-04 4554.00 0.25 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1F2 2675075632 19199310 13505314 5693996 0.00212854 469.00000000 5693996 0 0 0 0 0 0 4321937 2301668 9183377 3392328 23 0 8.60e-04 1162.00 0.68 0.00e+00 0.00 0.00
+CountVariants none eval none novel 1F9 2675075632 19199310 15508283 3691027 0.00137978 724.00000000 3691027 0 0 0 0 0 0 8428208 817540 7080075 2873487 64 0 3.06e-04 3272.00 0.28 0.00e+00 0.00 0.00
+CountVariants none eval none novel 20F 2675075632 19199310 13333612 5865698 0.00219272 456.00000000 5865698 0 0 0 0 0 0 4050860 2457785 9282752 3407913 205 0 9.19e-04 1088.00 0.72 0.00e+00 0.00 0.00
+CountVariants none eval none novel 20S 2675075632 19199310 16400770 2798540 0.00104615 955.00000000 2798540 0 0 0 0 0 0 10770437 503015 5630333 2295525 0 0 1.88e-04 5318.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none novel 21N 2675075632 19199310 14062191 5137119 0.00192036 520.00000000 5137119 0 0 0 0 0 0 5443416 1874461 8618775 3262658 37 0 7.01e-04 1427.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none novel 22H 2675075632 19199310 11659062 7540248 0.00281870 354.00000000 7540248 0 0 0 0 0 0 1600250 4233780 10058812 3306468 1439 0 1.58e-03 631.00 1.28 0.00e+00 0.00 0.00
+CountVariants none eval none novel 24B 2675075632 19199310 14460497 4738813 0.00177147 564.00000000 4738813 0 0 0 0 0 0 6419303 1689158 8041194 3049655 99 0 6.31e-04 1583.00 0.55 0.00e+00 0.00 0.00
+CountVariants none eval none novel 24V 2675075632 19199310 14543510 4655800 0.00174044 574.00000000 4655800 0 0 0 0 0 0 6586326 1616420 7957184 3039380 173 0 6.04e-04 1654.00 0.53 0.00e+00 0.00 0.00
+CountVariants none eval none novel 25L 2675075632 19199310 16668989 2530321 0.00094589 1057.00000000 2530321 0 0 0 0 0 0 11622104 462772 5046885 2067549 14 0 1.73e-04 5780.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none novel 25P 2675075632 19199310 10551524 8647786 0.00323273 309.00000000 8647786 0 0 0 0 0 0 160714 5490386 10390810 3157400 5881 0 2.05e-03 487.00 1.74 0.00e+00 0.00 0.00
+CountVariants none eval none novel 26P 2675075632 19199310 12321565 6877745 0.00257105 388.00000000 6877745 0 0 0 0 0 0 2470755 3490036 9850810 3387709 222 0 1.30e-03 766.00 1.03 0.00e+00 0.00 0.00
+CountVariants none eval none novel 28B 2675075632 19199310 14801741 4397569 0.00164390 608.00000000 4397569 0 0 0 0 0 0 7071647 1391599 7730094 3005970 114 0 5.20e-04 1922.00 0.46 0.00e+00 0.00 0.00
+CountVariants none eval none novel 28J 2675075632 19199310 15226166 3973144 0.00148525 673.00000000 3973144 0 0 0 0 0 0 7941355 1098510 7284811 2874634 9 0 4.11e-04 2435.00 0.38 0.00e+00 0.00 0.00
+CountVariants none eval none novel 29B 2675075632 19199310 14632464 4566846 0.00170718 585.00000000 4566846 0 0 0 0 0 0 6669976 1506203 7962488 3060643 27 0 5.63e-04 1776.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none novel 29V 2675075632 19199310 16223857 2975453 0.00111229 899.00000000 2975453 0 0 0 0 0 0 10403315 616553 5820542 2358900 28 0 2.30e-04 4338.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none novel 29Z 2675075632 19199310 13413294 5786016 0.00216294 462.00000000 5786016 0 0 0 0 0 0 4252148 2418350 9161146 3367666 107 0 9.04e-04 1106.00 0.72 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2A2 2675075632 19199310 15530231 3669079 0.00137158 729.00000000 3669079 0 0 0 0 0 0 8667981 940005 6862250 2729074 3 0 3.51e-04 2845.00 0.34 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2A5 2675075632 19199310 16790148 2409162 0.00090060 1110.00000000 2409162 0 0 0 0 0 0 11871953 380841 4918195 2028321 4 0 1.42e-04 7024.00 0.19 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2A7 2675075632 19199310 13535114 5664196 0.00211740 472.00000000 5664196 0 0 0 0 0 0 4384577 2283041 9150537 3381155 29 0 8.53e-04 1171.00 0.68 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2A8 2675075632 19199310 16384746 2814564 0.00105214 950.00000000 2814564 0 0 0 0 0 0 10726988 503184 5657758 2311380 5 0 1.88e-04 5316.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2C3 2675075632 19199310 15735035 3464275 0.00129502 772.00000000 3464275 0 0 0 0 0 0 9353027 964797 6382008 2499478 39 0 3.61e-04 2772.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2C4 2675075632 19199310 14175534 5023776 0.00187799 532.00000000 5023776 0 0 0 0 0 0 6068015 2059567 8107519 2964209 27 0 7.70e-04 1298.00 0.69 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2C8 2675075632 19199310 16672858 2526452 0.00094444 1058.00000000 2526452 0 0 0 0 0 0 11546210 405977 5126648 2120475 8 0 1.52e-04 6589.00 0.19 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2C9 2675075632 19199310 15810956 3388354 0.00126664 789.00000000 3388354 0 0 0 0 0 0 9386600 812811 6424356 2575543 44 0 3.04e-04 3291.00 0.32 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2D5 2675075632 19199310 16875168 2324142 0.00086881 1150.00000000 2324142 0 0 0 0 0 0 12090863 350143 4784305 1973999 16 0 1.31e-04 7639.00 0.18 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2F0 2675075632 19199310 16057296 3142014 0.00117455 851.00000000 3142014 0 0 0 0 0 0 9927249 650186 6130047 2491828 16 0 2.43e-04 4114.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2F2 2675075632 19199310 14634170 4565140 0.00170655 585.00000000 4565140 0 0 0 0 0 0 6629397 1465016 8004773 3100124 7 0 5.48e-04 1825.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2F9 2675075632 19199310 14718930 4480380 0.00167486 597.00000000 4480380 0 0 0 0 0 0 6899300 1449942 7819630 3030438 32 0 5.42e-04 1844.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none novel 2G2 2675075632 19199310 13619070 5580240 0.00208601 479.00000000 5580240 0 0 0 0 0 0 4631199 2274745 8987871 3305495 179 0 8.50e-04 1175.00 0.69 0.00e+00 0.00 0.00
+CountVariants none eval none novel 30C 2675075632 19199310 12293127 6906183 0.00258168 387.00000000 6906183 0 0 0 0 0 0 2648560 3606251 9644567 3299932 813 0 1.35e-03 741.00 1.09 0.00e+00 0.00 0.00
+CountVariants none eval none novel 30L 2675075632 19199310 12175962 7023348 0.00262548 380.00000000 7023348 0 0 0 0 0 0 2171072 3534490 10004890 3488858 1194 0 1.32e-03 756.00 1.01 0.00e+00 0.00 0.00
+CountVariants none eval none novel 31S 2675075632 19199310 13063627 6135683 0.00229365 435.00000000 6135683 0 0 0 0 0 0 3795303 2811315 9268324 3324368 1080 0 1.05e-03 951.00 0.85 0.00e+00 0.00 0.00
+CountVariants none eval none novel 32S 2675075632 19199310 15482306 3717004 0.00138949 719.00000000 3717004 0 0 0 0 0 0 8549202 950108 6933104 2766896 41 0 3.55e-04 2815.00 0.34 0.00e+00 0.00 0.00
+CountVariants none eval none novel 33T 2675075632 19199310 10525310 8674000 0.00324253 308.00000000 8674000 0 0 0 0 0 0 50977 5353806 10474333 3320194 4083 0 2.00e-03 499.00 1.61 0.00e+00 0.00 0.00
+CountVariants none eval none novel 33V 2675075632 19199310 11227243 7972067 0.00298013 335.00000000 7972067 0 0 0 0 0 0 691236 4525320 10536007 3446747 3657 0 1.69e-03 591.00 1.31 0.00e+00 0.00 0.00
+CountVariants none eval none novel 34N 2675075632 19199310 16449631 2749679 0.00102789 972.00000000 2749679 0 0 0 0 0 0 10957555 504463 5492076 2245216 1 0 1.89e-04 5302.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none novel 34P 2675075632 19199310 13964819 5234491 0.00195676 511.00000000 5234491 0 0 0 0 0 0 5318429 1996108 8646390 3238383 126 0 7.46e-04 1340.00 0.62 0.00e+00 0.00 0.00
+CountVariants none eval none novel 35N 2675075632 19199310 11788457 7410853 0.00277033 360.00000000 7410853 0 0 0 0 0 0 1585818 3937867 10202639 3472986 532 0 1.47e-03 679.00 1.13 0.00e+00 0.00 0.00
+CountVariants none eval none novel 35V 2675075632 19199310 10451754 8747556 0.00327002 305.00000000 8747556 0 0 0 0 0 0 51945 5587881 10399809 3159675 3184 0 2.09e-03 478.00 1.77 0.00e+00 0.00 0.00
+CountVariants none eval none novel 36T 2675075632 19199310 16042481 3156829 0.00118009 847.00000000 3156829 0 0 0 0 0 0 10320586 942036 5721895 2214793 178 0 3.52e-04 2839.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none novel 36Z 2675075632 19199310 16026792 3172518 0.00118595 843.00000000 3172518 0 0 0 0 0 0 9868016 671116 6158776 2501402 4 0 2.51e-04 3986.00 0.27 0.00e+00 0.00 0.00
+CountVariants none eval none novel 37N 2675075632 19199310 10561121 8638189 0.00322914 309.00000000 8638189 0 0 0 0 0 0 165521 5426547 10395600 3211642 6324 0 2.03e-03 492.00 1.69 0.00e+00 0.00 0.00
+CountVariants none eval none novel 37V 2675075632 19199310 15208837 3990473 0.00149172 670.00000000 3990473 0 0 0 0 0 0 7885661 1102987 7323176 2887486 25 0 4.12e-04 2425.00 0.38 0.00e+00 0.00 0.00
+CountVariants none eval none novel 3A9 2675075632 19199310 15389066 3810244 0.00142435 702.00000000 3810244 0 0 0 0 0 0 8508367 1122910 6880699 2687334 45 0 4.20e-04 2382.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none novel 3B9 2675075632 19199310 16065072 3134238 0.00117164 853.00000000 3134238 0 0 0 0 0 0 9936946 628813 6128126 2505425 11 0 2.35e-04 4254.00 0.25 0.00e+00 0.00 0.00
+CountVariants none eval none novel 3D9 2675075632 19199310 15176090 4023220 0.00150396 664.00000000 4023220 0 0 0 0 0 0 7752589 1096230 7423501 2926990 14 0 4.10e-04 2440.00 0.37 0.00e+00 0.00 0.00
+CountVariants none eval none novel 3E2 2675075632 19199310 13325802 5873508 0.00219564 455.00000000 5873508 0 0 0 0 0 0 4166673 2549617 9159129 3323891 147 0 9.53e-04 1049.00 0.77 0.00e+00 0.00 0.00
+CountVariants none eval none novel 3E4 2675075632 19199310 15179135 4020175 0.00150283 665.00000000 4020175 0 0 0 0 0 0 7985140 1196547 7193995 2823628 110 0 4.47e-04 2235.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none novel 3F4 2675075632 19199310 14810533 4388777 0.00164062 609.00000000 4388777 0 0 0 0 0 0 7156297 1465908 7654236 2922869 93 0 5.48e-04 1824.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none novel 40L 2675075632 19199310 14770130 4429180 0.00165572 603.00000000 4429180 0 0 0 0 0 0 7024668 1476091 7745462 2953089 18 0 5.52e-04 1812.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none novel 42L 2675075632 19199310 11453572 7745738 0.00289552 345.00000000 7745738 0 0 0 0 0 0 1315520 4360872 10138052 3384866 2377 0 1.63e-03 613.00 1.29 0.00e+00 0.00 0.00
+CountVariants none eval none novel 42T 2675075632 19199310 10621247 8578063 0.00320666 311.00000000 8578063 0 0 0 0 0 0 198743 5322077 10422504 3255986 6673 0 1.99e-03 502.00 1.63 0.00e+00 0.00 0.00
+CountVariants none eval none novel 43F 2675075632 19199310 16565749 2633561 0.00098448 1015.00000000 2633561 0 0 0 0 0 0 11208481 440374 5357268 2193187 2 0 1.65e-04 6074.00 0.20 0.00e+00 0.00 0.00
+CountVariants none eval none novel 43H 2675075632 19199310 14442978 4756332 0.00177802 562.00000000 4756332 0 0 0 0 0 0 6356611 1643209 8086367 3113123 112 0 6.14e-04 1627.00 0.53 0.00e+00 0.00 0.00
+CountVariants none eval none novel 43J 2675075632 19199310 14357871 4841439 0.00180983 552.00000000 4841439 0 0 0 0 0 0 6116170 1717560 8241701 3123879 91 0 6.42e-04 1557.00 0.55 0.00e+00 0.00 0.00
+CountVariants none eval none novel 43N 2675075632 19199310 15022961 4176349 0.00156121 640.00000000 4176349 0 0 0 0 0 0 7719221 1364947 7303740 2811402 35 0 5.10e-04 1959.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none novel 43P 2675075632 19199310 15279024 3920286 0.00146549 682.00000000 3920286 0 0 0 0 0 0 8006502 1037305 7272522 2882981 10 0 3.88e-04 2578.00 0.36 0.00e+00 0.00 0.00
+CountVariants none eval none novel 44J 2675075632 19199310 14369329 4829981 0.00180555 553.00000000 4829981 0 0 0 0 0 0 6010448 1656704 8358881 3173277 13 0 6.19e-04 1614.00 0.52 0.00e+00 0.00 0.00
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+CountVariants none eval none novel 46Z 2675075632 19199310 14036972 5162338 0.00192979 518.00000000 5162338 0 0 0 0 0 0 5348104 1861309 8688868 3301029 55 0 6.96e-04 1437.00 0.56 0.00e+00 0.00 0.00
+CountVariants none eval none novel 47Z 2675075632 19199310 15915953 3283357 0.00122739 814.00000000 3283357 0 0 0 0 0 0 9532774 685205 6383179 2598152 13 0 2.56e-04 3904.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none novel 48V 2675075632 19199310 15803205 3396105 0.00126954 787.00000000 3396105 0 0 0 0 0 0 9333332 783491 6469873 2612614 0 0 2.93e-04 3414.00 0.30 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4A9 2675075632 19199310 14668580 4530730 0.00169368 590.00000000 4530730 0 0 0 0 0 0 7080378 1665994 7588202 2864736 94 0 6.23e-04 1605.00 0.58 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4C1 2675075632 19199310 10582119 8617191 0.00322129 310.00000000 8617191 0 0 0 0 0 0 166980 5405119 10415139 3212072 1494 0 2.02e-03 494.00 1.68 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4C3 2675075632 19199310 15002544 4196766 0.00156884 637.00000000 4196766 0 0 0 0 0 0 7458316 1230926 7544228 2965840 4 0 4.60e-04 2173.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4C5 2675075632 19199310 14866944 4332366 0.00161953 617.00000000 4332366 0 0 0 0 0 0 7210726 1381704 7656218 2950662 53 0 5.17e-04 1936.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4D3 2675075632 19199310 10749644 8449666 0.00315866 316.00000000 8449666 0 0 0 0 0 0 298061 5191194 10451583 3258472 4528 0 1.94e-03 515.00 1.59 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4D8 2675075632 19199310 15210524 3988786 0.00149109 670.00000000 3988786 0 0 0 0 0 0 8060721 1198850 7149803 2789936 24 0 4.48e-04 2231.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none novel 4G8 2675075632 19199310 14986526 4212784 0.00157483 634.00000000 4212784 0 0 0 0 0 0 7486729 1295446 7499797 2917338 36 0 4.84e-04 2064.00 0.44 0.00e+00 0.00 0.00
+CountVariants none eval none novel 50S 2675075632 19199310 16199222 3000088 0.00112150 891.00000000 3000088 0 0 0 0 0 0 10587219 784956 5612003 2215132 40 0 2.93e-04 3407.00 0.35 0.00e+00 0.00 0.00
+CountVariants none eval none novel 51V 2675075632 19199310 15111573 4087737 0.00152808 654.00000000 4087737 0 0 0 0 0 0 7723890 1203687 7387683 2884050 53 0 4.50e-04 2222.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none novel 52P 2675075632 19199310 17289638 1909672 0.00071388 1400.00000000 1909672 0 0 0 0 0 0 13273977 229165 4015661 1680507 2 0 8.57e-05 11673.00 0.14 0.00e+00 0.00 0.00
+CountVariants none eval none novel 52Z 2675075632 19199310 15075637 4123673 0.00154152 648.00000000 4123673 0 0 0 0 0 0 7517504 1162133 7558133 2961540 2 0 4.34e-04 2301.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none novel 53E 2675075632 19199310 12248203 6951107 0.00259847 384.00000000 6951107 0 0 0 0 0 0 2463894 3615034 9784309 3336073 932 0 1.35e-03 739.00 1.08 0.00e+00 0.00 0.00
+CountVariants none eval none novel 53Z 2675075632 19199310 15093121 4106189 0.00153498 651.00000000 4106189 0 0 0 0 0 0 7675453 1208133 7417668 2898056 22 0 4.52e-04 2214.00 0.42 0.00e+00 0.00 0.00
+CountVariants none eval none novel 54N 2675075632 19199310 11858096 7341214 0.00274430 364.00000000 7341214 0 0 0 0 0 0 1727301 3937207 10130795 3404007 1508 0 1.47e-03 679.00 1.16 0.00e+00 0.00 0.00
+CountVariants none eval none novel 55J 2675075632 19199310 16388761 2810549 0.00105064 951.00000000 2810549 0 0 0 0 0 0 10786335 508947 5602426 2301602 0 0 1.90e-04 5256.00 0.22 0.00e+00 0.00 0.00
+CountVariants none eval none novel 55V 2675075632 19199310 14888499 4310811 0.00161147 620.00000000 4310811 0 0 0 0 0 0 7310769 1376448 7577730 2934363 60 0 5.15e-04 1943.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none novel 56E 2675075632 19199310 11267405 7931905 0.00296511 337.00000000 7931905 0 0 0 0 0 0 964459 4589759 10302946 3342146 2976 0 1.72e-03 582.00 1.37 0.00e+00 0.00 0.00
+CountVariants none eval none novel 56K 2675075632 19199310 15355540 3843770 0.00143688 695.00000000 3843770 0 0 0 0 0 0 8219819 1044849 7135721 2798921 42 0 3.91e-04 2560.00 0.37 0.00e+00 0.00 0.00
+CountVariants none eval none novel 57F 2675075632 19199310 11190907 8008403 0.00299371 334.00000000 8008403 0 0 0 0 0 0 856197 4599011 10334710 3409392 952 0 1.72e-03 581.00 1.35 0.00e+00 0.00 0.00
+CountVariants none eval none novel 57H 2675075632 19199310 14068359 5130951 0.00191806 521.00000000 5130951 0 0 0 0 0 0 5584706 1953561 8483653 3177390 82 0 7.30e-04 1369.00 0.61 0.00e+00 0.00 0.00
+CountVariants none eval none novel 59A 2675075632 19199310 14943033 4256277 0.00159109 628.00000000 4256277 0 0 0 0 0 0 7432188 1349515 7510845 2906762 54 0 5.04e-04 1982.00 0.46 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5B0 2675075632 19199310 15116121 4083189 0.00152638 655.00000000 4083189 0 0 0 0 0 0 7944910 1306230 7171211 2776959 38 0 4.88e-04 2047.00 0.47 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5B2 2675075632 19199310 10614384 8584926 0.00320923 311.00000000 8584926 0 0 0 0 0 0 186773 5378716 10427611 3206210 7284 0 2.01e-03 497.00 1.68 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5C0 2675075632 19199310 15434960 3764350 0.00140719 710.00000000 3764350 0 0 0 0 0 0 8393693 994809 7041267 2769541 15 0 3.72e-04 2689.00 0.36 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5E1 2675075632 19199310 15369296 3830014 0.00143174 698.00000000 3830014 0 0 0 0 0 0 8186210 982835 7183086 2847179 24 0 3.67e-04 2721.00 0.35 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5E4 2675075632 19199310 14001999 5197311 0.00194287 514.00000000 5197311 0 0 0 0 0 0 5247481 1872284 8754518 3325027 106 0 7.00e-04 1428.00 0.56 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5E8 2675075632 19199310 14417860 4781450 0.00178741 559.00000000 4781450 0 0 0 0 0 0 6163776 1611058 8254084 3170392 65 0 6.02e-04 1660.00 0.51 0.00e+00 0.00 0.00
+CountVariants none eval none novel 5G7 2675075632 19199310 15852952 3346358 0.00125094 799.00000000 3346358 0 0 0 0 0 0 9449154 771110 6403798 2575248 0 0 2.88e-04 3469.00 0.30 0.00e+00 0.00 0.00
+CountVariants none eval none novel 60E 2675075632 19199310 14735628 4463682 0.00166862 599.00000000 4463682 0 0 0 0 0 0 6887804 1445780 7847824 3017902 156 0 5.40e-04 1850.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none novel 60P 2675075632 19199310 14951964 4247346 0.00158775 629.00000000 4247346 0 0 0 0 0 0 7483652 1404184 7468312 2843162 252 0 5.25e-04 1905.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none novel 60R 2675075632 19199310 15959378 3239932 0.00121116 825.00000000 3239932 0 0 0 0 0 0 9714213 741840 6245165 2498092 34 0 2.77e-04 3606.00 0.30 0.00e+00 0.00 0.00
+CountVariants none eval none novel 60T 2675075632 19199310 10460278 8739032 0.00326684 306.00000000 8739032 0 0 0 0 0 0 51440 5500283 10408838 3238749 4759 0 2.06e-03 486.00 1.70 0.00e+00 0.00 0.00
+CountVariants none eval none novel 61D 2675075632 19199310 15122530 4076780 0.00152399 656.00000000 4076780 0 0 0 0 0 0 7652118 1153327 7470412 2923453 127 0 4.31e-04 2319.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none novel 61J 2675075632 19199310 14143089 5056221 0.00189012 529.00000000 5056221 0 0 0 0 0 0 5796267 1950348 8346822 3105873 69 0 7.29e-04 1371.00 0.63 0.00e+00 0.00 0.00
+CountVariants none eval none novel 61R 2675075632 19199310 11040304 8159006 0.00305001 327.00000000 8159006 0 0 0 0 0 0 535884 4791602 10504420 3367404 4122 0 1.79e-03 558.00 1.42 0.00e+00 0.00 0.00
+CountVariants none eval none novel 62R 2675075632 19199310 16703364 2495946 0.00093304 1071.00000000 2495946 0 0 0 0 0 0 11645355 413629 5058009 2082317 1 0 1.55e-04 6467.00 0.20 0.00e+00 0.00 0.00
+CountVariants none eval none novel 63V 2675075632 19199310 15669702 3529608 0.00131944 757.00000000 3529608 0 0 0 0 0 0 8984872 840359 6684830 2689249 23 0 3.14e-04 3183.00 0.31 0.00e+00 0.00 0.00
+CountVariants none eval none novel 64D 2675075632 19199310 15626806 3572504 0.00133548 748.00000000 3572504 0 0 0 0 0 0 8823507 835497 6803299 2737007 9 0 3.12e-04 3201.00 0.31 0.00e+00 0.00 0.00
+CountVariants none eval none novel 64P 2675075632 19199310 12019592 7179718 0.00268393 372.00000000 7179718 0 0 0 0 0 0 1903511 3756377 10116081 3423341 85 0 1.40e-03 712.00 1.10 0.00e+00 0.00 0.00
+CountVariants none eval none novel 64S 2675075632 19199310 14337063 4862247 0.00181761 550.00000000 4862247 0 0 0 0 0 0 6061285 1727196 8275778 3135051 118 0 6.46e-04 1548.00 0.55 0.00e+00 0.00 0.00
+CountVariants none eval none novel 68V 2675075632 19199310 16205785 2993525 0.00111904 893.00000000 2993525 0 0 0 0 0 0 10346370 610520 5859415 2383005 6 0 2.28e-04 4381.00 0.26 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6A8 2675075632 19199310 10529574 8669736 0.00324093 308.00000000 8669736 0 0 0 0 0 0 51552 5388895 10478022 3280841 5544 0 2.01e-03 496.00 1.64 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6B2 2675075632 19199310 16664121 2535189 0.00094771 1055.00000000 2535189 0 0 0 0 0 0 11519084 427604 5145037 2107585 9 0 1.60e-04 6255.00 0.20 0.00e+00 0.00 0.00
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+CountVariants none eval none novel 6C2 2675075632 19199310 14204688 4994622 0.00186710 535.00000000 4994622 0 0 0 0 0 0 5774412 1816321 8430276 3178301 74 0 6.79e-04 1472.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6C5 2675075632 19199310 11072386 8126924 0.00303802 329.00000000 8126924 0 0 0 0 0 0 534708 4686819 10537678 3440105 2929 0 1.75e-03 570.00 1.36 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6D4 2675075632 19199310 14941539 4257771 0.00159165 628.00000000 4257771 0 0 0 0 0 0 7197436 1240101 7744103 3017670 70 0 4.64e-04 2157.00 0.41 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6D6 2675075632 19199310 13991343 5207967 0.00194685 513.00000000 5207967 0 0 0 0 0 0 5383862 2007872 8607481 3200095 266 0 7.51e-04 1332.00 0.63 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6D9 2675075632 19199310 14814203 4385107 0.00163925 610.00000000 4385107 0 0 0 0 0 0 7145011 1449799 7669192 2935308 41 0 5.42e-04 1845.00 0.49 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6F2 2675075632 19199310 14458510 4740800 0.00177221 564.00000000 4740800 0 0 0 0 0 0 6180219 1534303 8278291 3206497 154 0 5.74e-04 1743.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none novel 6F6 2675075632 19199310 10580994 8618316 0.00322171 310.00000000 8618316 0 0 0 0 0 0 148433 5370537 10432561 3247779 5393 0 2.01e-03 498.00 1.65 0.00e+00 0.00 0.00
+CountVariants none eval none novel 72T 2675075632 19199310 15178467 4020843 0.00150308 665.00000000 4020843 0 0 0 0 0 0 7852281 1132918 7326186 2887925 91 0 4.24e-04 2361.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none novel 73V 2675075632 19199310 10575318 8623992 0.00322383 310.00000000 8623992 0 0 0 0 0 0 170084 5420808 10405234 3203184 1787 0 2.03e-03 493.00 1.69 0.00e+00 0.00 0.00
+CountVariants none eval none novel 73Z 2675075632 19199310 14481362 4717948 0.00176367 566.00000000 4717948 0 0 0 0 0 0 6388204 1631441 8093158 3086507 18 0 6.10e-04 1639.00 0.53 0.00e+00 0.00 0.00
+CountVariants none eval none novel 74S 2675075632 19199310 15990466 3208844 0.00119953 833.00000000 3208844 0 0 0 0 0 0 9758807 697276 6231659 2511568 10 0 2.61e-04 3836.00 0.28 0.00e+00 0.00 0.00
+CountVariants none eval none novel 77I 2675075632 19199310 15408858 3790452 0.00141695 705.00000000 3790452 0 0 0 0 0 0 8486821 1065667 6922037 2724785 71 0 3.98e-04 2510.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none novel 78I 2675075632 19199310 12097902 7101408 0.00265466 376.00000000 7101408 0 0 0 0 0 0 2201183 3744060 9896719 3357348 447 0 1.40e-03 714.00 1.12 0.00e+00 0.00 0.00
+CountVariants none eval none novel 78T 2675075632 19199310 11860913 7338397 0.00274325 364.00000000 7338397 0 0 0 0 0 0 1667547 3934695 10193366 3403702 963 0 1.47e-03 679.00 1.16 0.00e+00 0.00 0.00
+CountVariants none eval none novel 79Z 2675075632 19199310 14828231 4371079 0.00163400 611.00000000 4371079 0 0 0 0 0 0 6922364 1267131 7905867 3103948 12 0 4.74e-04 2111.00 0.41 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7B2 2675075632 19199310 14152320 5046990 0.00188667 530.00000000 5046990 0 0 0 0 0 0 5678004 1878306 8474316 3168684 157 0 7.02e-04 1424.00 0.59 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7B3 2675075632 19199310 15474107 3725203 0.00139256 718.00000000 3725203 0 0 0 0 0 0 8573445 1003647 6900662 2721556 9 0 3.75e-04 2665.00 0.37 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7B7 2675075632 19199310 14705417 4493893 0.00167991 595.00000000 4493893 0 0 0 0 0 0 6943437 1523864 7761980 2970029 97 0 5.70e-04 1755.00 0.51 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7C0 2675075632 19199310 11662257 7537053 0.00281751 354.00000000 7537053 0 0 0 0 0 0 3462073 4995808 8200184 2541245 243 0 1.87e-03 535.00 1.97 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7D7 2675075632 19199310 15565923 3633387 0.00135824 736.00000000 3633387 0 0 0 0 0 0 8717988 903530 6847935 2729857 6 0 3.38e-04 2960.00 0.33 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7D8 2675075632 19199310 15185699 4013611 0.00150037 666.00000000 4013611 0 0 0 0 0 0 7928440 1162254 7257259 2851357 11 0 4.34e-04 2301.00 0.41 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7F0 2675075632 19199310 14943953 4255357 0.00159074 628.00000000 4255357 0 0 0 0 0 0 7405406 1348299 7538547 2907058 14 0 5.04e-04 1984.00 0.46 0.00e+00 0.00 0.00
+CountVariants none eval none novel 7F5 2675075632 19199310 14172950 5026360 0.00187896 532.00000000 5026360 0 0 0 0 0 0 5948538 1976074 8224412 3050286 228 0 7.39e-04 1353.00 0.65 0.00e+00 0.00 0.00
+CountVariants none eval none novel 80S 2675075632 19199310 11305178 7894132 0.00295099 338.00000000 7894132 0 0 0 0 0 0 760819 4379374 10544359 3514758 2384 0 1.64e-03 610.00 1.25 0.00e+00 0.00 0.00
+CountVariants none eval none novel 80T 2675075632 19199310 14194785 5004525 0.00187080 534.00000000 5004525 0 0 0 0 0 0 5900270 1903150 8294515 3101375 452 0 7.11e-04 1405.00 0.61 0.00e+00 0.00 0.00
+CountVariants none eval none novel 81I 2675075632 19199310 12238770 6960540 0.00260200 384.00000000 6960540 0 0 0 0 0 0 2828033 3803198 9410737 3157342 856 0 1.42e-03 703.00 1.20 0.00e+00 0.00 0.00
+CountVariants none eval none novel 82A 2675075632 19199310 16428203 2771107 0.00103590 965.00000000 2771107 0 0 0 0 0 0 10846042 480536 5582161 2290571 2 0 1.80e-04 5566.00 0.21 0.00e+00 0.00 0.00
+CountVariants none eval none novel 82L 2675075632 19199310 14284504 4914806 0.00183726 544.00000000 4914806 0 0 0 0 0 0 6406394 2028125 7878110 2886681 147 0 7.58e-04 1318.00 0.70 0.00e+00 0.00 0.00
+CountVariants none eval none novel 85B 2675075632 19199310 11757034 7442276 0.00278208 359.00000000 7442276 0 0 0 0 0 0 1681604 4077630 10075430 3364646 617 0 1.52e-03 656.00 1.21 0.00e+00 0.00 0.00
+CountVariants none eval none novel 85T 2675075632 19199310 15639286 3560024 0.00133081 751.00000000 3560024 0 0 0 0 0 0 9024834 944150 6614452 2615874 27 0 3.53e-04 2833.00 0.36 0.00e+00 0.00 0.00
+CountVariants none eval none novel 86Z 2675075632 19199310 15337515 3861795 0.00144362 692.00000000 3861795 0 0 0 0 0 0 8199370 1027345 7138145 2834450 40 0 3.84e-04 2603.00 0.36 0.00e+00 0.00 0.00
+CountVariants none eval none novel 88I 2675075632 19199310 16819453 2379857 0.00088964 1124.00000000 2379857 0 0 0 0 0 0 11965304 370126 4854149 2009731 24 0 1.38e-04 7227.00 0.18 0.00e+00 0.00 0.00
+CountVariants none eval none novel 88N 2675075632 19199310 11917114 7282196 0.00272224 367.00000000 7282196 0 0 0 0 0 0 1878102 3882966 10039012 3399230 1130 0 1.45e-03 688.00 1.14 0.00e+00 0.00 0.00
+CountVariants none eval none novel 88T 2675075632 19199310 15656110 3543200 0.00132452 754.00000000 3543200 0 0 0 0 0 0 9092357 955823 6563753 2587377 30 0 3.57e-04 2798.00 0.37 0.00e+00 0.00 0.00
+CountVariants none eval none novel 8B0 2675075632 19199310 13750162 5449148 0.00203701 490.00000000 5449148 0 0 0 0 0 0 4817569 2129517 8932593 3319631 89 0 7.96e-04 1256.00 0.64 0.00e+00 0.00 0.00
+CountVariants none eval none novel 8B5 2675075632 19199310 14982853 4216457 0.00157620 634.00000000 4216457 0 0 0 0 0 0 7280946 1207787 7701907 3008670 59 0 4.51e-04 2214.00 0.40 0.00e+00 0.00 0.00
+CountVariants none eval none novel 8C0 2675075632 19199310 14444599 4754711 0.00177741 562.00000000 4754711 0 0 0 0 0 0 6123774 1551725 8320825 3202986 7 0 5.80e-04 1723.00 0.48 0.00e+00 0.00 0.00
+CountVariants none eval none novel 8C9 2675075632 19199310 15124850 4074460 0.00152312 656.00000000 4074460 0 0 0 0 0 0 7684446 1148804 7440404 2925656 32 0 4.29e-04 2328.00 0.39 0.00e+00 0.00 0.00
+CountVariants none eval none novel 8D6 2675075632 19199310 15047585 4151725 0.00155200 644.00000000 4151725 0 0 0 0 0 0 7768712 1378564 7278873 2773161 47 0 5.15e-04 1940.00 0.50 0.00e+00 0.00 0.00
+CountVariants none eval none novel 8E8 2675075632 19199310 15102784 4096526 0.00153137 653.00000000 4096526 0 0 0 0 0 0 7746507 1196490 7356277 2900036 12 0 4.47e-04 2235.00 0.41 0.00e+00 0.00 0.00
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+CountVariants none eval none novel 91V 2675075632 19199310 14315202 4884108 0.00182578 547.00000000 4884108 0 0 0 0 0 0 6092105 1767250 8223097 3116858 64 0 6.61e-04 1513.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none novel 92D 2675075632 19199310 10462993 8736317 0.00326582 306.00000000 8736317 0 0 0 0 0 0 54090 5579306 10408903 3157011 4879 0 2.09e-03 479.00 1.77 0.00e+00 0.00 0.00
+CountVariants none eval none novel 93O 2675075632 19199310 12426782 6772528 0.00253171 394.00000000 6772528 0 0 0 0 0 0 2917805 3566114 9508977 3206414 706 0 1.33e-03 750.00 1.11 0.00e+00 0.00 0.00
+CountVariants none eval none novel 93Z 2675075632 19199310 10621694 8577616 0.00320649 311.00000000 8577616 0 0 0 0 0 0 57084 5194352 10564610 3383264 2492 0 1.94e-03 514.00 1.54 0.00e+00 0.00 0.00
+CountVariants none eval none novel 94H 2675075632 19199310 11758640 7440670 0.00278148 359.00000000 7440670 0 0 0 0 0 0 1767565 4104951 9991075 3335719 1523 0 1.53e-03 651.00 1.23 0.00e+00 0.00 0.00
+CountVariants none eval none novel 96B 2675075632 19199310 12071535 7127775 0.00266451 375.00000000 7127775 0 0 0 0 0 0 2368316 3871869 9703219 3255906 363 0 1.45e-03 690.00 1.19 0.00e+00 0.00 0.00
+CountVariants none eval none novel 98T 2675075632 19199310 14258470 4940840 0.00184699 541.00000000 4940840 0 0 0 0 0 0 5992906 1782977 8265564 3157863 11 0 6.67e-04 1500.00 0.56 0.00e+00 0.00 0.00
+CountVariants none eval none novel 98Z 2675075632 19199310 14260370 4938940 0.00184628 541.00000000 4938940 0 0 0 0 0 0 5930566 1788460 8329804 3150480 56 0 6.69e-04 1495.00 0.57 0.00e+00 0.00 0.00
+CountVariants none eval none novel 99L 2675075632 19199310 11192625 8006685 0.00299307 334.00000000 8006685 0 0 0 0 0 0 863009 4687390 10329616 3319295 493 0 1.75e-03 570.00 1.41 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9A4 2675075632 19199310 12184136 7015174 0.00262242 381.00000000 7015174 0 0 0 0 0 0 2360745 3639470 9823391 3375704 56 0 1.36e-03 735.00 1.08 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9C1 2675075632 19199310 10651094 8548216 0.00319550 312.00000000 8548216 0 0 0 0 0 0 156840 5223548 10494254 3324668 8171 0 1.95e-03 512.00 1.57 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9C2 2675075632 19199310 15987040 3212270 0.00120081 832.00000000 3212270 0 0 0 0 0 0 9788501 701344 6198539 2510926 0 0 2.62e-04 3814.00 0.28 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9C5 2675075632 19199310 15468430 3730880 0.00139468 717.00000000 3730880 0 0 0 0 0 0 8446742 925823 7021688 2805057 40 0 3.46e-04 2889.00 0.33 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9C6 2675075632 19199310 11951580 7247730 0.00270936 369.00000000 7247730 0 0 0 0 0 0 2028743 3907158 9922837 3340572 1049 0 1.46e-03 684.00 1.17 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9D4 2675075632 19199310 10533680 8665630 0.00323940 308.00000000 8665630 0 0 0 0 0 0 172702 5474631 10360978 3190999 7780 0 2.05e-03 488.00 1.72 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9D8 2675075632 19199310 15990180 3209130 0.00119964 833.00000000 3209130 0 0 0 0 0 0 9732786 675398 6257394 2533732 8 0 2.52e-04 3960.00 0.27 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9E3 2675075632 19199310 16672045 2527265 0.00094475 1058.00000000 2527265 0 0 0 0 0 0 11534257 416721 5137788 2110544 0 0 1.56e-04 6419.00 0.20 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9E5 2675075632 19199310 15381572 3817738 0.00142715 700.00000000 3817738 0 0 0 0 0 0 8256731 991312 7124841 2826426 20 0 3.71e-04 2698.00 0.35 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9E6 2675075632 19199310 16493981 2705329 0.00101131 988.00000000 2705329 0 0 0 0 0 0 11099891 503557 5394090 2201772 2 0 1.88e-04 5312.00 0.23 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9E8 2675075632 19199310 14973049 4226261 0.00157987 632.00000000 4226261 0 0 0 0 0 0 7398021 1262026 7575028 2964235 58 0 4.72e-04 2119.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9F5 2675075632 19199310 16102812 3096498 0.00115754 863.00000000 3096498 0 0 0 0 0 0 10031776 622006 6071036 2474492 0 0 2.33e-04 4300.00 0.25 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9H7 2675075632 19199310 15343768 3855542 0.00144128 693.00000000 3855542 0 0 0 0 0 0 8270772 1055198 7072996 2800344 21 0 3.94e-04 2535.00 0.38 0.00e+00 0.00 0.00
+CountVariants none eval none novel 9H9 2675075632 19199310 15015267 4184043 0.00156408 639.00000000 4184043 0 0 0 0 0 0 7470378 1254640 7544889 2929403 18 0 4.69e-04 2132.00 0.43 0.00e+00 0.00 0.00
+CountVariants none eval none novel K00 2675075632 19199310 10463695 8735615 0.00326556 306.00000000 8735615 0 0 0 0 0 0 58126 5566363 10405569 3169252 10539 0 2.08e-03 480.00 1.76 0.00e+00 0.00 0.00
+CountVariants none eval none novel N12 2675075632 19199310 16286454 2912856 0.00108889 918.00000000 2912856 0 0 0 0 0 0 10535878 568570 5750576 2344286 3 0 2.13e-04 4704.00 0.24 0.00e+00 0.00 0.00
+CountVariants none eval none novel O34 2675075632 19199310 12214768 6984542 0.00261097 382.00000000 6984542 0 0 0 0 0 0 2254651 3566964 9960117 3417578 2752 0 1.33e-03 749.00 1.04 0.00e+00 0.00 0.00
+CountVariants none eval none novel O52 2675075632 19199310 15035211 4164099 0.00155663 642.00000000 4164099 0 0 0 0 0 0 7638552 1313346 7396659 2850753 51 0 4.91e-04 2036.00 0.46 0.00e+00 0.00 0.00
+CountVariants none eval none novel T84 2675075632 19199310 11731218 7468092 0.00279173 358.00000000 7468092 0 0 0 0 0 0 1694223 4155159 10036995 3312933 636 0 1.55e-03 643.00 1.25 0.00e+00 0.00 0.00
+CountVariants none eval none novel V36 2675075632 19199310 15015844 4183466 0.00156387 639.00000000 4183466 0 0 0 0 0 0 7446368 1207152 7569476 2976314 120 0 4.51e-04 2216.00 0.41 0.00e+00 0.00 0.00
+CountVariants none eval none novel X44 2675075632 19199310 16429814 2769496 0.00103530 965.00000000 2769496 0 0 0 0 0 0 10923014 523637 5506800 2245859 12 0 1.96e-04 5108.00 0.23 0.00e+00 0.00 0.00
+CountVariants none eval none novel X58 2675075632 19199310 11251932 7947378 0.00297090 336.00000000 7947378 0 0 0 0 0 0 918674 4606315 10333258 3341063 2922 0 1.72e-03 580.00 1.38 0.00e+00 0.00 0.00
+CountVariants none eval none novel Z46 2675075632 19199310 11777388 7421922 0.00277447 360.00000000 7421922 0 0 0 0 0 0 1695659 4066929 10081729 3354993 111 0 1.52e-03 657.00 1.21 0.00e+00 0.00 0.00
+CountVariants none eval none novel all 2675075632 19199310 0 19199310 0.00717711 139.00000000 19199310 0 0 0 0 0 0 1330372586 466564538 1747450553 641061903 158691 0 1.74e-01 5.00 0.73 0.00e+00 0.00 0.00
+
+#:GATKTable:15:657:%s:%s:%s:%s:%s:%s:%d:%d:%.2f:%d:%d:%.2f:%d:%d:%.2f:;
+#:GATKTable:TiTvVariantEvaluator:Ti/Tv Variant Evaluator
+TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty Sample nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio
+TiTvVariantEvaluator none eval none all 00O 2584117 1108447 2.33 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 00V 3031776 1324413 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 01K 4776615 2119892 2.25 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 03J 5748647 2692720 2.13 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 04I 2361976 1017715 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 04T 5966987 2788930 2.14 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 04Z 3571948 1572089 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 07D 5948288 2782300 2.14 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0A2 5577026 2541681 2.19 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0A4 1800039 762952 2.36 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0A9 2360739 1009380 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0B4 2577663 1128533 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0B6 1530365 664847 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0C6 3144389 1368066 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0D3 3762615 1658031 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0F6 5418801 2450243 2.21 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0G9 2823894 1226176 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 0I5 2798980 1211214 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 10S 5102195 2275973 2.24 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 12O 5264563 2380577 2.21 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 14I 3139269 1352807 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 14L 3624511 1589948 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 17C 3468728 1485897 2.33 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 17K 3353373 1457040 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 17L 3351022 1469931 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 18Z 3732693 1622674 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 19A 3003893 1306179 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 19T 3110237 1355314 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1A3 3123736 1321618 2.36 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1A6 3206677 1404303 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1B0 2479559 1074706 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1B1 881472 391426 2.25 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1C0 3185094 1392466 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1C2 3484648 1516830 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1C5 2768851 1184349 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1E2 3468208 1512566 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1E3 5578736 2540391 2.20 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1E5 3410056 1490925 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1E6 2028684 875289 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1F2 3949017 1742579 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 1F9 2564447 1125680 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 20F 4071526 1791569 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 20S 1945675 852340 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 21N 3558180 1577004 2.26 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 22H 5205915 2329659 2.23 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 24B 3305923 1430950 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 24V 3250917 1403072 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 25L 1771731 758087 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 25P 5904554 2737214 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 26P 4749419 2124589 2.24 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 28B 3066385 1329724 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 28J 2758040 1213978 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 29B 3185890 1379305 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 29V 2082509 892254 2.33 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 29Z 4016546 1766924 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2A2 2559695 1108404 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2A5 1680379 728376 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2A7 3923256 1738568 2.26 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2A8 1956699 857284 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2C3 2428735 1034466 2.35 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2C4 3517889 1503560 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2C8 1755743 770285 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2C9 2365724 1021772 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2D5 1622452 701248 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2F0 2194977 946278 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2F2 3179278 1384196 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2F9 3123343 1355434 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 2G2 3874767 1702984 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 30C 4787706 2114587 2.26 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 30L 4851333 2168046 2.24 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 31S 4261083 1871651 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 32S 2586169 1129811 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 33T 5902553 2765361 2.13 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 33V 5477221 2490074 2.20 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 34N 1915770 833370 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 34P 3643963 1588309 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 35N 5110976 2295768 2.23 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 35V 5956540 2784721 2.14 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 36T 2231572 924091 2.41 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 36Z 2207706 964079 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 37N 5897571 2734606 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 37V 2780305 1208955 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 3A9 2667044 1141953 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 3B9 2181588 951949 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 3D9 2799201 1222769 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 3E2 4085013 1785639 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 3E4 2802314 1216582 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 3F4 3062956 1324128 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 40L 3087683 1339850 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 42L 5337018 2403885 2.22 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 42T 5857877 2714091 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 43F 1833582 799477 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 43H 3312659 1441839 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 43J 3374207 1465372 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 43N 2926086 1248692 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 43P 2726383 1192762 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 44J 3361449 1466640 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 46N 5869209 2721586 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 46Z 3583100 1577240 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 47Z 2281600 1000972 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 48V 2371371 1023809 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4A9 3172614 1356260 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4C1 5883872 2727265 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4C3 2918009 1277395 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4C5 3025828 1305070 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4D3 5784795 2659293 2.18 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4D8 2785992 1201472 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 4G8 2936115 1275207 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 50S 2112084 887120 2.38 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 51V 2849595 1236844 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 52P 1331459 577943 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 52Z 2870917 1251485 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 53E 4813275 2134022 2.26 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 53Z 2859924 1244861 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 54N 5069684 2267159 2.24 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 55J 1954852 855114 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 55V 3010507 1298748 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 56E 5450284 2476509 2.20 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 56K 2679587 1163006 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 57F 5501194 2502171 2.20 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 57H 3572572 1556247 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 59A 2972046 1282783 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5B0 2852479 1229312 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5B2 5860010 2718835 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5C0 2624247 1138958 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5E1 2669188 1159703 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5E4 3611201 1584124 2.28 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5E8 3324823 1454815 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 5G7 2330509 1015028 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 60E 3109532 1352577 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 60P 2975108 1270722 2.34 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 60R 2261947 977122 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 60T 5951037 2781872 2.14 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 61D 2840911 1234612 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 61J 3529423 1524572 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 61R 5599030 2554952 2.19 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 62R 1740079 755400 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 63V 2460397 1068256 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 64D 2487321 1084215 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 64P 4958090 2217552 2.24 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 64S 3382876 1477472 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 68V 2088479 904374 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6A8 5899680 2763931 2.13 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6B2 1767609 767087 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6C0 3337672 1418158 2.35 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6C2 3477679 1514968 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6C5 5578058 2543762 2.19 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6D4 2961328 1295069 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6D6 3623312 1582414 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6D9 3058850 1324646 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6F2 3290561 1448642 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 6F6 5883414 2728875 2.16 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 72T 2797421 1222197 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 73V 5882263 2735800 2.15 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 73Z 3284013 1432116 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 74S 2235738 972370 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 77I 2649405 1139880 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 78I 4918207 2178958 2.26 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 78T 5056274 2278003 2.22 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 79Z 3040763 1328936 2.29 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 7B2 3514039 1530871 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 7B3 2596999 1127087 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 7B7 3131549 1360653 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 7C0 5257305 2275010 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 7D7 2532693 1099644 2.30 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none all 7D8 2798131 1214198 2.30 0 0 0.00 0 0 0.00
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+TiTvVariantEvaluator none eval none novel N12 2031233 880969 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel O34 4825075 2155618 2.24 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel O52 2906692 1255997 2.31 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel T84 5152459 2311058 2.23 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel V36 2901332 1280854 2.27 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel X44 1935242 833666 2.32 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel X58 5458129 2484343 2.20 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel Z46 5121173 2296301 2.23 0 0 0.00 0 0 0.00
+TiTvVariantEvaluator none eval none novel all 13160478 5982016 2.20 0 0 0.00 0 0 0.00
+
diff -r 000000000000 -r 3bad335ccea9 test-data/gatk_varianteval_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk_varianteval_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample deletions insertions known_titv snps symbolic novel_titv complex mnps titv_reference mixed nocalls
+gatk_varianteval 0 0 0.0 19199310 0 2.2 0 0 none 0 1330372586
diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_deduplicator.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_deduplicator.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,7 @@
+File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques
+Sample-1.A007.C8DRAANXX.s_2.r_1_2.filt.bam 7029431 6978457 876396 4591811 1510250
+Sample-1.A002.C8DRAANXX.s_2.r_1_2.filt.bam 8935388 8864466 1159324 5742469 1962673
+Sample-1.A005.C8DRAANXX.s_2.r_1_2.filt.bam 11314841 11219537 1495237 7243835 2480465
+Sample-1.A019.C8DRAANXX.s_2.r_1_2.filt.bam 11766363 11658185 1811982 7779338 2066865
+Sample-1.A012.C8DRAANXX.s_2.r_1_2.filt.bam 11705308 11609411 1261011 7003201 3345199
+Sample-1.A006.C8DRAANXX.s_2.r_1_2.filt.bam 13106391 12998003 2043926 8107586 2846491
diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_filter.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_filter.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,7 @@
+File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size
+Sample-1.A002.C8DRAANXX.s_2.r_1_2.pair.bam 14383198 8935388 1169666 5787588 1978134 5447810 136087 530246 2442480 834795 48328 1455874
+Sample-1.A007.C8DRAANXX.s_2.r_1_2.pair.bam 14621513 7029431 882929 4625450 1521052 7592082 157241 452563 4031859 771757 37367 2141295
+Sample-1.A005.C8DRAANXX.s_2.r_1_2.pair.bam 15245021 11314841 1509270 7304795 2500776 3930180 187236 298334 1580105 924315 59919 880271
+Sample-1.A019.C8DRAANXX.s_2.r_1_2.pair.bam 16053923 11766363 1830414 7850293 2085656 4287560 223187 305385 1541376 1070842 72067 1074703
+Sample-1.A006.C8DRAANXX.s_2.r_1_2.pair.bam 18473566 13106391 2063334 8173491 2869566 5367175 220527 408217 2075370 961388 65086 1636587
+Sample-1.A012.C8DRAANXX.s_2.r_1_2.pair.bam 19070455 11705308 1272882 7060212 3372214 7365147 163868 663463 3810160 976378 55368 1695910
diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_mapper.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_mapper.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,13 @@
+File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired
+Sample-1.A006.C8DRAANXX.s_2.r_1.trunc.fastq.gz 34760244 579570 1.7 25926210 74.6 5230796 15.0 3023668 8.7 18473566 53.1
+Sample-1.A006.C8DRAANXX.s_2.r_2.trunc.fastq.gz 34760244 539500 1.6 25637256 73.8 5121683 14.7 3461805 10.0 18473566 53.1
+Sample-1.A005.C8DRAANXX.s_2.r_1.trunc.fastq.gz 26780491 431302 1.6 20379141 76.1 4263954 15.9 1706094 6.4 15245021 56.9
+Sample-1.A005.C8DRAANXX.s_2.r_2.trunc.fastq.gz 26780491 407260 1.5 20071745 74.9 4167422 15.6 2134064 8.0 15245021 56.9
+Sample-1.A012.C8DRAANXX.s_2.r_1.trunc.fastq.gz 35472550 526747 1.5 26504291 74.7 5362349 15.1 3079163 8.7 19070455 53.8
+Sample-1.A012.C8DRAANXX.s_2.r_2.trunc.fastq.gz 35472550 494718 1.4 26142222 73.7 5264577 14.8 3571033 10.1 19070455 53.8
+Sample-1.A002.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28754600 751623 2.6 21072845 73.3 4475271 15.6 2454861 8.5 14383198 50.0
+Sample-1.A002.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28754600 698375 2.4 20505141 71.3 4336149 15.1 3214935 11.2 14383198 50.0
+Sample-1.A007.C8DRAANXX.s_2.r_1.trunc.fastq.gz 31000250 368533 1.2 22327487 72.0 4263821 13.8 4040409 13.0 14621513 47.2
+Sample-1.A007.C8DRAANXX.s_2.r_2.trunc.fastq.gz 31000250 338254 1.1 21828226 70.4 4140992 13.4 4692778 15.1 14621513 47.2
+Sample-1.A019.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28583413 519100 1.8 21667602 75.8 4404215 15.4 1992496 7.0 16053923 56.2
+Sample-1.A019.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28583413 488517 1.7 21491634 75.2 4342639 15.2 2260623 7.9 16053923 56.2
diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_truncater.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicup_truncater.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,13 @@
+File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence
+Sample-1.A002.C8DRAANXX.s_2.r_1.fq 28754600 7548969 26.25 21205631 73.75 58.69
+Sample-1.A002.C8DRAANXX.s_2.r_2.fq 28754600 7446167 25.90 21308433 74.10 59.65
+Sample-1.A006.C8DRAANXX.s_2.r_2.fq 34760244 10523907 30.28 24236337 69.72 66.68
+Sample-1.A012.C8DRAANXX.s_2.r_2.fq 35472550 9050477 25.51 26422073 74.49 66.30
+Sample-1.A006.C8DRAANXX.s_2.r_1.fq 34760244 10420308 29.98 24339936 70.02 65.67
+Sample-1.A012.C8DRAANXX.s_2.r_1.fq 35472550 8999621 25.37 26472929 74.63 65.39
+Sample-1.A005.C8DRAANXX.s_2.r_2.fq 26780491 8436781 31.50 18343710 68.50 67.02
+Sample-1.A005.C8DRAANXX.s_2.r_1.fq 26780491 8361813 31.22 18418678 68.78 66.22
+Sample-1.A019.C8DRAANXX.s_2.r_2.fq 28583413 9321837 32.61 19261576 67.39 66.38
+Sample-1.A019.C8DRAANXX.s_2.r_1.fq 28583413 9151107 32.02 19432306 67.98 65.11
+Sample-1.A007.C8DRAANXX.s_2.r_1.fq 31000250 6212988 20.04 24787262 79.96 65.01
+Sample-1.A007.C8DRAANXX.s_2.r_2.fq 31000250 6187239 19.96 24813011 80.04 65.94
diff -r 000000000000 -r 3bad335ccea9 test-data/hisat2_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hisat2_1.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,6 @@
+HISAT2 summary stats:
+ Total reads: 99978
+ Aligned 0 time: 3849 (3.85%)
+ Aligned 1 time: 86176 (86.19%)
+ Aligned >1 times: 9953 (9.96%)
+ Overall alignment rate: 96.15%
diff -r 000000000000 -r 3bad335ccea9 test-data/hisat2_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hisat2_2.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,6 @@
+HISAT2 summary stats:
+ Total reads: 99978
+ Aligned 0 time: 3849 (3.85%)
+ Aligned 1 time: 86176 (86.19%)
+ Aligned >1 times: 9953 (9.96%)
+ Overall alignment rate: 96.15%
diff -r 000000000000 -r 3bad335ccea9 test-data/hisat2_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hisat2_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,3 @@
+Sample overall_alignment_rate unpaired_aligned_none unpaired_aligned_multi unpaired_total unpaired_aligned_one
+hisat2_1 96.15 3849 9953 99978 86176
+hisat2_2 96.15 3849 9953 99978 86176
diff -r 000000000000 -r 3bad335ccea9 test-data/htseq.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/htseq.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,5 @@
+__no_feature 19
+__ambiguous 0
+__too_low_aQual 0
+__not_aligned 1336
+__alignment_not_unique 0
diff -r 000000000000 -r 3bad335ccea9 test-data/htseq_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/htseq_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample ambiguous percent_assigned too_low_aQual total_count no_feature alignment_not_unique assigned not_aligned
+htseq 0 0.0 0 1355 19 0 0 1336
diff -r 000000000000 -r 3bad335ccea9 test-data/kallisto_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_1.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,489 @@
+
+--------------------------------------------------------------------------------
+Module: fastqc
+Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
+Job ID: cf_fastq_kallisto_1463255307_fastqc_732
+Previous Job ID: start_000
+Date & Time: 20:48, 14-05-2016
+--------------------------------------------------------------------------------
+
+---------- FastQC version information ----------
+FastQC v0.11.5
+
+------- End of FastQC version information ------
+
+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
+
+###CF FastQC successfully ran, took 12 minutes
+
+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
+
+###CF FastQC successfully ran, took 11 minutes, 16 seconds
+
+
+
+
+--------------------------------------------------------------------------------
+Module: trim_galore
+Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
+Job ID: cf_fastq_kallisto_1463255307_trim_galore_659
+Previous Job ID: start_000
+Date & Time: 20:48, 14-05-2016
+--------------------------------------------------------------------------------
+
+---------- Cutadapt version information ----------
+1.8.1
+
+------- End of Cutadapt version information ------
+---------- Trim Galore! version information ----------
+
+ Quality-/Adapter-/RRBS-Trimming
+ (powered by Cutadapt)
+ version 0.4.1
+
+ Last update: 20 07 2015
+
+
+------- End of Trim Galore! version information ------
+
+###CFCMD trim_galore --paired --gzip --phred33 --fastqc HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
+
+Path to Cutadapt set as: 'cutadapt' (default)
+1.8.1
+Cutadapt seems to be working fine (tested command 'cutadapt --version')
+
+
+AUTO-DETECTING ADAPTER TYPE
+===========================
+Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz <<)
+
+Found perfect matches for the following adapter sequences:
+Adapter type Count Sequence Sequences analysed Percentage
+Illumina 4591 AGATCGGAAGAGC 1000000 0.46
+Nextera 4 CTGTCTCTTATA 1000000 0.00
+smallRNA 2 TGGAATTCTCGG 1000000 0.00
+Using Illumina adapter for trimming (count: 4591). Second best hit was Nextera (count: 4)
+
+Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_trimming_report.txt'
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.4.1
+Cutadapt version: 1.8.1
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+Running FastQC on the data once trimming has completed
+Output file(s) will be GZIP compressed
+
+Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz
+
+
+ >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz <<<
+10000000 sequences processed
+20000000 sequences processed
+30000000 sequences processed
+40000000 sequences processed
+50000000 sequences processed
+60000000 sequences processed
+This is cutadapt 1.8.1 with Python 2.7.5
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
+Trimming 1 adapter with at most 10.0% errors in single-end mode ...
+Finished in 1129.68 s (19 us/read; 3.20 M reads/minute).
+
+=== Summary ===
+
+Total reads processed: 60,339,006
+Reads with adapters: 19,773,783 (32.8%)
+Reads written (passing filters): 60,339,006 (100.0%)
+
+Total basepairs processed: 6,094,239,606 bp
+Quality-trimmed: 318,558,927 bp (5.2%)
+Total written (filtered): 5,735,844,499 bp (94.1%)
+
+=== Adapter 1 ===
+
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19773783 times.
+
+No. of allowed errors:
+0-9 bp: 0; 10-13 bp: 1
+
+Bases preceding removed adapters:
+ A: 29.4%
+ C: 32.6%
+ G: 21.6%
+ T: 16.2%
+ none/other: 0.2%
+
+Overview of removed sequences
+length count expect max.err error counts
+1 13107583 15084751.5 0 13107583
+2 4517008 3771187.9 0 4517008
+3 1168959 942797.0 0 1168959
+4 281663 235699.2 0 281663
+5 104792 58924.8 0 104792
+6 69263 14731.2 0 69263
+7 51851 3682.8 0 51851
+8 51844 920.7 0 51844
+9 41855 230.2 0 41073 782
+10 36637 57.5 1 35344 1293
+11 29587 14.4 1 28680 907
+12 28042 3.6 1 27586 456
+13 22536 0.9 1 22227 309
+14 19927 0.9 1 19661 266
+15 17329 0.9 1 17095 234
+16 15643 0.9 1 15353 290
+17 13807 0.9 1 13539 268
+18 11603 0.9 1 11389 214
+19 8338 0.9 1 8198 140
+20 8131 0.9 1 8001 130
+21 6942 0.9 1 6778 164
+22 5839 0.9 1 5731 108
+23 5474 0.9 1 5341 133
+24 4736 0.9 1 4599 137
+25 4504 0.9 1 4393 111
+26 3852 0.9 1 3728 124
+27 4425 0.9 1 4203 222
+28 3575 0.9 1 3433 142
+29 3316 0.9 1 3165 151
+30 3370 0.9 1 3209 161
+31 2266 0.9 1 2167 99
+32 2158 0.9 1 2035 123
+33 2462 0.9 1 2308 154
+34 2879 0.9 1 2595 284
+35 3667 0.9 1 3330 337
+36 4027 0.9 1 3697 330
+37 2582 0.9 1 2341 241
+38 2056 0.9 1 1830 226
+39 2926 0.9 1 2733 193
+40 1401 0.9 1 1278 123
+41 1847 0.9 1 1733 114
+42 1508 0.9 1 1413 95
+43 1211 0.9 1 1130 81
+44 1112 0.9 1 975 137
+45 1507 0.9 1 1329 178
+46 1640 0.9 1 1514 126
+47 1116 0.9 1 1028 88
+48 1158 0.9 1 1060 98
+49 1375 0.9 1 1274 101
+50 1121 0.9 1 1020 101
+51 1703 0.9 1 1474 229
+52 1994 0.9 1 1755 239
+53 2141 0.9 1 1984 157
+54 919 0.9 1 835 84
+55 822 0.9 1 721 101
+56 1428 0.9 1 1252 176
+57 1649 0.9 1 1438 211
+58 1372 0.9 1 1179 193
+59 1835 0.9 1 1664 171
+60 1510 0.9 1 1296 214
+61 1538 0.9 1 1240 298
+62 2471 0.9 1 1928 543
+63 3805 0.9 1 3104 701
+64 4243 0.9 1 3806 437
+65 2208 0.9 1 1851 357
+66 2382 0.9 1 1899 483
+67 3595 0.9 1 2610 985
+68 6338 0.9 1 4553 1785
+69 10826 0.9 1 7037 3789
+70 15641 0.9 1 13860 1781
+71 6064 0.9 1 5031 1033
+72 2588 0.9 1 2271 317
+73 1010 0.9 1 855 155
+74 466 0.9 1 379 87
+75 232 0.9 1 169 63
+76 133 0.9 1 87 46
+77 123 0.9 1 83 40
+78 109 0.9 1 73 36
+79 67 0.9 1 38 29
+80 62 0.9 1 33 29
+81 63 0.9 1 21 42
+82 77 0.9 1 33 44
+83 59 0.9 1 22 37
+84 67 0.9 1 23 44
+85 62 0.9 1 23 39
+86 72 0.9 1 33 39
+87 73 0.9 1 22 51
+88 79 0.9 1 24 55
+89 54 0.9 1 22 32
+90 66 0.9 1 31 35
+91 62 0.9 1 30 32
+92 85 0.9 1 32 53
+93 70 0.9 1 27 43
+94 61 0.9 1 27 34
+95 56 0.9 1 25 31
+96 79 0.9 1 35 44
+97 78 0.9 1 39 39
+98 125 0.9 1 50 75
+99 87 0.9 1 43 44
+100 137 0.9 1 79 58
+101 547 0.9 1 329 218
+
+
+RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
+=============================================
+60339006 sequences processed in total
+The length threshold of paired-end sequences gets evaluated later on (in the validation step)
+
+Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz_trimming_report.txt'
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.4.1
+Cutadapt version: 1.8.1
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+Running FastQC on the data once trimming has completed
+Output file(s) will be GZIP compressed
+
+Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz
+
+
+ >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz <<<
+10000000 sequences processed
+20000000 sequences processed
+30000000 sequences processed
+40000000 sequences processed
+50000000 sequences processed
+60000000 sequences processed
+This is cutadapt 1.8.1 with Python 2.7.5
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
+Trimming 1 adapter with at most 10.0% errors in single-end mode ...
+Finished in 1357.49 s (22 us/read; 2.67 M reads/minute).
+
+=== Summary ===
+
+Total reads processed: 60,339,006
+Reads with adapters: 17,101,385 (28.3%)
+Reads written (passing filters): 60,339,006 (100.0%)
+
+Total basepairs processed: 6,094,239,606 bp
+Quality-trimmed: 1,861,214,185 bp (30.5%)
+Total written (filtered): 4,202,697,623 bp (69.0%)
+
+=== Adapter 1 ===
+
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17101385 times.
+
+No. of allowed errors:
+0-9 bp: 0; 10-13 bp: 1
+
+Bases preceding removed adapters:
+ A: 30.1%
+ C: 33.1%
+ G: 21.0%
+ T: 15.6%
+ none/other: 0.2%
+
+Overview of removed sequences
+length count expect max.err error counts
+1 10224232 15084751.5 0 10224232
+2 5630139 3771187.9 0 5630139
+3 824951 942797.0 0 824951
+4 237457 235699.2 0 237457
+5 42614 58924.8 0 42614
+6 8620 14731.2 0 8620
+7 4051 3682.8 0 4051
+8 2491 920.7 0 2491
+9 2860 230.2 0 1848 1012
+10 4289 57.5 1 2932 1357
+11 1923 14.4 1 1196 727
+12 3234 3.6 1 2884 350
+13 1974 0.9 1 1769 205
+14 3402 0.9 1 3193 209
+15 1303 0.9 1 1215 88
+16 1677 0.9 1 1563 114
+17 3501 0.9 1 3304 197
+18 753 0.9 1 662 91
+19 1959 0.9 1 1820 139
+20 1348 0.9 1 1256 92
+21 807 0.9 1 745 62
+22 1343 0.9 1 1262 81
+23 1485 0.9 1 1358 127
+24 3748 0.9 1 3541 207
+25 1313 0.9 1 1219 94
+26 1605 0.9 1 1405 200
+27 1260 0.9 1 1122 138
+28 2828 0.9 1 2673 155
+29 1187 0.9 1 1064 123
+30 4440 0.9 1 4243 197
+31 383 0.9 1 326 57
+32 1491 0.9 1 1382 109
+33 753 0.9 1 683 70
+34 736 0.9 1 649 87
+35 1840 0.9 1 1717 123
+36 923 0.9 1 835 88
+37 1792 0.9 1 1685 107
+38 875 0.9 1 795 80
+39 2158 0.9 1 2040 118
+40 1496 0.9 1 1370 126
+41 2113 0.9 1 1958 155
+42 4026 0.9 1 3801 225
+43 837 0.9 1 761 76
+44 2041 0.9 1 1906 135
+45 3100 0.9 1 2934 166
+46 687 0.9 1 630 57
+47 1082 0.9 1 1003 79
+48 1398 0.9 1 1297 101
+49 1470 0.9 1 1380 90
+50 2185 0.9 1 2046 139
+51 3600 0.9 1 3427 173
+52 786 0.9 1 712 74
+53 343 0.9 1 290 53
+54 1810 0.9 1 1687 123
+55 1581 0.9 1 1462 119
+56 662 0.9 1 605 57
+57 1454 0.9 1 1336 118
+58 2899 0.9 1 2636 263
+59 1818 0.9 1 1633 185
+60 1593 0.9 1 1376 217
+61 1968 0.9 1 1722 246
+62 2449 0.9 1 2062 387
+63 4233 0.9 1 3609 624
+64 5813 0.9 1 4609 1204
+65 9498 0.9 1 7807 1691
+66 5265 0.9 1 4540 725
+67 755 0.9 1 565 190
+68 303 0.9 1 257 46
+69 106 0.9 1 84 22
+70 86 0.9 1 55 31
+71 51 0.9 1 26 25
+72 40 0.9 1 20 20
+73 54 0.9 1 38 16
+74 32 0.9 1 21 11
+76 1 0.9 1 0 1
+77 2 0.9 1 1 1
+79 3 0.9 1 2 1
+
+
+RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
+=============================================
+60339006 sequences processed in total
+The length threshold of paired-end sequences gets evaluated later on (in the validation step)
+
+Validate paired-end files HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz
+file_1: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz, file_2: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz
+
+
+>>>>> Now validing the length of the 2 paired-end infiles: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz <<<<<
+Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+
+Total number of sequences analysed: 60339006
+
+Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2322959 (3.85%)
+
+
+ >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz<<<
+
+Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+
+ >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz<<<
+
+Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+Deleting both intermediate output files HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz
+
+====================================================================================================
+
+###CF Trim galore (PE mode) successfully exited, took 1 hours, 45 minutes, 38 seconds..
+
+
+
+
+--------------------------------------------------------------------------------
+Module: kallisto
+Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
+Job ID: cf_fastq_kallisto_1463255307_kallisto_017
+Previous Job ID: cf_fastq_kallisto_1463255307_trim_galore_659
+Date & Time: 22:34, 14-05-2016
+--------------------------------------------------------------------------------
+
+
+Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx
+
+---------- Kallisto version information ----------
+kallisto 0.42.5
+
+------- End of Kallisto version information ------
+
+###CFCMD kallisto quant -t 1 --pseudobam -i /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx -o HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz_kallisto_output -b 100 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz | samtools view -Sb - > HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz_kallisto.bam
+
+
+[quant] fragment length distribution will be estimated from the data
+[index] k-mer length: 31
+[index] number of targets: 176,241
+[index] number of k-mers: 104,600,239
+[index] number of equivalence classes: 702,950
+[quant] running in paired-end mode
+[quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
+ HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
+[quant] finding pseudoalignments for the reads ... done
+[quant] processed 58,016,047 reads, 48,531,088 reads pseudoaligned
+[quant] estimated average fragment length: 167.866
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 1,210 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
[bstrp] running EM for the bootstrap: 6
[bstrp] running EM for the bootstrap: 7
[bstrp] running EM for the bootstrap: 8
[bstrp] running EM for the bootstrap: 9
[bstrp] running EM for the bootstrap: 10
[bstrp] running EM for the bootstrap: 11
[bstrp] running EM for the bootstrap: 12
[bstrp] running EM for the bootstrap: 13
[bstrp] running EM for the bootstrap: 14
[bstrp] running EM for the bootstrap: 15
[bstrp] running EM for the bootstrap: 16
[bstrp] running EM for the bootstrap: 17
[bstrp] running EM for the bootstrap: 18
[bstrp] running EM for the bootstrap: 19
[bstrp] running EM for the bootstrap: 20
[bstrp] running EM for the bootstrap: 21
[bstrp] running EM for the bootstrap: 22
[bstrp] running EM for the bootstrap: 23
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[bstrp] running EM for the bootstrap: 26
[bstrp] running EM for the bootstrap: 27
[bstrp] running EM for the bootstrap: 28
[bstrp] running EM for the bootstrap: 29
[bstrp] running EM for the bootstrap: 30
[bstrp] running EM for the bootstrap: 31
[bstrp] running EM for the bootstrap: 32
[bstrp] running EM for the bootstrap: 33
[bstrp] running EM for the bootstrap: 34
[bstrp] running EM for the bootstrap: 35
[bstrp] running EM for the bootstrap: 36
[bstrp] running EM for the bootstrap: 37
[bstrp] running EM for the bootstrap: 38
[bstrp] running EM for the bootstrap: 39
[bstrp] running EM for the bootstrap: 40
[bstrp] running EM for the bootstrap: 41
[bstrp] running EM for the bootstrap: 42
[bstrp] running EM for the bootstrap: 43
[bstrp] running EM for the bootstrap: 44
[bstrp] running EM for the bootstrap: 45
[bstrp] running EM for the bootstrap: 46
[bstrp] running EM for the bootstrap: 47
[bstrp] running EM for the bootstrap: 48
[bstrp] running EM for the bootstrap: 49
[bstrp] running EM for the bootstrap: 50
[bstrp] running EM for the bootstrap: 51
[bstrp] running EM for the bootstrap: 52
[bstrp] running EM for the bootstrap: 53
[bstrp] running EM for the bootstrap: 54
[bstrp] running EM for the bootstrap: 55
[bstrp] running EM for the bootstrap: 56
[bstrp] running EM for the bootstrap: 57
[bstrp] running EM for the bootstrap: 58
[bstrp] running EM for the bootstrap: 59
[bstrp] running EM for the bootstrap: 60
[bstrp] running EM for the bootstrap: 61
[bstrp] running EM for the bootstrap: 62
[bstrp] running EM for the bootstrap: 63
[bstrp] running EM for the bootstrap: 64
[bstrp] running EM for the bootstrap: 65
[bstrp] running EM for the bootstrap: 66
[bstrp] running EM for the bootstrap: 67
[bstrp] running EM for the bootstrap: 68
[bstrp] running EM for the bootstrap: 69
[bstrp] running EM for the bootstrap: 70
[bstrp] running EM for the bootstrap: 71
[bstrp] running EM for the bootstrap: 72
[bstrp] running EM for the bootstrap: 73
[bstrp] running EM for the bootstrap: 74
[bstrp] running EM for the bootstrap: 75
[bstrp] running EM for the bootstrap: 76
[bstrp] running EM for the bootstrap: 77
[bstrp] running EM for the bootstrap: 78
[bstrp] running EM for the bootstrap: 79
[bstrp] running EM for the bootstrap: 80
[bstrp] running EM for the bootstrap: 81
[bstrp] running EM for the bootstrap: 82
[bstrp] running EM for the bootstrap: 83
[bstrp] running EM for the bootstrap: 84
[bstrp] running EM for the bootstrap: 85
[bstrp] running EM for the bootstrap: 86
[bstrp] running EM for the bootstrap: 87
[bstrp] running EM for the bootstrap: 88
[bstrp] running EM for the bootstrap: 89
[bstrp] running EM for the bootstrap: 90
[bstrp] running EM for the bootstrap: 91
[bstrp] running EM for the bootstrap: 92
[bstrp] running EM for the bootstrap: 93
[bstrp] running EM for the bootstrap: 94
[bstrp] running EM for the bootstrap: 95
[bstrp] running EM for the bootstrap: 96
[bstrp] running EM for the bootstrap: 97
[bstrp] running EM for the bootstrap: 98
[bstrp] running EM for the bootstrap: 99
[bstrp] running EM for the bootstrap: 100
+
+###CF kallisto (PE mode) successfully exited, took 2 hours, 30 minutes, 54 seconds..
+
+
+
+
+================================================================================
+
+
+
+
+
+###CF Run finished at 01:06 15-05-2016
diff -r 000000000000 -r 3bad335ccea9 test-data/kallisto_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_2.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,496 @@
+
+--------------------------------------------------------------------------------
+Module: fastqc
+Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
+Job ID: cf_fastq_kallisto_1463255307_fastqc_792
+Previous Job ID: start_000
+Date & Time: 20:48, 14-05-2016
+--------------------------------------------------------------------------------
+
+---------- FastQC version information ----------
+FastQC v0.11.5
+
+------- End of FastQC version information ------
+
+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
+
+###CF FastQC successfully ran, took 13 minutes, 29 seconds
+
+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
+
+###CF FastQC successfully ran, took 12 minutes, 27 seconds
+
+
+
+
+--------------------------------------------------------------------------------
+Module: trim_galore
+Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
+Job ID: cf_fastq_kallisto_1463255307_trim_galore_160
+Previous Job ID: start_000
+Date & Time: 20:48, 14-05-2016
+--------------------------------------------------------------------------------
+
+---------- Cutadapt version information ----------
+1.8.1
+
+------- End of Cutadapt version information ------
+---------- Trim Galore! version information ----------
+
+ Quality-/Adapter-/RRBS-Trimming
+ (powered by Cutadapt)
+ version 0.4.1
+
+ Last update: 20 07 2015
+
+
+------- End of Trim Galore! version information ------
+
+###CFCMD trim_galore --paired --gzip --phred33 --fastqc HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
+
+Path to Cutadapt set as: 'cutadapt' (default)
+1.8.1
+Cutadapt seems to be working fine (tested command 'cutadapt --version')
+
+
+AUTO-DETECTING ADAPTER TYPE
+===========================
+Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz <<)
+
+Found perfect matches for the following adapter sequences:
+Adapter type Count Sequence Sequences analysed Percentage
+Illumina 7610 AGATCGGAAGAGC 1000000 0.76
+Nextera 8 CTGTCTCTTATA 1000000 0.00
+smallRNA 3 TGGAATTCTCGG 1000000 0.00
+Using Illumina adapter for trimming (count: 7610). Second best hit was Nextera (count: 8)
+
+Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_trimming_report.txt'
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.4.1
+Cutadapt version: 1.8.1
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+Running FastQC on the data once trimming has completed
+Output file(s) will be GZIP compressed
+
+Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz
+
+
+ >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz <<<
+10000000 sequences processed
+20000000 sequences processed
+30000000 sequences processed
+40000000 sequences processed
+50000000 sequences processed
+60000000 sequences processed
+70000000 sequences processed
+This is cutadapt 1.8.1 with Python 2.7.5
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
+Trimming 1 adapter with at most 10.0% errors in single-end mode ...
+Finished in 1418.14 s (19 us/read; 3.14 M reads/minute).
+
+=== Summary ===
+
+Total reads processed: 74,203,167
+Reads with adapters: 24,438,848 (32.9%)
+Reads written (passing filters): 74,203,167 (100.0%)
+
+Total basepairs processed: 7,494,519,867 bp
+Quality-trimmed: 512,942,133 bp (6.8%)
+Total written (filtered): 6,915,434,043 bp (92.3%)
+
+=== Adapter 1 ===
+
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24438848 times.
+
+No. of allowed errors:
+0-9 bp: 0; 10-13 bp: 1
+
+Bases preceding removed adapters:
+ A: 29.1%
+ C: 32.5%
+ G: 21.5%
+ T: 15.6%
+ none/other: 1.2%
+
+Overview of removed sequences
+length count expect max.err error counts
+1 15780739 18550791.8 0 15780739
+2 5577733 4637697.9 0 5577733
+3 1416646 1159424.5 0 1416646
+4 357832 289856.1 0 357832
+5 146943 72464.0 0 146943
+6 108165 18116.0 0 108165
+7 80461 4529.0 0 80461
+8 82845 1132.3 0 82845
+9 70563 283.1 0 69432 1131
+10 60090 70.8 1 58009 2081
+11 47646 17.7 1 46210 1436
+12 46325 4.4 1 45426 899
+13 36297 1.1 1 35620 677
+14 33206 1.1 1 32517 689
+15 30200 1.1 1 29537 663
+16 26650 1.1 1 25941 709
+17 23883 1.1 1 23175 708
+18 22814 1.1 1 22206 608
+19 15317 1.1 1 14942 375
+20 14734 1.1 1 14316 418
+21 12981 1.1 1 12572 409
+22 10726 1.1 1 10386 340
+23 10585 1.1 1 10145 440
+24 8211 1.1 1 7813 398
+25 7776 1.1 1 7401 375
+26 6577 1.1 1 6226 351
+27 7824 1.1 1 7188 636
+28 6995 1.1 1 6562 433
+29 5964 1.1 1 5450 514
+30 6235 1.1 1 5759 476
+31 4001 1.1 1 3651 350
+32 4002 1.1 1 3591 411
+33 3627 1.1 1 3171 456
+34 4898 1.1 1 3703 1195
+35 5262 1.1 1 4277 985
+36 5078 1.1 1 3913 1165
+37 5358 1.1 1 4348 1010
+38 4700 1.1 1 3853 847
+39 4403 1.1 1 3314 1089
+40 5420 1.1 1 3916 1504
+41 6469 1.1 1 5586 883
+42 3392 1.1 1 2865 527
+43 2475 1.1 1 2072 403
+44 2456 1.1 1 1563 893
+45 4035 1.1 1 2956 1079
+46 3992 1.1 1 3345 647
+47 2424 1.1 1 1858 566
+48 2639 1.1 1 1947 692
+49 2945 1.1 1 2271 674
+50 2427 1.1 1 1771 656
+51 3773 1.1 1 2342 1431
+52 5065 1.1 1 3343 1722
+53 4906 1.1 1 4300 606
+54 1870 1.1 1 1307 563
+55 1999 1.1 1 1388 611
+56 2968 1.1 1 1945 1023
+57 3724 1.1 1 2617 1107
+58 3918 1.1 1 2489 1429
+59 4730 1.1 1 3582 1148
+60 4028 1.1 1 2633 1395
+61 4988 1.1 1 3106 1882
+62 8736 1.1 1 4240 4496
+63 14165 1.1 1 8720 5445
+64 12661 1.1 1 10106 2555
+65 6864 1.1 1 4432 2432
+66 8136 1.1 1 4501 3635
+67 13203 1.1 1 6497 6706
+68 25197 1.1 1 12465 12732
+69 50150 1.1 1 22596 27554
+70 57190 1.1 1 45540 11650
+71 24203 1.1 1 17833 6370
+72 10860 1.1 1 7925 2935
+73 4677 1.1 1 3765 912
+74 1417 1.1 1 1054 363
+75 588 1.1 1 413 175
+76 488 1.1 1 343 145
+77 560 1.1 1 379 181
+78 531 1.1 1 361 170
+79 280 1.1 1 172 108
+80 252 1.1 1 156 96
+81 202 1.1 1 123 79
+82 186 1.1 1 100 86
+83 165 1.1 1 93 72
+84 176 1.1 1 81 95
+85 196 1.1 1 110 86
+86 217 1.1 1 116 101
+87 235 1.1 1 119 116
+88 256 1.1 1 137 119
+89 249 1.1 1 132 117
+90 276 1.1 1 140 136
+91 278 1.1 1 138 140
+92 347 1.1 1 176 171
+93 314 1.1 1 171 143
+94 333 1.1 1 205 128
+95 361 1.1 1 228 133
+96 461 1.1 1 237 224
+97 505 1.1 1 250 255
+98 640 1.1 1 312 328
+99 628 1.1 1 330 298
+100 1356 1.1 1 726 630
+101 6374 1.1 1 3751 2623
+
+
+RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
+=============================================
+74203167 sequences processed in total
+The length threshold of paired-end sequences gets evaluated later on (in the validation step)
+
+Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz_trimming_report.txt'
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.4.1
+Cutadapt version: 1.8.1
+Quality Phred score cutoff: 20
+Quality encoding type selected: ASCII+33
+Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
+Maximum trimming error rate: 0.1 (default)
+Minimum required adapter overlap (stringency): 1 bp
+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
+Running FastQC on the data once trimming has completed
+Output file(s) will be GZIP compressed
+
+Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz
+
+
+ >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz <<<
+10000000 sequences processed
+20000000 sequences processed
+30000000 sequences processed
+40000000 sequences processed
+50000000 sequences processed
+60000000 sequences processed
+70000000 sequences processed
+This is cutadapt 1.8.1 with Python 2.7.5
+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
+Trimming 1 adapter with at most 10.0% errors in single-end mode ...
+Finished in 1721.22 s (23 us/read; 2.59 M reads/minute).
+
+=== Summary ===
+
+Total reads processed: 74,203,167
+Reads with adapters: 21,064,160 (28.4%)
+Reads written (passing filters): 74,203,167 (100.0%)
+
+Total basepairs processed: 7,494,519,867 bp
+Quality-trimmed: 2,366,541,609 bp (31.6%)
+Total written (filtered): 5,082,419,690 bp (67.8%)
+
+=== Adapter 1 ===
+
+Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21064160 times.
+
+No. of allowed errors:
+0-9 bp: 0; 10-13 bp: 1
+
+Bases preceding removed adapters:
+ A: 30.1%
+ C: 33.0%
+ G: 20.7%
+ T: 15.2%
+ none/other: 0.9%
+
+Overview of removed sequences
+length count expect max.err error counts
+1 12550241 18550791.8 0 12550241
+2 6853426 4637697.9 0 6853426
+3 1004381 1159424.5 0 1004381
+4 288343 289856.1 0 288343
+5 51798 72464.0 0 51798
+6 12267 18116.0 0 12267
+7 5590 4529.0 0 5590
+8 3548 1132.3 0 3548
+9 4029 283.1 0 2533 1496
+10 5830 70.8 1 4021 1809
+11 2853 17.7 1 1580 1273
+12 4735 4.4 1 4249 486
+13 2911 1.1 1 2430 481
+14 4856 1.1 1 4434 422
+15 1804 1.1 1 1593 211
+16 2368 1.1 1 2059 309
+17 4669 1.1 1 4321 348
+18 1030 1.1 1 866 164
+19 2547 1.1 1 2321 226
+20 1754 1.1 1 1600 154
+21 950 1.1 1 868 82
+22 1594 1.1 1 1455 139
+23 1951 1.1 1 1677 274
+24 4690 1.1 1 4305 385
+25 1690 1.1 1 1476 214
+26 2584 1.1 1 1543 1041
+27 1859 1.1 1 1414 445
+28 3527 1.1 1 3194 333
+29 1791 1.1 1 1440 351
+30 5381 1.1 1 4997 384
+31 567 1.1 1 440 127
+32 1756 1.1 1 1597 159
+33 999 1.1 1 858 141
+34 1029 1.1 1 911 118
+35 2074 1.1 1 1899 175
+36 1288 1.1 1 1109 179
+37 2081 1.1 1 1892 189
+38 1339 1.1 1 1197 142
+39 2811 1.1 1 2570 241
+40 2661 1.1 1 2354 307
+41 3432 1.1 1 3016 416
+42 6993 1.1 1 6439 554
+43 1468 1.1 1 1286 182
+44 2728 1.1 1 2432 296
+45 4923 1.1 1 4561 362
+46 1119 1.1 1 989 130
+47 1665 1.1 1 1489 176
+48 1946 1.1 1 1791 155
+49 1932 1.1 1 1752 180
+50 4384 1.1 1 4019 365
+51 3873 1.1 1 3633 240
+52 1010 1.1 1 918 92
+53 506 1.1 1 432 74
+54 2117 1.1 1 1959 158
+55 2453 1.1 1 2286 167
+56 1117 1.1 1 995 122
+57 2284 1.1 1 2007 277
+58 5593 1.1 1 5183 410
+59 3875 1.1 1 3516 359
+60 4107 1.1 1 3667 440
+61 5724 1.1 1 5107 617
+62 8646 1.1 1 7513 1133
+63 18293 1.1 1 16357 1936
+64 29353 1.1 1 24721 4632
+65 54668 1.1 1 47835 6833
+66 30607 1.1 1 28229 2378
+67 4181 1.1 1 3499 682
+68 1785 1.1 1 1607 178
+69 649 1.1 1 581 68
+70 386 1.1 1 331 55
+71 201 1.1 1 149 52
+72 181 1.1 1 161 20
+73 238 1.1 1 203 35
+74 116 1.1 1 100 16
+75 1 1.1 1 0 1
+79 2 1.1 1 1 1
+80 2 1.1 1 1 1
+
+
+RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
+=============================================
+74203167 sequences processed in total
+The length threshold of paired-end sequences gets evaluated later on (in the validation step)
+
+Validate paired-end files HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz
+file_1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz, file_2: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz
+
+
+>>>>> Now validing the length of the 2 paired-end infiles: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz <<<<<
+Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+
+Total number of sequences analysed: 74203167
+
+Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4050544 (5.46%)
+
+
+ >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz<<<
+
+Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+
+ >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz<<<
+
+Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+Deleting both intermediate output files HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz
+
+====================================================================================================
+
+###CF Trim galore (PE mode) successfully exited, took 2 hours, 14 minutes, 51 seconds..
+
+
+
+
+--------------------------------------------------------------------------------
+Module: kallisto
+Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
+Job ID: cf_fastq_kallisto_1463255307_kallisto_460
+Previous Job ID: cf_fastq_kallisto_1463255307_trim_galore_160
+Date & Time: 23:03, 14-05-2016
+--------------------------------------------------------------------------------
+
+
+Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx
+
+---------- Kallisto version information ----------
+kallisto 0.42.5
+
+------- End of Kallisto version information ------
+
+###CFCMD kallisto quant -t 1 --pseudobam -i /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx -o HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz_kallisto_output -b 100 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz | samtools view -Sb - > HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz_kallisto.bam
+
+
+[quant] fragment length distribution will be estimated from the data
+[index] k-mer length: 31
+[index] number of targets: 176,241
+[index] number of k-mers: 104,600,239
+[index] number of equivalence classes: 702,950
+[quant] running in paired-end mode
+[quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
+ HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
+[quant] finding pseudoalignments for the reads ... done
+[quant] processed 70,152,623 reads, 59,280,920 reads pseudoaligned
+[quant] estimated average fragment length: 169.418
+[ em] quantifying the abundances ... done
+[ em] the Expectation-Maximization algorithm ran for 1,380 rounds
+[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
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[bstrp] running EM for the bootstrap: 36
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[bstrp] running EM for the bootstrap: 38
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[bstrp] running EM for the bootstrap: 40
[bstrp] running EM for the bootstrap: 41
[bstrp] running EM for the bootstrap: 42
[bstrp] running EM for the bootstrap: 43
[bstrp] running EM for the bootstrap: 44
[bstrp] running EM for the bootstrap: 45
[bstrp] running EM for the bootstrap: 46
[bstrp] running EM for the bootstrap: 47
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[bstrp] running EM for the bootstrap: 50
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[bstrp] running EM for the bootstrap: 52
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[bstrp] running EM for the bootstrap: 54
[bstrp] running EM for the bootstrap: 55
[bstrp] running EM for the bootstrap: 56
[bstrp] running EM for the bootstrap: 57
[bstrp] running EM for the bootstrap: 58
[bstrp] running EM for the bootstrap: 59
[bstrp] running EM for the bootstrap: 60
[bstrp] running EM for the bootstrap: 61
[bstrp] running EM for the bootstrap: 62
[bstrp] running EM for the bootstrap: 63
[bstrp] running EM for the bootstrap: 64
[bstrp] running EM for the bootstrap: 65
[bstrp] running EM for the bootstrap: 66
[bstrp] running EM for the bootstrap: 67
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[bstrp] running EM for the bootstrap: 69
[bstrp] running EM for the bootstrap: 70
[bstrp] running EM for the bootstrap: 71
[bstrp] running EM for the bootstrap: 72
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[bstrp] running EM for the bootstrap: 74
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[bstrp] running EM for the bootstrap: 80
[bstrp] running EM for the bootstrap: 81
[bstrp] running EM for the bootstrap: 82
[bstrp] running EM for the bootstrap: 83
[bstrp] running EM for the bootstrap: 84
[bstrp] running EM for the bootstrap: 85
[bstrp] running EM for the bootstrap: 86
[bstrp] running EM for the bootstrap: 87
[bstrp] running EM for the bootstrap: 88
[bstrp] running EM for the bootstrap: 89
[bstrp] running EM for the bootstrap: 90
[bstrp] running EM for the bootstrap: 91
[bstrp] running EM for the bootstrap: 92
[bstrp] running EM for the bootstrap: 93
[bstrp] running EM for the bootstrap: 94
[bstrp] running EM for the bootstrap: 95
[bstrp] running EM for the bootstrap: 96
[bstrp] running EM for the bootstrap: 97
[bstrp] running EM for the bootstrap: 98
[bstrp] running EM for the bootstrap: 99
[bstrp] running EM for the bootstrap: 100
+
+###CF kallisto (PE mode) successfully exited, took 2 hours, 44 minutes, 36 seconds..
+
+
+
+================================================================================
+
+
+
+
+
+###CF Run finished at 01:48 15-05-2016
+
+
+###CF Pipeline fastq_kallisto finished at 01:59 15-05-2016
+
+Sending HTML e-mail with sendmail..
+Sent a pipeline e-mail notification to rsh46@cam.ac.uk
diff -r 000000000000 -r 3bad335ccea9 test-data/kallisto_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kallisto_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,3 @@
+Sample fragment_length percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads
+HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.6511456908 58016047.0 9484959.0 48531088.0
+HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.5027847355 70152623.0 10871703.0 59280920.0
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_AlignmentSummaryMetrics_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_AlignmentSummaryMetrics_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample PF_HQ_ALIGNED_READS READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH BAD_CYCLES PF_INDEL_RATE PCT_READS_ALIGNED_IN_PAIRS TOTAL_READS PCT_CHIMERAS PF_HQ_ERROR_RATE PF_ALIGNED_BASES PCT_PF_READS LIBRARY PF_READS PCT_ADAPTER PCT_PF_READS_ALIGNED READ_GROUP SAMPLE PF_NOISE_READS STRAND_BALANCE PF_HQ_ALIGNED_Q20_BASES CATEGORY PF_HQ_MEDIAN_MISMATCHES PF_HQ_ALIGNED_BASES PF_MISMATCH_RATE PF_READS_ALIGNED
+D11_H4K16ac_Rep1_R1_fastq_gz 11288718.0 0.0 74.733459 0.0 0.000848 0.0 16199126.0 0.0 0.006165 1189439864.0 1.0 16199126.0 1.4e-05 0.983085 112.0 0.494061 802235299.0 UNPAIRED 0.0 843872901.0 0.011597 15925118.0
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectAlignmentSummaryMetrics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectAlignmentSummaryMetrics.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,10 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false REFERENCE_SEQUENCE=/data/repository/organisms/GRCm38_ensembl/genome_fasta/genome.fa INPUT=D11_H4K16ac_Rep1_R1_fastq_gz OUTPUT=/data/galaxy2/files/000/163/dataset_163662.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri Apr 21 14:00:55 CEST 2017
+
+## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
+CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP
+UNPAIRED 16199126 16199126 1 112 15925118 0.983085 1189439864 11288718 843872901 802235299 0 0.011597 0.006165 0.000848 74.733459 0 0 0 0.494061 0 0.000014
+
+
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectBaseDistributionByCycle.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectBaseDistributionByCycle.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,84 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectBaseDistributionByCycle CHART_OUTPUT=/data/galaxy2/files/000/163/dataset_163657.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=D11_H4K16ac_Rep1_R1_fastq_gz OUTPUT=/data/galaxy2/files/000/163/dataset_163656.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/data/repository/organisms/GRCm38_ensembl/genome_fasta/genome.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Fri Apr 21 13:59:56 CEST 2017
+
+## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics
+READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N
+1 1 45.534532 6.100294 6.278409 41.942176 0.144589
+1 2 18.642016 31.079914 32.291905 17.974837 0.011328
+1 3 25.118841 24.321879 26.15791 24.401106 0.000264
+1 4 22.612561 27.464826 27.30928 22.606024 0.007309
+1 5 27.970543 22.96859 21.970694 27.090173 0
+1 6 28.405874 22.976144 21.741647 26.875952 0.000383
+1 7 31.150444 19.648545 20.094438 29.10656 0.000013
+1 8 31.215988 19.341113 20.496087 28.946812 0
+1 9 31.733121 18.755302 20.342562 29.169015 0
+1 10 31.51068 19.338274 20.26157 28.889475 0
+1 11 31.155932 19.344704 20.729096 28.770267 0
+1 12 28.641307 21.681095 22.115748 27.561843 0.000006
+1 13 28.644403 21.190688 21.233551 28.931359 0
+1 14 27.912176 22.509522 21.398893 28.179408 0
+1 15 29.987269 20.65125 20.583967 28.777514 0
+1 16 30.695446 20.751024 19.720664 28.832866 0
+1 17 32.301494 19.466964 19.056719 29.174754 0.000069
+1 18 31.991424 19.465319 19.428886 29.114371 0
+1 19 31.223398 19.283091 20.843846 28.649665 0
+1 20 30.001159 20.431045 21.682439 27.885357 0
+1 21 30.268972 20.128608 21.518529 28.08389 0
+1 22 29.507609 20.991486 21.551678 27.949227 0
+1 23 29.228924 20.961638 22.202396 27.607042 0
+1 24 28.895271 21.140428 22.773371 27.190931 0
+1 25 30.220087 20.183506 21.007244 28.589163 0
+1 26 30.747733 19.55149 20.989765 28.711005 0.000006
+1 27 30.618992 19.162575 20.686703 29.531698 0.000031
+1 28 31.561628 19.651299 20.291748 28.495305 0.000019
+1 29 31.889741 19.244628 20.387671 28.477401 0.000559
+1 30 30.01585 20.370968 21.669604 27.943339 0.000239
+1 31 29.948939 20.187892 21.74697 28.116198 0
+1 32 29.83526 20.721207 21.226889 28.216644 0
+1 33 28.951574 21.118594 21.807089 28.122743 0
+1 34 29.250508 21.589012 20.80903 28.351444 0.000006
+1 35 29.741069 20.846087 21.339816 28.073028 0
+1 36 29.685575 20.657699 21.409349 28.247377 0
+1 37 30.435943 19.845352 21.605325 28.11328 0.0001
+1 38 31.52442 19.566381 20.859275 28.049918 0.000006
+1 39 31.915805 19.322889 20.315213 28.445698 0.000396
+1 40 31.415236 19.831291 20.60081 28.152663 0
+1 41 31.151606 20.007274 19.953602 28.887329 0.000188
+1 42 29.605015 21.700164 21.132809 27.561943 0.000069
+1 43 28.856192 21.690732 21.620633 27.832141 0.000302
+1 44 28.354815 21.89939 21.789262 27.956319 0.000214
+1 45 28.785938 21.376155 22.083299 27.443347 0.311262
+1 46 30.020967 20.974608 20.997153 28.006939 0.000333
+1 47 30.905677 19.834877 21.050285 28.209156 0.000006
+1 48 31.123254 20.025503 20.781792 28.068879 0.000572
+1 49 32.061167 19.135286 20.210972 28.592399 0.000176
+1 50 31.368968 19.831498 20.33522 28.464018 0.000295
+1 51 30.241493 20.530902 21.628272 27.599157 0.000176
+1 52 29.272115 21.228524 22.138875 27.360278 0.000208
+1 53 28.876831 20.985166 22.109191 28.028328 0.000484
+1 54 28.25128 21.263287 22.617006 27.868106 0.000321
+1 55 29.677859 20.048159 21.516525 28.756368 0.001089
+1 56 31.025964 19.638994 21.162354 28.1717 0.000988
+1 57 32.3089 19.022943 19.727314 28.939987 0.000856
+1 58 33.069967 18.780516 19.315424 28.832859 0.001234
+1 59 32.5634 19.018873 19.681712 28.735624 0.000391
+1 60 31.033388 19.63991 20.28236 29.043106 0.001235
+1 61 28.877884 21.063797 22.54864 27.508242 0.001437
+1 62 28.206236 21.933072 21.756687 28.103248 0.000757
+1 63 28.076144 21.765468 22.13245 28.025345 0.000593
+1 64 28.444021 21.930975 21.519278 28.105031 0.000694
+1 65 30.427586 20.515343 21.251214 27.804511 0.001345
+1 66 30.96119 20.454946 20.819432 27.764078 0.000354
+1 67 31.55559 19.752271 19.98091 28.7104 0.000829
+1 68 30.884355 19.787006 21.169721 28.158438 0.000481
+1 69 29.915794 19.951388 21.827419 28.302832 0.002566
+1 70 29.720163 20.878848 21.185973 28.214947 0.00007
+1 71 28.563014 21.296438 21.558676 28.580233 0.001639
+1 72 27.775812 22.725309 21.897851 27.599987 0.001041
+1 73 28.801882 22.042398 21.835818 27.319535 0.000367
+1 74 29.842933 21.375107 20.192959 28.587638 0.001363
+1 75 28.875221 21.990286 22.042923 27.09157 0
+
+
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectInsertSizeMetrics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectInsertSizeMetrics.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,737 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/omaha-beach/cloud_26/files/000/dataset_199.dat DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_198.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon May 23 09:33:00 UTC 2016
+
+## METRICS CLASS picard.analysis.InsertSizeMetrics
+MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
+194 63 100 5331452 271.809759 196.076488 311788 FR 25 47 69 91 127 343 941 1515 2585 16663
+
+## HISTOGRAM java.lang.Integer
+insert_size All_Reads.fr_count
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+
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectRnaSeqMetrics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,113 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Thu Dec 08 10:55:06 CET 2016
+
+## METRICS CLASS picard.analysis.RnaSeqMetrics
+PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP
+48870 48712 0 38786 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829
+
+## HISTOGRAM java.lang.Integer
+normalized_position All_Reads.normalized_coverage
+0 0.313906
+1 0.333933
+2 0.365536
+3 0.344525
+4 0.371353
+5 0.378606
+6 0.518015
+7 0.51266
+8 0.500497
+9 0.690539
+10 0.829611
+11 0.784227
+12 0.825037
+13 0.730533
+14 0.73133
+15 0.693057
+16 0.873759
+17 0.774195
+18 0.721989
+19 0.791727
+20 0.697702
+21 0.698451
+22 0.568885
+23 0.689955
+24 0.580475
+25 0.602348
+26 0.657286
+27 0.600594
+28 0.48185
+29 0.478605
+30 0.646053
+31 0.689366
+32 0.740073
+33 0.695415
+34 0.708419
+35 0.714707
+36 0.707421
+37 0.793703
+38 0.84384
+39 0.819497
+40 0.982412
+41 1.172387
+42 1.28116
+43 1.379184
+44 1.416285
+45 1.32892
+46 1.248258
+47 1.308676
+48 1.085518
+49 1.006687
+50 0.851309
+51 0.693805
+52 0.672921
+53 0.684999
+54 0.62579
+55 0.529832
+56 0.546564
+57 0.566014
+58 0.615824
+59 0.565042
+60 0.547677
+61 0.642067
+62 0.83636
+63 0.937071
+64 1.057465
+65 1.168829
+66 1.375228
+67 1.489487
+68 1.530099
+69 1.287542
+70 1.442585
+71 1.347823
+72 1.424913
+73 1.468345
+74 1.796846
+75 1.79639
+76 1.747908
+77 1.76867
+78 1.773528
+79 1.670178
+80 1.740083
+81 1.809632
+82 2.019967
+83 2.201517
+84 2.150455
+85 2.327367
+86 2.261259
+87 1.929731
+88 1.936627
+89 1.80697
+90 1.789004
+91 1.642341
+92 1.408203
+93 1.159737
+94 0.990047
+95 0.697842
+96 0.377809
+97 0.243433
+98 0.218816
+99 0.223665
+100 0.225079
+
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_MarkDuplicates.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_MarkDuplicates.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,112 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.sam.markduplicates.MarkDuplicates INPUT=[/omaha-beach/cloud_26/files/000/dataset_114.dat] OUTPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat METRICS_FILE=/omaha-beach/cloud_26/files/000/dataset_196.dat REMOVE_DUPLICATES=false ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon May 23 09:32:41 UTC 2016
+
+## METRICS CLASS picard.sam.DuplicationMetrics
+LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
+Unknown Library 2900 313405 0 2257 629 0 0.005582 77973949
+
+## HISTOGRAM java.lang.Double
+BIN VALUE
+1.0 1
+2.0 1.995989
+3.0 2.987982
+4.0 3.975997
+5.0 4.960048
+6.0 5.940152
+7.0 6.916324
+8.0 7.88858
+9.0 8.856937
+10.0 9.821409
+11.0 10.782013
+12.0 11.738763
+13.0 12.691676
+14.0 13.640766
+15.0 14.586049
+16.0 15.52754
+17.0 16.465254
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+77.0 66.357519
+78.0 67.09134
+79.0 67.822217
+80.0 68.550163
+81.0 69.275188
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+83.0 70.716526
+84.0 71.432862
+85.0 72.146324
+86.0 72.856924
+87.0 73.564674
+88.0 74.269585
+89.0 74.971668
+90.0 75.670935
+91.0 76.367397
+92.0 77.061066
+93.0 77.751952
+94.0 78.440066
+95.0 79.12542
+96.0 79.808025
+97.0 80.487892
+98.0 81.165032
+99.0 81.839456
+100.0 82.511174
+
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_RnaSeqMetrics_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_RnaSeqMetrics_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample PCT_CODING_BASES RIBOSOMAL_BASES PF_NOT_ALIGNED_BASES PCT_MRNA_BASES CORRECT_STRAND_READS MEDIAN_CV_COVERAGE PCT_RIBOSOMAL_BASES PCT_INTRONIC_BASES MEDIAN_3PRIME_BIAS PF_ALIGNED_BASES LIBRARY MEDIAN_5PRIME_BIAS PCT_USABLE_BASES PF_BASES READ_GROUP IGNORED_READS SAMPLE INTERGENIC_BASES INTRONIC_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_INTERGENIC_BASES PCT_CORRECT_STRAND_READS INCORRECT_STRAND_READS CODING_BASES UTR_BASES PCT_UTR_BASES
+picard_CollectRnaSeqMetrics_bam 0.0 158.0 79.6231 0.0 0.91593 0.0 0.235755 48712.0 0.430026 79.3657 48870.0 0.0 9926.0 0.0 1.402829 20.3769 0.0 0.0 0.0 38786.0 79.6231
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_baseContent_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_baseContent_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample sum_pct_n mean_pct_t sum_pct_g sum_pct_a sum_pct_c mean_pct_a sum_pct_t mean_pct_c cycle_count mean_pct_g
+D11_H4K16ac_Rep1_R1_fastq_gz 0.499258 28.1544206133 1590.390797 2251.590365 1545.938026 30.0212048667 2111.581546 20.6125070133 75 21.2052106267
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_collectGcBias.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_collectGcBias.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,110 @@
+## htsjdk.samtools.metrics.StringHeader
+# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_195.dat SUMMARY_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_193.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/omaha-beach/cloud_26/files/000/dataset_114.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_194.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
+## htsjdk.samtools.metrics.StringHeader
+# Started on: Mon May 23 09:32:30 UTC 2016
+
+## METRICS CLASS picard.analysis.GcBiasDetailMetrics
+ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP
+All Reads 0 0 0 0 0 0
+All Reads 1 0 0 0 0 0
+All Reads 2 0 0 0 0 0
+All Reads 3 10 0 0 0 0
+All Reads 4 7 0 0 0 0
+All Reads 5 6 0 0 0 0
+All Reads 6 4 0 0 0 0
+All Reads 7 9 0 0 0 0
+All Reads 8 22 0 0 0 0
+All Reads 9 15 0 0 0 0
+All Reads 10 20 0 0 0 0
+All Reads 11 18 0 0 0 0
+All Reads 12 101 0 0 0 0
+All Reads 13 118 0 0 0 0
+All Reads 14 137 1 20 0.110575 0.110575
+All Reads 15 243 4 19 0.249362 0.124681
+All Reads 16 366 10 21 0.4139 0.130887
+All Reads 17 468 9 24 0.291322 0.097107
+All Reads 18 689 25 24 0.549664 0.109933
+All Reads 19 1087 40 26 0.557451 0.088141
+All Reads 20 2152 95 25 0.668741 0.068611
+All Reads 21 3279 127 23 0.586731 0.052064
+All Reads 22 5106 178 23 0.528099 0.039583
+All Reads 23 7817 319 23 0.618197 0.034612
+All Reads 24 11933 630 24 0.799774 0.031864
+All Reads 25 17449 759 25 0.658943 0.023918
+All Reads 26 25272 1414 26 0.847591 0.02254
+All Reads 27 34926 1806 25 0.783331 0.018433
+All Reads 28 48489 2889 26 0.90257 0.016792
+All Reads 29 64950 4285 26 0.99942 0.015268
+All Reads 30 84452 5453 26 0.978142 0.013246
+All Reads 31 107535 6476 26 0.912291 0.011337
+All Reads 32 134982 7953 26 0.892548 0.010008
+All Reads 33 165941 9475 26 0.864972 0.008886
+All Reads 34 199087 11437 26 0.870253 0.008137
+All Reads 35 233144 12856 26 0.83533 0.007367
+All Reads 36 266049 14918 26 0.849426 0.006955
+All Reads 37 298999 17019 26 0.862265 0.00661
+All Reads 38 327958 20230 26 0.934446 0.00657
+All Reads 39 350801 22684 26 0.97957 0.006504
+All Reads 40 369841 23670 26 0.969527 0.006302
+All Reads 41 383262 25527 26 1.008975 0.006315
+All Reads 42 392470 26131 25 1.008617 0.006239
+All Reads 43 395234 25603 25 0.981326 0.006133
+All Reads 44 392428 26425 25 1.020074 0.006275
+All Reads 45 386569 25213 25 0.988039 0.006222
+All Reads 46 376763 25980 25 1.044594 0.006481
+All Reads 47 363422 24801 25 1.033795 0.006564
+All Reads 48 348339 24838 25 1.080167 0.006854
+All Reads 49 331960 24992 24 1.140491 0.007214
+All Reads 50 315781 23793 24 1.141405 0.0074
+All Reads 51 297249 22601 24 1.151818 0.007662
+All Reads 52 278159 19653 24 1.070317 0.007635
+All Reads 53 263713 19395 24 1.114127 0.008
+All Reads 54 247317 19047 24 1.166673 0.008453
+All Reads 55 230663 17922 23 1.177023 0.008792
+All Reads 56 215458 16244 23 1.142107 0.008961
+All Reads 57 198515 14904 23 1.137329 0.009316
+All Reads 58 180718 13720 23 1.150083 0.009819
+All Reads 59 165914 11940 23 1.090179 0.009977
+All Reads 60 152561 10775 23 1.069917 0.010307
+All Reads 61 138857 9746 23 1.063249 0.01077
+All Reads 62 125804 9067 22 1.091807 0.011466
+All Reads 63 112222 7148 22 0.964902 0.011413
+All Reads 64 99218 6056 23 0.924638 0.011882
+All Reads 65 85414 5612 24 0.995326 0.013286
+All Reads 66 72999 4286 23 0.88943 0.013586
+All Reads 67 61396 3631 23 0.895907 0.014868
+All Reads 68 52109 3341 22 0.971271 0.016804
+All Reads 69 45121 2735 21 0.918238 0.017558
+All Reads 70 38925 1675 21 0.651873 0.015928
+All Reads 71 32225 1053 22 0.495008 0.015254
+All Reads 72 27537 721 22 0.396639 0.014772
+All Reads 73 23481 483 22 0.311607 0.014179
+All Reads 74 20300 423 22 0.315661 0.015348
+All Reads 75 17785 245 22 0.208684 0.013332
+All Reads 76 15846 236 22 0.225615 0.014686
+All Reads 77 13683 230 22 0.254638 0.01679
+All Reads 78 11733 217 23 0.280174 0.019019
+All Reads 79 10547 188 22 0.270026 0.019694
+All Reads 80 9314 151 22 0.245594 0.019986
+All Reads 81 7659 149 23 0.294707 0.024143
+All Reads 82 5813 56 25 0.145937 0.019502
+All Reads 83 4687 46 23 0.148676 0.021921
+All Reads 84 3505 18 23 0.077797 0.018337
+All Reads 85 2385 8 23 0.050813 0.017965
+All Reads 86 1424 5 21 0.053191 0.023788
+All Reads 87 859 3 20 0.052906 0.030545
+All Reads 88 529 0 0 0 0
+All Reads 89 411 0 0 0 0
+All Reads 90 348 0 0 0 0
+All Reads 91 138 0 0 0 0
+All Reads 92 40 0 0 0 0
+All Reads 93 7 0 0 0 0
+All Reads 94 7 0 0 0 0
+All Reads 95 12 0 0 0 0
+All Reads 96 17 0 0 0 0
+All Reads 97 8 0 0 0 0
+All Reads 98 9 0 0 0 0
+All Reads 99 5 0 0 0 0
+All Reads 100 30 0 0 0 0
+
+
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_dups_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_dups_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample UNMAPPED_READS ESTIMATED_LIBRARY_SIZE READ_PAIR_OPTICAL_DUPLICATES READ_PAIRS_EXAMINED UNPAIRED_READS_EXAMINED PERCENT_DUPLICATION LIBRARY READ_PAIR_DUPLICATES UNPAIRED_READ_DUPLICATES
+dataset_114 0.0 77973949.0 0.0 313405.0 2900.0 0.005582 Unknown Library 629.0 2257.0
diff -r 000000000000 -r 3bad335ccea9 test-data/picard_insertSize_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_insertSize_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample SAMPLE_NAME MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
+dataset_197_FR dataset_197 194.0 63.0 100.0 5331452.0 271.809759 196.076488 311788.0 FR 25.0 47.0 69.0 91.0 127.0 343.0 941.0 1515.0 2585.0 16663.0
diff -r 000000000000 -r 3bad335ccea9 test-data/post_aligner_soft_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/post_aligner_soft_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,21 @@
+Sample QUAST_N50 QUAST_Total_length featureCounts_percent_assigned featureCounts_Assigned Picard_PCT_PF_READS_ALIGNED Prokka_organism Prokka_contigs Prokka_bases Prokka_CDS Bcftools Stats_number_of_records Bcftools Stats_number_of_SNPs Bcftools Stats_number_of_indels Bcftools Stats_tstv Bcftools Stats_number_of_MNPs Bamtools_duplicates_pct Bamtools_mapped_reads_pct Picard_PERCENT_DUPLICATION Picard_summed_median Picard_summed_mean GATK VariantEval_known_titv GATK VariantEval_novel_titv HTSeq Count_percent_assigned HTSeq Count_assigned Picard_PCT_RIBOSOMAL_BASES Picard_PCT_MRNA_BASES Samtools Flagstat_mapped_passed Samtools Stats_error_rate Samtools Stats_non_primary_alignments Samtools Stats_reads_mapped Samtools Stats_reads_mapped_percent Samtools Stats_raw_total_sequences Samblaster_pct_dups
+14892_1#15 115136.0 18435361.0
+70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797
+75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012
+80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981
+85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485
+90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170
+95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929
+D11_H4K16ac_Rep1_R1_fastq_gz 0.983085
+Sample1 Helicobacter pylori 30 1629978 1548
+Sample2 Escherichia coli 52 162997532523 1548
+Test1 5522770.0 4474244.0 902934.0 1.97 72330.0
+bamtools 0.0 93.125
+dataset_114 0.005582
+dataset_197 176 271.809759
+gatk_varianteval 0.0 2.2
+htseq 0.0 0
+picard_CollectRnaSeqMetrics_bam 79.62310000000001
+samtools_flagstat 20689039
+samtools_stats 0.004248509 12111.0 641821.0 100.0 641821.0
+virtual-normal 1.28
diff -r 000000000000 -r 3bad335ccea9 test-data/pre_alignment_soft_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pre_alignment_soft_log.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,75 @@
+[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc2/lib/python2.7/site-packages/multiqc-1.2-py2.7.egg/multiqc_config.yaml
+[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml
+[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml
+[2017-09-28 17:24:01,554] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir
+[2017-09-28 17:24:02,209] multiqc [DEBUG ] Latest MultiQC version is v1.2
+[2017-09-28 17:24:02,210] multiqc [INFO ] This is MultiQC v1.2
+[2017-09-28 17:24:02,210] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir
+[2017-09-28 17:24:02,210] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc
+[2017-09-28 17:24:02,210] multiqc [INFO ] Template : default
+[2017-09-28 17:24:02,210] multiqc [INFO ] Searching 'multiqc_WDir'
+[2017-09-28 17:24:02,211] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rseqc, busco, goleft_indexcov, disambiguate, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bismark, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq
+[2017-09-28 17:24:02,249] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig
+[2017-09-28 17:24:05,021] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,098] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found
+[2017-09-28 17:24:05,144] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,235] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,259] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,306] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50
+[2017-09-28 17:24:05,306] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,315] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,329] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,347] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,394] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,424] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,430] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,469] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('multiqc_WDir',)
+[2017-09-28 17:24:05,475] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,499] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,513] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,552] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,571] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,637] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,693] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,757] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,787] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,868] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,874] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,881] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',)
+[2017-09-28 17:24:05,915] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,931] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:05,942] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('multiqc_WDir',)
+[2017-09-28 17:24:06,029] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,064] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,083] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',)
+[2017-09-28 17:24:06,107] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',)
+[2017-09-28 17:24:06,145] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,187] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.
+[2017-09-28 17:24:06,207] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,225] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,238] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,245] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,250] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,263] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,273] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,299] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports
+[2017-09-28 17:24:06,351] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs
+[2017-09-28 17:24:06,378] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs
+[2017-09-28 17:24:06,403] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',)
+[2017-09-28 17:24:06,421] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs
+[2017-09-28 17:24:06,441] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,448] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,605] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
+[2017-09-28 17:24:06,908] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('multiqc_WDir',)
+[2017-09-28 17:24:06,914] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('multiqc_WDir',)
+[2017-09-28 17:24:06,923] multiqc [INFO ] Compressing plot data
+[2017-09-28 17:24:07,121] multiqc [INFO ] Report : multiqc_report.html
+[2017-09-28 17:24:07,121] multiqc [INFO ] Data : multiqc_data
+[2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data'
+[2017-09-28 17:24:07,952] multiqc [INFO ] MultiQC complete
diff -r 000000000000 -r 3bad335ccea9 test-data/pre_alignment_soft_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pre_alignment_soft_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,7 @@
+Sample SortMeRNA_rRNA_pct Trimmomatic_dropped_pct Cutadapt_percent_trimmed FastQC_percent_duplicates FastQC_percent_gc FastQC_avg_sequence_length FastQC_total_sequences FastQC_percent_fails Flexbar_removed_bases_pct
+25839_merged 1.09929975002
+C2 17.98
+dataset_33 10.7768204362
+poulet5_1 36.3059115993 48.0 101.0 267849.0 8.33333333333
+poulet5_2 36.1733887481 48.0 101.0 267849.0 8.33333333333
+result_right 45.2606635071
diff -r 000000000000 -r 3bad335ccea9 test-data/prokka_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/prokka_1.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,9 @@
+organism: Helicobacter pylori Sample1
+contigs: 30
+bases: 1629978
+tmRNA: 1
+tRNA: 36
+repeat_region: 15
+sig_peptide: 88
+rRNA: 2
+CDS: 1548
diff -r 000000000000 -r 3bad335ccea9 test-data/prokka_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/prokka_2.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,6 @@
+organism: Escherichia coli Sample2
+contigs: 52
+bases: 162997532523
+rRNA: 2
+CDS: 1548
+misc_RNA: 5152
diff -r 000000000000 -r 3bad335ccea9 test-data/prokka_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/prokka_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,3 @@
+Sample contigs tmRNA tRNA repeat_region sig_peptide bases rRNA CDS organism misc_RNA
+Sample1 30 1 36 15 88 1629978 2 1548 Helicobacter pylori
+Sample2 52 162997532523 2 1548 Escherichia coli 5152
diff -r 000000000000 -r 3bad335ccea9 test-data/quast.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/quast.tsv Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,48 @@
+Assembly 14892_1#15
+# contigs (>= 0 bp) 545
+# contigs (>= 1000 bp) 376
+# contigs (>= 5000 bp) 242
+# contigs (>= 10000 bp) 215
+# contigs (>= 25000 bp) 181
+# contigs (>= 50000 bp) 123
+Total length (>= 0 bp) 18465341
+Total length (>= 1000 bp) 18373173
+Total length (>= 5000 bp) 18079934
+Total length (>= 10000 bp) 17893099
+Total length (>= 25000 bp) 17353907
+Total length (>= 50000 bp) 15112131
+# contigs 467
+Largest contig 435484
+Total length 18435361
+Reference length 18916112
+GC (%) 48.17
+Reference GC (%) 48.21
+N50 115136
+NG50 112874
+N75 62262
+NG75 56990
+L50 48
+LG50 50
+L75 100
+LG75 106
+# misassemblies 107
+# misassembled contigs 82
+Misassembled contigs length 4540800
+# local misassemblies 132
+# unaligned contigs 8 + 59 part
+Unaligned length 88446
+Genome fraction (%) 95.482
+Duplication ratio 1.016
+# N's per 100 kbp 929.55
+# mismatches per 100 kbp 262.21
+# indels per 100 kbp 33.75
+# genes 7280 + 968 part
+Largest alignment 356982
+NA50 102129
+NGA50 99244
+NA75 54365
+NGA75 51757
+LA50 56
+LGA50 59
+LA75 117
+LGA75 124
diff -r 000000000000 -r 3bad335ccea9 test-data/quast_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/quast_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample L50 Duplication ratio GC (%) LG75 # misassemblies # contigs (>= 25000 bp) L75 Total length (>= 10000 bp) # genes # mismatches per 100 kbp # indels per 100 kbp # contigs (>= 5000 bp) Unaligned length Total length # unaligned contigs # local misassemblies Reference GC (%) # N's per 100 kbp Total length (>= 25000 bp) # contigs (>= 0 bp) # genes_partial NGA50 NGA75 Largest contig # contigs # unaligned contigs_partial NG75 # contigs (>= 50000 bp) Total length (>= 0 bp) NG50 # contigs (>= 10000 bp) LGA50 NA75 Total length (>= 5000 bp) Genome fraction (%) LGA75 LG50 N75 Total length (>= 1000 bp) NA50 # contigs (>= 1000 bp) N50 Total length (>= 50000 bp) Largest alignment LA75 LA50 Misassembled contigs length Reference length # misassembled contigs
+14892_1#15 48.0 1.016 48.17 106.0 107.0 181.0 100.0 17893099.0 7280.0 262.21 33.75 242.0 88446.0 18435361.0 8.0 132.0 48.21 929.55 17353907.0 545.0 968.0 99244.0 51757.0 435484.0 467.0 59.0 56990.0 123.0 18465341.0 112874.0 215.0 59.0 54365.0 18079934.0 95.482 124.0 50.0 62262.0 18373173.0 102129.0 376.0 115136.0 15112131.0 356982.0 117.0 56.0 4540800.0 18916112.0 82.0
diff -r 000000000000 -r 3bad335ccea9 test-data/report_manual_custom_content.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report_manual_custom_content.html Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,4806 @@
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Report generated on 2017-10-02, 14:14 based on data in:
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diff -r 000000000000 -r 3bad335ccea9 test-data/rsem.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rsem.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,57 @@
+2302013 30752387 0 33054400
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+65457099 3
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+29 37
+30 56
+31 115
+32 146
+33 210
+34 18
+35 128
+36 5
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+39 81
+40 1231
+41 284
+42 27
+43 112
+44 6
+45 4
+46 1
+47 1
+48 7
+53 2
+71 24
+73 1
+77 6
+Inf 0
diff -r 000000000000 -r 3bad335ccea9 test-data/rseqc.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rseqc.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,53 @@
+GC% read_count
+60.78 829481
+27.45 703668
+50.98 2379493
+1.96 261
+7.84 634
+35.29 2846032
+15.69 24491
+84.31 5518
+98.04 16
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+80.39 13695
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+92.16 437
+0.00 268
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+90.20 920
+21.57 178359
+45.10 3299529
+76.47 33755
+3.92 253
+41.18 3524191
+56.86 1272852
+54.90 1460810
+37.25 3180062
+100.00 4
+70.59 209856
+68.63 246416
+86.27 3040
+39.22 3812147
+5.88 382
+11.76 4123
+33.33 2269744
diff -r 000000000000 -r 3bad335ccea9 test-data/salmon.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/salmon.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
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1.08428e-05 8.1754e-06 6.07466e-06 5.15208e-06 5.38196e-06 6.08604e-06 6.00756e-06 6.48509e-06 7.17523e-06 6.32834e-06 6.30781e-06 8.63972e-06 1.17246e-05 1.42171e-05 1.44737e-05 1.39417e-05 1.49739e-05 1.34774e-05 8.48393e-06 6.52076e-06 8.59729e-06 9.88876e-06 8.73588e-06 7.19017e-06 6.60393e-06 7.90853e-06 1.35146e-05 1.90635e-05 1.72624e-05 1.36599e-05 1.41403e-05 1.24135e-05 6.29769e-06 1.70231e-06 7.93462e-07 1.51668e-06 3.70154e-06 8.90089e-06 1.39394e-05 1.39214e-05 1.01037e-05 8.39903e-06 1.28578e-05 1.63268e-05 1.0656e-05 3.04466e-06 6.80488e-07 5.69187e-07 1.65732e-06 6.6409e-06 1.56287e-05 2.36638e-05 2.25498e-05 1.19664e-05 2.65332e-06 2.12142e-06 8.85763e-06 1.46954e-05 1.30284e-05 8.9613e-06 9.41787e-06 1.24864e-05 1.32299e-05 1.09039e-05 8.40077e-06 7.40911e-06 6.38258e-06 3.74339e-06 1.43927e-06 1.13906e-06 1.29372e-06 1.33564e-06 2.46596e-06 4.46963e-06 5.67218e-06 4.90606e-06 4.04313e-06 6.34515e-06 8.88379e-06 6.95433e-06 3.65637e-06 2.94153e-06 4.17195e-06 5.5028e-06 4.74869e-06 2.17937e-06 7.82578e-07 2.43841e-06 6.8549e-06 1.06683e-05 9.78123e-06 5.28579e-06 1.99386e-06 2.50526e-06 6.54417e-06 1.11548e-05 1.14234e-05 7.26258e-06 4.4539e-06 5.43921e-06 7.07614e-06 6.63592e-06 4.78539e-06 3.19464e-06 2.10155e-06 1.72895e-06 2.37028e-06 3.47349e-06 3.77081e-06 2.39965e-06 8.38368e-07 4.67798e-07 5.94779e-07 1.01159e-06 2.03373e-06 2.50506e-06 1.69265e-06 2.01259e-06 5.0072e-06 6.87755e-06 5.0568e-06 2.80961e-06 2.54084e-06 3.53985e-06 4.11274e-06 3.3652e-06 2.96116e-06 3.00754e-06 2.25854e-06 2.07636e-06 2.45488e-06 1.63659e-06 4.09147e-07 3.85885e-07 1.56387e-06 2.86285e-06 3.53111e-06 3.46887e-06 2.69838e-06 1.85779e-06 1.49693e-06 1.22314e-06 1.21479e-06 2.31806e-06 3.28215e-06 3.84767e-06 6.78209e-06 9.55348e-06 7.76424e-06 4.57611e-06 3.32036e-06 3.40193e-06 4.69867e-06 5.48751e-06 3.69654e-06 1.2805e-06 2.89866e-07 7.83975e-08 2.6148e-07 1.06334e-06 1.74289e-06 1.52401e-06 9.07056e-07 5.1625e-07 8.31187e-07 2.47749e-06 4.2339e-06 3.97655e-06 2.17198e-06 7.20291e-07 1.50117e-07 8.41709e-07 3.65886e-06 6.7976e-06 7.03373e-06 4.57005e-06 1.9335e-06 1.12986e-06 3.40076e-06 7.19508e-06 7.86113e-06 4.68721e-06 2.46511e-06 2.39414e-06 1.93741e-06 1.27594e-06 1.48226e-06 2.30749e-06 2.97352e-06 2.52344e-06 2.31968e-06 4.53879e-06 6.29353e-06 4.15418e-06 1.99749e-06 4.0946e-06 6.78898e-06 5.42395e-06 2.19728e-06 1.49087e-06 3.60187e-06 5.48598e-06 5.55927e-06 4.70616e-06 3.05027e-06 1.49419e-06 1.77041e-06 3.28006e-06 4.91242e-06 5.31697e-06 3.27109e-06 8.17772e-07 2.0556e-09 8.22241e-09 2.73776e-08 6.83982e-08 1.19281e-07 1.68023e-07 1.78207e-07 1.13419e-07 3.08581e-07 1.09862e-06 2.20692e-06 3.35688e-06 4.99332e-06 7.74224e-06 9.23651e-06 6.38429e-06 2.64563e-06 4.40649e-06 1.09547e-05 1.3498e-05 9.01164e-06 5.95876e-06 6.76799e-06 6.08158e-06 5.24991e-06 6.45314e-06 5.96304e-06 2.93128e-06 6.59683e-07 7.47147e-08 1.99209e-08 9.9379e-10 4.56574e-07 1.8253e-06 2.73935e-06 1.83091e-06 8.73364e-07 1.64011e-06 2.45315e-06 3.43558e-06 7.7112e-06 1.19341e-05 1.2711e-05 1.45177e-05 1.4914e-05 8.6575e-06 1.98422e-06 8.47947e-08 3.3357e-07 1.23407e-06 3.26845e-06 4.48571e-06 2.93488e-06 7.3372e-07 8.48451e-20 8.96793e-07 3.59294e-06 5.40385e-06 3.63152e-06 9.58739e-07 6.40541e-08 3.88541e-08 4.80455e-08 3.30967e-07 9.40549e-07 1.21916e-06 7.48889e-07 1.77639e-07 8.48451e-20 8.48451e-20 3.74019e-10 1.24594e-07 4.9984e-07 1.65769e-06 4.85254e-06 8.49019e-06 8.04065e-06 3.86231e-06 7.51093e-07 3.88541e-08 1.42289e-07 3.74887e-07 5.13763e-07 5.22964e-07 1.3609e-06 3.23852e-06 3.92375e-06 2.4373e-06 1.49085e-06 2.52107e-06 3.62893e-06 3.89446e-06 3.4838e-06 2.38137e-06 2.43245e-06 4.29959e-06 5.14334e-06 4.42458e-06 5.07748e-06 7.05396e-06 6.70794e-06 3.56321e-06 1.09354e-06 5.94004e-07 2.23031e-06 6.82104e-06 9.6855e-06 6.31699e-06 1.55824e-06 2.43299e-08 9.73194e-08 1.45979e-07 9.73194e-08 2.43299e-08 5.65959e-07 2.86045e-06 5.78219e-06 5.87574e-06 3.0814e-06 7.90119e-07 4.3638e-07 1.26769e-06 1.86803e-06 3.32101e-06 8.55452e-06 1.2341e-05 8.22336e-06 2.0626e-06 2.28594e-07 8.46747e-07 1.23631e-06 8.12933e-07 2.01542e-07 8.48451e-20 6.62153e-07 2.64861e-06 3.97306e-06 2.64918e-06 6.63001e-07 5.65634e-10 1.41408e-10 5.08647e-07 2.69674e-06 5.74233e-06 6.20182e-06 3.51613e-06 9.91274e-07 1.49684e-07 2.94087e-08 9.78813e-09 1.46822e-08 2.48321e-08 1.24873e-07 4.67214e-07 9.51419e-07 1.05552e-06 6.09723e-07 1.51734e-07 8.0021e-09 8.22241e-09 7.6778e-07 3.48633e-06 6.56158e-06 6.56591e-06 3.83529e-06 1.87558e-06 2.86313e-06 5.46522e-06 6.77583e-06 6.76114e-06 5.96453e-06 3.46521e-06 8.60546e-07 8.57557e-07 3.41456e-06 5.12027e-06 3.97947e-06 3.37465e-06 5.5051e-06 8.12692e-06 8.17751e-06 4.99229e-06 1.70417e-06 4.16364e-07 1.04091e-07 8.48451e-20 8.48451e-20 1.03855e-06 4.17877e-06 7.31893e-06 8.25894e-06 7.07274e-06 3.98182e-06 1.10885e-06 4.78174e-07 7.17261e-07 4.78174e-07 1.06162e-06 3.76832e-06 5.65248e-06 3.76832e-06 1.00433e-06 9.46158e-07 3.69878e-06 6.57856e-06 6.0715e-06 2.84656e-06 5.40835e-07 6.62769e-07 2.64063e-06 3.95989e-06 2.63993e-06 6.65929e-07 2.3786e-08 3.5679e-08 2.3786e-08 5.9465e-09 8.48451e-20 8.48451e-20 1.05325e-06 4.213e-06 6.31951e-06 4.213e-06 1.74237e-06 2.75646e-06 4.14557e-06 2.79999e-06 7.54417e-07 4.35348e-08 1.08837e-08 1.62467e-06 6.4987e-06 9.74804e-06 6.4987e-06 1.62467e-06 2.42376e-07 9.69503e-07 1.45515e-06 9.73101e-07 2.47772e-07 3.59728e-09 2.08228e-06 8.32552e-06 1.25152e-05 8.43337e-06 2.53305e-06 1.26743e-06 1.76634e-06 1.16823e-06 9.73446e-07 2.64779e-06 3.92848e-06 2.60459e-06 6.81238e-07 1.34953e-07 2.17296e-07 1.64686e-07 5.60377e-08 2.95843e-07 1.15959e-06 1.82339e-06 2.39241e-06 4.38112e-06 6.7061e-06 7.6585e-06 6.95299e-06 4.13776e-06 1.10966e-06 5.44951e-07 2.05945e-06 3.08987e-06 2.06224e-06 5.19564e-07 4.87571e-09 1.20166e-07 4.67429e-07 7.15222e-07 5.67288e-07 3.57226e-07 7.34211e-07 1.98274e-06 2.77314e-06 1.8253e-06 5.34391e-07 3.12261e-07 4.68391e-07 3.12261e-07 7.80652e-08 4.91325e-08 1.9653e-07 2.94795e-07 1.96778e-07 5.01263e-08 1.49069e-09 9.9379e-10 2.48448e-10 8.48451e-20 8.48451e-20 1.28319e-06 5.13871e-06 7.72294e-06 5.16845e-06 1.30698e-06 5.9465e-09 6.45033e-08 4.1415e-07 1.01157e-06 1.21721e-06 7.78569e-07 2.90415e-07 8.9519e-08 1.62661e-06 7.55928e-06 1.41948e-05 1.33201e-05 6.37014e-06 1.43714e-06 1.9653e-07 4.91325e-08 8.48451e-20 1.40225e-09 3.01961e-08 1.06762e-07 1.53132e-07 1.48883e-07 2.21117e-07 2.94795e-07 1.9653e-07 1.52023e-07 1.4224e-06 4.66068e-06 6.47657e-06 4.14623e-06 1.2079e-06 7.88265e-07 1.1824e-06 7.88265e-07 1.97066e-07 1.13356e-09 4.53426e-09 7.40038e-08 8.39303e-07 2.66819e-06 3.66457e-06 2.33104e-06 5.65959e-07 8.48451e-20 5.75979e-08 2.30392e-07 3.45587e-07 2.32447e-07 6.58203e-08 1.23336e-08 1.27549e-08 2.01854e-08 2.71947e-08 1.81298e-08 4.53244e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 1.56137e-07 6.82145e-07 1.16721e-06 9.70134e-07 3.86528e-07 5.75979e-08 9.89308e-07 3.95723e-06 5.95252e-06 4.56652e-06 3.25974e-06 3.32229e-06 2.6434e-06 2.3679e-06 2.73795e-06 1.8253e-06 4.56325e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 4.52923e-08 1.81169e-07 2.71754e-07 1.81169e-07 4.52923e-08 8.48451e-20 2.42376e-07 9.69503e-07 1.45426e-06 9.69503e-07 2.42376e-07 8.48451e-20 1.27948e-07 5.11793e-07 7.72222e-07 5.29923e-07 3.56237e-07 8.22506e-07 1.2111e-06 8.04377e-07 2.01094e-07 1.19543e-07 4.85833e-07 7.47897e-07 5.59316e-07 2.9093e-07 2.18785e-07 1.4075e-07 3.51876e-08 8.48451e-20 1.7085e-09 6.83399e-09 1.0251e-08 4.48392e-07 1.76794e-06 2.64935e-06 1.76623e-06 4.41558e-07 2.28063e-07 9.20891e-07 1.40294e-06 9.70858e-07 3.1919e-07 1.67271e-07 2.04131e-07 9.36586e-07 3.27659e-06 4.87062e-06 3.25897e-06 8.59342e-07 7.1358e-08 4.7572e-08 1.1893e-08 8.48451e-20 1.19543e-07 4.78174e-07 7.17261e-07 4.78174e-07 1.19543e-07 8.48451e-20 8.48451e-20 8.48451e-20 3.652e-07 1.4608e-06 2.1912e-06 1.4608e-06 3.652e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 2.88646e-09 1.31089e-07 4.95492e-07 7.28806e-07 4.8106e-07 1.19543e-07 8.48451e-20 2.11966e-06 8.47864e-06 1.2718e-05 8.49079e-06 2.16829e-06 3.62843e-07 1.88217e-06 4.44733e-06 5.20328e-06 2.98569e-06 6.76004e-07 8.22241e-09 1.23336e-08 8.22241e-09 4.1112e-09 8.22241e-09 1.23336e-08 8.22241e-09 2.0556e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 5.08647e-07 2.89843e-06 6.66338e-06 7.84217e-06 4.90082e-06 2.61356e-05 9.87451e-05 0.000147884
+
diff -r 000000000000 -r 3bad335ccea9 test-data/samblaster.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samblaster.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,15 @@
+samblaster: Version 0.1.22
+samblaster: Inputting from stdin
+samblaster: Outputting to stdout
+samblaster: Opening /vagrant/test-out6/virtual-normal-samblaster-markdups.txt for write.
+[bam_header_read] EOF marker is absent. The input is probably truncated.
+[M::mem_pestat] skip orientation FF as there are not enough pairs
+[M::mem_pestat] skip orientation FR as there are not enough pairs
+[M::mem_pestat] skip orientation RF as there are not enough pairs
+[M::mem_pestat] skip orientation RR as there are not enough pairs
+samblaster: Loaded 86 header sequence entries.
+samblaster: Removed 1 of 78 (1.28%) read ids as duplicates using 1724k memory in 0.000S CPU seconds and 31S wall time.
+[main] Version: 0.7.7-r441
+[main] CMD:[samopen] SAM header is present: 86 sequences.
+ bwa mem -M -v 1 -R @RG\tID:virtual-normal\tSM:virtual-normal\tLB:virtual-normal\tPL:ILLUMINA -t 2 /proj/b2010040/private/nobackup/autoseq-genome/bwa/human_g1k_v37_decoy.fasta /vagrant/test-out6/skewer/virtual-normal_1.fastq.gz /vagrant/test-out6/skewer/virtual-normal_2.fastq.gz
+[main] Real time: 30.780 sec; CPU: 13.292 sec
diff -r 000000000000 -r 3bad335ccea9 test-data/samblaster_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samblaster_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample n_dups pct_dups n_tot n_nondups
+virtual-normal 1 1.28 78 77
diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_flagstat.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_flagstat.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,13 @@
+21040602 + 0 in total (QC-passed reads + QC-failed reads)
+0 + 0 secondary
+0 + 0 supplementary
+5448463 + 0 duplicates
+20689039 + 0 mapped (98.33%:-nan%)
+0 + 0 paired in sequencing
+0 + 0 read1
+0 + 0 read2
+0 + 0 properly paired (-nan%:-nan%)
+0 + 0 with itself and mate mapped
+0 + 0 singletons (-nan%:-nan%)
+0 + 0 with mate mapped to a different chr
+0 + 0 with mate mapped to a different chr (mapQ>=5)
diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_flagstat_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_flagstat_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample mapped_passed duplicates_failed secondary_passed paired in sequencing_failed duplicates_passed read2_passed read1_failed read1_passed with mate mapped to a different chr_passed total_failed properly paired_passed_pct singletons_passed supplementary_passed singletons_passed_pct mapped_failed_pct mapped_passed_pct supplementary_failed with itself and mate mapped_failed mapped_failed total_passed properly paired_failed flagstat_total with mate mapped to a different chr (mapQ >= 5)_passed properly paired_failed_pct with mate mapped to a different chr (mapQ >= 5)_failed with itself and mate mapped_passed read2_failed with mate mapped to a different chr_failed properly paired_passed paired in sequencing_passed singletons_failed secondary_failed singletons_failed_pct
+samtools_flagstat 20689039 0 0 0 5448463 0 0 0 0 0 nan 0 0 nan nan 98.33 0 0 0 21040602 0 21040602 0 nan 0 0 0 0 0 0 0 0 nan
diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_idxstats.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_idxstats.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,67 @@
+1 195471971 977171 0
+10 130694993 637405 0
+11 122082543 557954 0
+12 120129022 822778 0
+13 120421639 595176 0
+14 124902244 1179793 0
+15 104043685 474303 0
+16 98207768 450478 0
+17 94987271 442543 0
+18 90702639 423431 0
+19 61431566 269193 0
+2 182113224 2369317 0
+3 160039680 802543 0
+4 156508116 738160 0
+5 151834684 703632 0
+6 149736546 768256 0
+7 145441459 685296 0
+8 129401213 895718 0
+9 124595110 1144967 0
+MT 16299 141 0
+X 171031299 506800 0
+Y 91744698 132190 0
+JH584299.1 953012 2185 0
+GL456233.1 336933 1053 0
+JH584301.1 259875 303 0
+GL456211.1 241735 2348 0
+GL456350.1 227966 283 0
+JH584293.1 207968 236 0
+GL456221.1 206961 2196 0
+JH584297.1 205776 366 0
+JH584296.1 199368 368 0
+GL456354.1 195993 591 0
+JH584294.1 191905 313 0
+JH584298.1 184189 277 0
+JH584300.1 182347 230 0
+GL456219.1 175968 622 0
+GL456210.1 169725 1661 0
+JH584303.1 158099 214 0
+JH584302.1 155838 185 0
+GL456212.1 153618 1979 0
+JH584304.1 114452 278844 0
+GL456379.1 72385 210 0
+GL456216.1 66673 341 0
+GL456393.1 55711 629 0
+GL456366.1 47073 244 0
+GL456367.1 42057 245 0
+GL456239.1 40056 214 0
+GL456213.1 39340 99 0
+GL456383.1 38659 848 0
+GL456385.1 35240 155 0
+GL456360.1 31704 165 0
+GL456378.1 31602 444 0
+GL456389.1 28772 6166 0
+GL456372.1 28664 211 0
+GL456370.1 26764 502 0
+GL456381.1 25871 55 0
+GL456387.1 24685 156 0
+GL456390.1 24668 780 0
+GL456394.1 24323 114 0
+GL456392.1 23629 21116 0
+GL456382.1 23158 57 0
+GL456359.1 22974 85 0
+GL456396.1 21240 20375 0
+GL456368.1 20208 319 0
+JH584292.1 14945 85 0
+JH584295.1 1976 4 0
+* 0 0 274008
diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_stats.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,9736 @@
+# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats
+# 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 /omaha-beach/cloud_26/files/000/dataset_20.dat /omaha-beach/cloud_26/files/000/dataset_114.dat
+# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
+# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
+CHK 7742088d 2cf80e59 99341a6a
+# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
+SN raw total sequences: 641821
+SN filtered sequences: 0
+SN sequences: 641821
+SN is sorted: 1
+SN 1st fragments: 320981
+SN last fragments: 320840
+SN reads mapped: 641821
+SN reads mapped and paired: 638746 # paired-end technology bit set + both mates mapped
+SN reads unmapped: 0
+SN reads properly paired: 635626 # proper-pair bit set
+SN reads paired: 641821 # paired-end technology bit set
+SN reads duplicated: 0 # PCR or optical duplicate bit set
+SN reads MQ0: 70 # mapped and MQ=0
+SN reads QC failed: 0
+SN non-primary alignments: 12111
+SN total length: 64823921 # ignores clipping
+SN bases mapped: 64823921 # ignores clipping
+SN bases mapped (cigar): 64823921 # more accurate
+SN bases trimmed: 0
+SN bases duplicated: 0
+SN mismatches: 275405 # from NM fields
+SN error rate: 4.248509e-03 # mismatches / bases mapped (cigar)
+SN average length: 101
+SN maximum length: 101
+SN average quality: 26.0
+SN insert size average: 719.7
+SN insert size standard deviation: 1223.0
+SN inward oriented pairs: 317512
+SN outward oriented pairs: 1294
+SN pairs with other orientation: 30
+SN pairs on different chromosomes: 0
+# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to cycles. First column is the cycle number.
+FFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 113 0 0 0 0 320725 143 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 4 320810 71 91 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 3 320877 25 75 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 5 320905 26 44 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 8 320816 67 86 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 8 320839 42 84 5 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 6 320867 57 47 1 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 8 320845 59 64 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 2 320851 46 78 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 4 320836 57 77 3 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 7 320849 46 67 5 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 8 320812 80 78 2 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 9 320826 56 82 4 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 0 10 320774 77 107 7 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 7 320808 60 95 3 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 12 320786 68 101 6 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 8 320758 89 116 6 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 9 320768 86 106 6 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 12 320795 77 91 4 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 11 320739 99 110 14 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 16 320681 115 143 21 0 0 0 0 0 0 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 5 0 0 0 0 11 320699 111 144 11 0 0 0 0 0 0 0 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 10 1 0 0 0 14 320659 111 171 15 0 0 0 0 0 0 0 0 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 1 11 1 0 0 0 18 320626 139 165 20 0 0 0 0 0 0 0 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 9 1 0 0 0 13 320630 125 180 23 0 0 0 0 0 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 9 1 0 0 1 32 320502 176 228 32 0 0 0 0 0 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 10 1 0 0 0 25 320413 219 270 43 0 0 0 0 0 0 0 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 5 0 0 0 0 40 320323 222 317 74 0 0 0 0 0 0 0 0 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 2 14 0 0 0 0 33 320324 240 300 68 0 0 0 0 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 7 0 0 0 0 32 320438 208 249 47 0 0 0 0 0 0 0 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 12 2 0 0 0 30 320518 136 220 63 0 0 0 0 0 0 0 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 2 7 2 0 0 0 22 320539 158 199 52 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 3 0 0 0 31 320501 143 234 58 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 14 5 0 0 0 28 320475 168 216 73 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 14 2 0 0 2 14 320498 164 217 65 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 6 7 0 0 0 25 320419 210 229 82 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 10 2 0 0 0 27 320497 146 216 79 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 2 15 2 0 0 0 35 320379 186 277 85 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 1 0 11 4 0 0 2 36 320412 186 271 58 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 8 4 0 0 0 31 320420 187 261 67 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 4 6 0 0 0 19 320375 205 268 92 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 2 0 0 0 34 320376 202 287 65 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 2 8 0 0 0 33 320367 206 289 68 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 4 13 0 0 2 41 320230 279 330 78 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 15 8 0 0 0 58 320276 209 341 68 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 8 0 0 0 53 320197 275 342 87 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 14 6 0 0 1 55 320225 219 388 67 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 11 9 0 0 0 53 320120 302 394 80 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 10 18 0 0 2 84 320118 260 419 63 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 10 12 0 0 0 60 319973 337 492 84 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 10 15 0 0 0 52 319932 333 537 90 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 5 18 0 0 0 61 319903 320 573 94 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 8 22 0 0 0 62 319897 359 544 78 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 14 25 0 0 0 89 319808 371 575 91 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 7 24 0 0 3 121 319810 320 633 57 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 4 42 0 0 0 66 319481 518 657 199 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 5 36 0 0 0 80 319309 575 777 183 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 7 40 0 0 0 79 319345 609 700 191 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 19 35 0 0 0 112 319419 487 785 110 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 9 54 0 0 0 88 319097 574 901 246 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 10 55 0 0 10 169 319174 475 997 74 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 7 75 0 0 0 111 318749 787 986 248 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 22 56 0 0 10 188 318870 589 1150 76 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 19 76 0 0 11 189 318737 648 1195 91 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 21 79 0 0 0 197 318550 705 1284 121 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 25 79 0 0 0 195 318333 783 1439 107 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 18 85 0 0 0 208 318101 829 1584 130 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 19 96 0 0 0 231 317865 961 1679 116 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 36 133 0 0 0 238 317621 994 1809 132 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 29 123 0 0 0 258 317369 1087 1947 143 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 32 0 123 0 0 109 316709 1180 1344 1464 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 35 0 133 0 0 125 316372 1317 1408 1576 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 34 138 0 0 7 406 316605 1310 2392 65 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 31 181 0 0 0 342 316340 1442 2510 108 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 36 187 0 0 8 395 316006 1568 2662 95 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 54 179 0 0 0 386 315780 1618 2865 77 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 77 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 46 206 0 0 11 436 315719 1579 2889 72 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 38 0 236 0 11 125 314395 1803 1935 2415 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 33 249 0 0 0 490 315017 1824 3294 60 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 42 285 0 0 8 548 314760 1875 3393 51 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 47 289 0 0 9 585 314291 2036 3653 55 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 2 46 359 0 0 14 604 313542 2274 4102 24 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 17 42 363 0 0 28 773 312837 2442 4461 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 61 357 0 0 22 706 312428 2610 4730 50 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 16 45 386 0 0 21 839 311516 2872 5269 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 27 57 431 0 0 31 937 310762 3053 5665 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 19 50 507 0 0 16 1056 309721 3328 6266 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 26 56 554 0 0 12 1030 309021 3568 6694 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 18 35 604 0 0 36 1137 308241 3708 7186 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 12 41 672 0 0 10 1127 307003 4124 7976 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 20 56 744 0 0 15 1358 305669 4425 8679 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 16 71 854 0 0 10 1290 304360 4896 9472 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 52 22 943 0 0 13 1582 302737 5311 10315 1 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 38 13 1011 0 0 13 1659 301116 5731 11394 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 48 1119 0 0 2 1835 299128 6219 12604 20 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 21 1338 0 0 0 1858 6469 296623 13924 730 12 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 8 1383 0 0 0 1987 6972 294224 15758 636 11 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 1574 0 0 6 2448 8066 291197 17253 422 6 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1610 2 0 0 2835 8983 8498 298741 142 169 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1699 0 0 0 3197 10141 285195 20749 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1758 0 0 0 3382 281089 11576 23176 0 0 0 0 0 0 0 0 0 0 0 0 0
+FFQ 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part.
+# Columns correspond to qualities and rows to cycles. First column is the cycle number.
+LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 0 0 0 0 0 319823 972 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 15 0 0 0 5 320305 160 321 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 20 320305 132 370 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 6 0 0 17 320360 134 308 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 22 320335 165 301 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 20 320442 112 243 18 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 30 320503 109 179 9 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 7 320490 131 197 9 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 12 320539 123 159 2 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 11 320465 112 240 4 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 1 0 0 0 27 320344 160 278 10 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0 0 25 320389 169 236 10 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 14 320331 166 308 8 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 3 0 0 0 24 320389 142 250 22 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 1 0 0 0 23 320394 156 236 15 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 30 320296 190 295 16 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 36 320300 198 269 19 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 32 320348 176 253 21 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 25 320363 163 250 26 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 8 1 0 0 0 39 320215 196 348 32 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 25 320265 187 327 23 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 36 320227 192 334 33 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 13 0 0 0 0 38 320161 240 349 38 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 2 0 0 0 41 320111 237 400 34 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 4 0 0 0 39 320085 261 392 48 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 1 0 0 0 34 320076 240 426 54 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 16 0 0 0 0 35 319993 298 427 68 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 14 1 0 0 0 42 319952 300 452 75 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 18 2 0 0 0 58 320012 286 377 83 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 5 0 0 0 52 319979 266 407 105 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 1 0 0 0 54 319959 299 411 96 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 0 0 1 51 319853 293 495 120 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 18 2 0 0 0 50 319892 295 436 143 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 14 5 0 0 0 47 320114 237 316 105 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 16 6 0 0 0 43 320038 226 401 109 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 25 3 0 0 0 37 320030 269 375 98 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 17 6 0 0 0 46 320071 254 344 98 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 10 5 0 0 0 30 320128 221 342 101 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 14 5 0 0 0 46 320016 258 387 108 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 19 14 0 0 4 68 319787 318 497 130 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 7 8 0 0 0 46 319976 278 397 123 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 15 7 0 0 1 51 319947 287 430 93 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 12 8 0 0 2 68 319889 291 486 76 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 1 8 13 0 0 3 72 319747 351 503 131 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 11 16 0 0 3 91 319807 302 533 74 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 14 12 0 0 4 101 319743 327 538 97 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 1 13 14 0 0 1 78 319747 337 546 90 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 7 12 0 0 0 75 319710 365 550 113 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 18 15 0 0 0 86 319656 366 578 109 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 2 22 0 0 1 77 319439 451 638 198 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 1 13 0 22 0 3 87 319532 327 590 253 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 14 28 0 0 0 114 319528 327 709 105 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 16 28 0 0 2 118 319515 341 724 82 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 31 0 0 0 76 319533 411 686 73 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 3 12 32 0 0 7 131 319452 389 735 69 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 12 32 0 0 0 103 319491 396 716 82 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 18 31 0 0 0 111 319284 502 801 81 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 9 61 0 0 0 70 318992 590 866 234 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 15 51 0 0 0 123 319167 473 919 79 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 14 42 0 0 0 147 318983 560 989 90 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 15 48 0 0 7 186 318820 580 1099 69 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 20 56 0 0 0 143 318718 602 1177 110 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 2 3 79 0 0 4 185 318381 755 1179 230 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 0 24 74 0 0 5 224 318275 723 1381 104 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 25 77 0 0 0 171 318184 802 1452 112 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 23 102 0 0 0 215 317842 881 1622 123 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 31 91 0 0 0 209 317749 900 1742 106 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 35 111 0 0 0 237 317543 965 1818 108 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 9 142 0 0 0 217 316914 1239 1936 363 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 24 130 0 0 0 321 317017 1154 2057 113 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 34 126 0 0 0 306 316905 1223 2124 96 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 31 154 0 0 0 318 316601 1277 2345 90 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 34 170 0 0 0 374 316178 1406 2546 114 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 33 157 0 0 0 399 315995 1484 2677 77 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 40 0 203 0 0 122 314680 1678 1928 2164 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 37 220 0 0 0 421 315186 1691 3158 101 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 77 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 44 232 0 0 0 500 314756 1810 3390 83 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 38 268 0 0 12 485 314348 2042 3541 81 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 40 323 0 0 12 582 313860 2068 3849 84 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 28 49 333 0 0 8 685 313142 2394 4103 98 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 3 54 371 0 0 23 729 312644 2505 4455 36 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 2 55 390 0 0 20 776 311868 2687 4972 49 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 53 64 441 0 0 21 837 311048 3011 5347 18 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 47 435 0 0 14 1018 310127 3319 5825 24 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 13 52 519 0 0 23 1054 309351 3540 6271 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 16 59 624 0 0 17 1089 308409 3668 6934 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 9 56 606 0 0 13 1206 307277 4043 7612 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 16 58 687 0 0 21 1265 306234 4400 8140 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 70 775 0 0 4 1284 305283 4424 8967 19 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 13 53 783 0 0 19 1478 303756 5133 9591 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 52 24 932 0 0 27 1532 302457 5466 10336 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 18 55 975 0 0 5 1597 300687 6045 11442 0 0 0 0 0 0 0 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 7 44 41 1139 0 0 16 1871 299027 6326 12349 20 0 0 0 0 0 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 11 30 45 1208 0 0 10 2042 297077 6923 13475 19 0 0 0 0 0 0 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 6 33 31 1338 0 0 13 2162 294534 7554 15153 16 0 0 0 0 0 0 0 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 3 27 1558 0 0 0 2210 7901 291792 16495 836 18 0 0 0 0 0 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 3 15 1627 0 0 0 2458 8586 288861 18599 681 10 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 12 1851 9 0 0 2912 9641 9013 296492 435 468 7 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 4 1919 1 0 0 3335 11040 10164 294027 177 171 2 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2077 0 0 0 3829 12449 278167 24318 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2027 0 0 0 3852 274224 14024 26713 0 0 0 0 0 0 0 0 0 0 0 0 0
+LFQ 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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
+MPC 1 157 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 98405 282 0 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 2 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 2 83677 42 82 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 6 82286 28 70 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 4 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 2 82418 21 68 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 7 81217 31 82 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 6 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 6 81340 32 62 5 0 0 0 0 0 0 0 0 0 0 0
+MPC 7 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 6 81247 27 39 2 0 0 0 0 0 0 0 0 0 0 0
+MPC 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 4 81087 40 50 3 0 0 0 0 0 0 0 0 0 0 0
+MPC 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 2 79830 37 46 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 10 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 6 81033 36 63 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 9 80885 35 70 8 0 0 0 0 0 0 0 0 0 0 0
+MPC 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 2 82102 55 54 2 0 0 0 0 0 0 0 0 0 0 0
+MPC 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 5 81994 46 69 2 0 0 0 0 0 0 0 0 0 0 0
+MPC 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 0 0 7 82435 51 74 7 0 0 0 0 0 0 0 0 0 0 0
+MPC 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 5 82095 38 96 4 0 0 0 0 0 0 0 0 0 0 0
+MPC 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 0 11 82142 44 85 4 0 0 0 0 0 0 0 0 0 0 0
+MPC 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 7 82554 45 91 4 0 0 0 0 0 0 0 0 0 0 0
+MPC 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 8 82379 41 88 3 0 0 0 0 0 0 0 0 0 0 0
+MPC 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 0 0 0 8 81995 38 84 4 0 0 0 0 0 0 0 0 0 0 0
+MPC 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 6 0 0 0 0 8 82708 44 126 11 0 0 0 0 0 0 0 0 0 0 0
+MPC 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 9 82903 57 103 6 0 0 0 0 0 0 0 0 0 0 0
+MPC 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 11 83189 44 109 5 0 0 0 0 0 0 0 0 0 0 0
+MPC 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 8 82967 56 110 16 0 0 0 0 0 0 0 0 0 0 0
+MPC 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 9 82668 59 137 4 0 0 0 0 0 0 0 0 0 0 0
+MPC 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 6 83255 58 136 20 0 0 0 0 0 0 0 0 0 0 0
+MPC 26 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 10 83007 71 163 22 0 0 0 0 0 0 0 0 0 0 0
+MPC 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 11 82689 97 145 22 0 0 0 0 0 0 0 0 0 0 0
+MPC 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 5 0 0 0 0 13 83144 101 185 33 0 0 0 0 0 0 0 0 0 0 0
+MPC 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 28 84129 97 178 29 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 6 1 0 0 0 10 83162 82 159 28 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 5 1 0 0 0 20 83511 87 146 33 0 0 0 0 0 0 0 0 0 0 0
+MPC 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 1 13 83904 73 143 36 0 0 0 0 0 0 0 0 0 0 0
+MPC 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 0 0 0 12 83287 83 141 38 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 9 2 0 0 0 6 84022 71 94 36 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 1 0 11 3 0 0 1 9 83453 89 128 26 0 0 0 0 0 0 0 0 0 0 0
+MPC 36 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 2 0 0 0 13 83649 81 103 36 0 0 0 0 0 0 0 0 0 0 0
+MPC 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 1 0 0 0 10 83548 73 88 35 0 0 0 0 0 0 0 0 0 0 0
+MPC 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 1 0 0 0 12 84925 76 109 33 0 0 0 0 0 0 0 0 0 0 0
+MPC 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 9 0 0 0 1 12 83561 96 122 45 0 0 0 0 0 0 0 0 0 0 0
+MPC 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 7 4 0 0 1 20 84791 88 168 42 0 0 0 0 0 0 0 0 0 0 0
+MPC 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 2 0 0 0 14 84150 74 124 45 0 0 0 0 0 0 0 0 0 0 0
+MPC 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 2 0 0 0 13 83774 98 123 28 0 0 0 0 0 0 0 0 0 0 0
+MPC 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 2 0 0 2 28 83771 94 159 32 0 0 0 0 0 0 0 0 0 0 0
+MPC 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 5 0 0 1 23 83722 104 175 39 0 0 0 0 0 0 0 0 0 0 0
+MPC 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 6 0 0 1 41 84261 93 160 25 0 0 0 0 0 0 0 0 0 0 0
+MPC 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 7 1 0 0 0 39 84627 104 160 42 0 0 0 0 0 0 0 0 0 0 0
+MPC 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 7 3 0 0 0 34 84297 101 169 36 0 0 0 0 0 0 0 0 0 0 0
+MPC 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 5 0 0 0 15 84963 121 171 48 0 0 0 0 0 0 0 0 0 0 0
+MPC 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 6 3 0 0 1 39 83942 137 169 32 0 0 0 0 0 0 0 0 0 0 0
+MPC 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 9 0 0 0 28 84075 143 194 66 0 0 0 0 0 0 0 0 0 0 0
+MPC 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 2 0 1 34 83331 123 177 64 0 0 0 0 0 0 0 0 0 0 0
+MPC 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 5 8 0 0 0 33 84009 111 218 49 0 0 0 0 0 0 0 0 0 0 0
+MPC 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 6 7 0 0 1 43 84258 125 209 35 0 0 0 0 0 0 0 0 0 0 0
+MPC 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 9 0 0 0 25 84920 133 194 29 0 0 0 0 0 0 0 0 0 0 0
+MPC 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 4 7 0 0 7 62 84793 109 211 26 0 0 0 0 0 0 0 0 0 0 0
+MPC 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 12 0 0 0 25 84246 173 244 47 0 0 0 0 0 0 0 0 0 0 0
+MPC 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 6 0 0 0 44 84546 193 256 53 0 0 0 0 0 0 0 0 0 0 0
+MPC 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 16 0 0 0 23 84043 200 294 57 0 0 0 0 0 0 0 0 0 0 0
+MPC 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 10 7 0 0 0 46 85272 172 310 30 0 0 0 0 0 0 0 0 0 0 0
+MPC 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 12 0 0 0 45 84534 200 308 64 0 0 0 0 0 0 0 0 0 0 0
+MPC 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 7 6 0 0 5 90 84509 185 343 32 0 0 0 0 0 0 0 0 0 0 0
+MPC 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 15 0 0 0 37 84802 260 354 65 0 0 0 0 0 0 0 0 0 0 0
+MPC 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 5 11 0 0 3 86 84937 241 420 51 0 0 0 0 0 0 0 0 0 0 0
+MPC 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 9 9 0 0 7 84 84776 280 455 38 0 0 0 0 0 0 0 0 0 0 0
+MPC 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 6 14 0 0 0 65 83919 322 428 61 0 0 0 0 0 0 0 0 0 0 0
+MPC 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 12 19 0 0 0 58 84493 325 511 47 0 0 0 0 0 0 0 0 0 0 0
+MPC 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 7 23 0 0 0 58 84399 362 558 45 0 0 0 0 0 0 0 0 0 0 0
+MPC 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 10 16 0 0 0 68 83573 371 585 57 0 0 0 0 0 0 0 0 0 0 0
+MPC 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 7 43 0 0 0 85 84135 412 599 101 0 0 0 0 0 0 0 0 0 0 0
+MPC 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 6 36 0 0 0 89 84584 409 665 43 0 0 0 0 0 0 0 0 0 0 0
+MPC 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 10 0 0 60 84237 450 528 301 0 0 0 0 0 0 0 0 0 0 0
+MPC 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 8 17 16 0 0 75 82936 493 605 299 0 0 0 0 0 0 0 0 0 0 0
+MPC 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 17 44 0 0 2 157 84054 528 844 22 0 0 0 0 0 0 0 0 0 0 0
+MPC 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 12 54 0 0 0 96 83448 556 848 43 0 0 0 0 0 0 0 0 0 0 0
+MPC 75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 8 31 33 0 1 97 83325 652 739 350 0 0 0 0 0 0 0 0 0 0 0
+MPC 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 19 34 0 0 0 130 82830 678 946 40 0 0 0 0 0 0 0 0 0 0 0
+MPC 77 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 13 41 0 0 0 143 82891 633 981 19 0 0 0 0 0 0 0 0 0 0 0
+MPC 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 13 43 27 0 2 100 82562 693 858 401 0 0 0 0 0 0 0 0 0 0 0
+MPC 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 16 82 0 0 3 163 82688 729 1061 25 0 0 0 0 0 0 0 0 0 0 0
+MPC 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 16 71 0 0 2 175 82962 828 1165 25 0 0 0 0 0 0 0 0 0 0 0
+MPC 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 3 17 74 0 0 8 231 82689 870 1289 15 0 0 0 0 0 0 0 0 0 0 0
+MPC 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 17 111 0 0 13 216 82308 966 1392 13 0 0 0 0 0 0 0 0 0 0 0
+MPC 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 4 25 99 0 0 9 267 81839 1044 1442 5 0 0 0 0 0 0 0 0 0 0 0
+MPC 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 20 85 0 0 1 232 81465 1231 1663 7 0 0 0 0 0 0 0 0 0 0 0
+MPC 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 17 99 0 0 10 268 81759 1291 1819 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 6 19 117 0 0 10 316 81327 1341 1988 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 3 19 117 0 0 4 349 81046 1483 2232 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 2 25 159 0 0 7 363 80978 1554 2285 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 4 25 182 0 0 9 338 80443 1644 2682 2 0 0 0 0 0 0 0 0 0 0 0
+MPC 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 2 17 214 0 0 4 430 79591 1772 2930 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 7 17 208 0 0 11 441 80129 1730 3233 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 5 17 211 0 0 3 446 78437 2002 3480 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 14 8 254 0 0 7 572 78615 1997 3749 3 0 0 0 0 0 0 0 0 0 0 0
+MPC 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 5 8 251 0 0 1 462 77866 2241 4048 6 0 0 0 0 0 0 0 0 0 0 0
+MPC 95 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 9 314 0 0 6 655 76430 2514 4695 7 0 0 0 0 0 0 0 0 0 0 0
+MPC 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 12 391 0 0 0 566 2098 76969 5222 211 4 0 0 0 0 0 0 0 0 0 0 0
+MPC 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 401 0 0 0 614 2396 75564 5776 229 6 0 0 0 0 0 0 0 0 0 0 0
+MPC 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 271 219 0 0 406 1727 2800 77304 3035 141 1 0 0 0 0 0 0 0 0 0 0 0
+MPC 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 504 0 0 0 928 2885 3413 78669 64 44 1 0 0 0 0 0 0 0 0 0 0 0
+MPC 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 536 0 0 0 979 3339 73408 7776 0 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 728 0 0 0 1072 73777 4856 10378 0 0 0 0 0 0 0 0 0 0 0 0
+MPC 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 7.29 0
+GCF 15.08 2
+GCF 16.08 3
+GCF 17.09 7
+GCF 18.59 17
+GCF 20.10 33
+GCF 21.11 42
+GCF 22.11 52
+GCF 23.12 114
+GCF 24.12 164
+GCF 25.13 326
+GCF 26.13 507
+GCF 27.14 691
+GCF 28.14 899
+GCF 29.15 1591
+GCF 30.15 1949
+GCF 31.16 2308
+GCF 32.16 2736
+GCF 32.91 3088
+GCF 33.67 3685
+GCF 34.67 4605
+GCF 35.68 5091
+GCF 36.68 6131
+GCF 37.69 6883
+GCF 38.69 7964
+GCF 39.70 8636
+GCF 40.70 10761
+GCF 41.71 12194
+GCF 42.71 12911
+GCF 43.72 13386
+GCF 44.72 13260
+GCF 45.73 13698
+GCF 46.73 13439
+GCF 47.74 15308
+GCF 48.74 14928
+GCF 49.75 14412
+GCF 50.75 13332
+GCF 51.76 12903
+GCF 52.76 11945
+GCF 53.77 12084
+GCF 54.77 11708
+GCF 55.78 9649
+GCF 56.78 9361
+GCF 57.79 8367
+GCF 58.79 6859
+GCF 59.80 5753
+GCF 60.80 4662
+GCF 61.81 4213
+GCF 62.81 3894
+GCF 63.82 3063
+GCF 64.82 2456
+GCF 65.83 1920
+GCF 66.58 1398
+GCF 67.34 1419
+GCF 68.34 1253
+GCF 69.35 963
+GCF 70.35 713
+GCF 71.36 414
+GCF 72.36 265
+GCF 73.37 187
+GCF 74.37 115
+GCF 75.38 74
+GCF 76.38 50
+GCF 77.39 32
+GCF 78.39 23
+GCF 79.90 14
+GCF 81.41 19
+GCF 82.41 13
+GCF 83.42 5
+GCF 84.42 2
+GCF 85.43 1
+# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
+GCL 6.78 0
+GCL 14.57 1
+GCL 16.08 3
+GCL 17.09 4
+GCL 18.09 7
+GCL 19.10 14
+GCL 20.10 31
+GCL 21.11 43
+GCL 22.11 65
+GCL 23.12 110
+GCL 24.12 186
+GCL 25.13 318
+GCL 26.13 565
+GCL 27.14 698
+GCL 28.14 919
+GCL 29.15 1512
+GCL 30.15 1962
+GCL 31.16 2348
+GCL 32.16 2693
+GCL 32.91 3148
+GCL 33.67 3657
+GCL 34.67 4472
+GCL 35.68 5072
+GCL 36.68 5943
+GCL 37.69 6932
+GCL 38.69 7875
+GCL 39.70 8778
+GCL 40.70 10644
+GCL 41.71 11773
+GCL 42.71 12979
+GCL 43.72 13566
+GCL 44.72 13217
+GCL 45.73 13362
+GCL 46.73 13338
+GCL 47.74 15116
+GCL 48.74 14791
+GCL 49.75 14361
+GCL 50.75 13389
+GCL 51.76 12939
+GCL 52.76 12428
+GCL 53.77 12023
+GCL 54.77 11736
+GCL 55.78 9713
+GCL 56.78 9335
+GCL 57.79 8514
+GCL 58.79 6846
+GCL 59.80 5874
+GCL 60.80 4865
+GCL 61.81 4274
+GCL 62.81 3973
+GCL 63.82 3008
+GCL 64.82 2400
+GCL 65.83 1929
+GCL 66.58 1438
+GCL 67.34 1428
+GCL 68.34 1299
+GCL 69.35 988
+GCL 70.35 739
+GCL 71.36 392
+GCL 72.36 258
+GCL 73.37 156
+GCL 74.37 118
+GCL 75.38 81
+GCL 76.38 51
+GCL 77.39 28
+GCL 78.39 32
+GCL 79.40 25
+GCL 80.40 21
+GCL 81.41 12
+GCL 82.41 14
+GCL 83.92 4
+GCL 85.43 2
+# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%]
+GCC 1 12.32 37.19 37.45 13.05
+GCC 2 30.22 19.07 19.01 31.70
+GCC 3 23.59 25.79 25.71 24.90
+GCC 4 24.89 24.36 24.80 25.95
+GCC 5 26.37 23.14 23.40 27.09
+GCC 6 27.80 21.60 21.70 28.90
+GCC 7 27.71 21.52 21.77 29.00
+GCC 8 25.01 24.21 24.68 26.10
+GCC 9 25.54 23.74 23.93 26.79
+GCC 10 27.83 21.53 21.61 29.03
+GCC 11 22.59 26.73 26.96 23.72
+GCC 12 24.80 24.68 24.80 25.72
+GCC 13 26.25 23.19 22.90 27.66
+GCC 14 25.68 23.77 23.72 26.83
+GCC 15 25.57 23.95 23.87 26.61
+GCC 16 25.07 24.41 24.49 26.03
+GCC 17 25.26 24.27 24.24 26.23
+GCC 18 25.39 24.07 23.99 26.55
+GCC 19 25.14 24.57 24.36 25.93
+GCC 20 25.54 23.86 23.89 26.71
+GCC 21 25.45 23.91 24.04 26.60
+GCC 22 25.38 23.88 24.40 26.34
+GCC 23 25.68 23.61 24.05 26.65
+GCC 24 25.78 23.77 23.42 27.03
+GCC 25 25.33 24.02 24.16 26.49
+GCC 26 25.76 23.85 23.76 26.63
+GCC 27 25.79 23.86 23.85 26.50
+GCC 28 25.39 24.28 24.11 26.23
+GCC 29 25.76 24.03 23.60 26.62
+GCC 30 25.85 23.95 23.84 26.35
+GCC 31 25.55 24.04 24.10 26.31
+GCC 32 25.91 23.72 23.70 26.66
+GCC 33 25.71 23.88 23.80 26.62
+GCC 34 25.47 24.24 24.41 25.87
+GCC 35 25.73 23.66 23.83 26.78
+GCC 36 25.56 23.78 23.97 26.69
+GCC 37 25.71 24.17 23.94 26.18
+GCC 38 25.76 23.66 23.92 26.66
+GCC 39 25.66 23.95 23.94 26.45
+GCC 40 25.54 24.12 24.01 26.33
+GCC 41 25.47 23.92 23.71 26.90
+GCC 42 25.78 23.69 23.74 26.79
+GCC 43 25.41 24.09 24.14 26.36
+GCC 44 25.94 23.70 23.59 26.77
+GCC 45 25.84 23.84 23.78 26.54
+GCC 46 25.47 24.14 24.07 26.32
+GCC 47 25.69 23.93 23.94 26.44
+GCC 48 25.71 24.00 23.78 26.51
+GCC 49 25.25 23.94 24.25 26.57
+GCC 50 25.78 23.80 23.68 26.74
+GCC 51 25.46 23.99 23.90 26.66
+GCC 52 25.32 23.97 24.09 26.62
+GCC 53 25.76 23.74 23.72 26.79
+GCC 54 25.69 23.87 23.88 26.55
+GCC 55 25.34 24.00 24.22 26.44
+GCC 56 25.68 23.94 23.77 26.61
+GCC 57 25.68 23.82 23.92 26.57
+GCC 58 25.74 23.69 24.16 26.41
+GCC 59 25.69 23.87 23.83 26.61
+GCC 60 25.83 23.70 23.85 26.63
+GCC 61 25.57 23.87 24.19 26.37
+GCC 62 25.87 23.75 23.88 26.51
+GCC 63 26.09 23.89 23.56 26.46
+GCC 64 25.68 24.31 23.96 26.06
+GCC 65 25.74 24.02 23.86 26.38
+GCC 66 25.73 23.92 23.70 26.65
+GCC 67 25.44 24.05 24.26 26.26
+GCC 68 25.76 23.92 23.83 26.49
+GCC 69 25.58 23.96 23.74 26.72
+GCC 70 25.91 23.86 24.02 26.21
+GCC 71 25.93 23.70 23.76 26.61
+GCC 72 25.95 23.42 23.76 26.87
+GCC 73 25.36 24.10 24.11 26.42
+GCC 74 25.91 23.79 23.67 26.64
+GCC 75 25.67 23.81 23.92 26.59
+GCC 76 25.79 23.88 24.29 26.05
+GCC 77 25.80 23.81 23.66 26.74
+GCC 78 26.11 23.71 23.57 26.61
+GCC 79 25.69 24.25 23.89 26.17
+GCC 80 25.79 23.81 23.80 26.60
+GCC 81 25.91 23.89 23.56 26.64
+GCC 82 25.47 23.98 23.96 26.59
+GCC 83 25.76 23.85 23.90 26.49
+GCC 84 26.10 23.65 23.62 26.63
+GCC 85 25.35 24.06 24.19 26.39
+GCC 86 26.07 23.85 23.69 26.39
+GCC 87 26.02 23.96 23.45 26.57
+GCC 88 25.63 24.31 23.85 26.20
+GCC 89 25.89 23.88 23.55 26.69
+GCC 90 25.81 24.05 23.77 26.37
+GCC 91 25.36 24.23 24.29 26.12
+GCC 92 25.90 23.55 23.90 26.65
+GCC 93 25.85 23.76 23.75 26.65
+GCC 94 25.50 24.35 24.15 26.00
+GCC 95 25.77 23.83 23.88 26.52
+GCC 96 25.71 23.78 23.88 26.62
+GCC 97 25.67 24.09 24.05 26.19
+GCC 98 25.81 23.71 23.97 26.51
+GCC 99 25.43 23.88 24.11 26.58
+GCC 100 25.46 23.99 24.27 26.28
+GCC 101 25.52 24.12 24.24 26.11
+# 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 5 4 1 0
+IS 102 537 308 229 0
+IS 103 481 296 185 0
+IS 104 401 345 56 0
+IS 105 348 332 16 0
+IS 106 367 358 9 0
+IS 107 346 346 0 0
+IS 108 356 356 0 0
+IS 109 391 391 0 0
+IS 110 349 349 0 0
+IS 111 368 368 0 0
+IS 112 452 452 0 0
+IS 113 461 461 0 0
+IS 114 474 474 0 0
+IS 115 515 515 0 0
+IS 116 481 481 0 0
+IS 117 521 521 0 0
+IS 118 561 561 0 0
+IS 119 601 601 0 0
+IS 120 605 605 0 0
+IS 121 605 605 0 0
+IS 122 702 702 0 0
+IS 123 707 707 0 0
+IS 124 658 658 0 0
+IS 125 755 755 0 0
+IS 126 738 738 0 0
+IS 127 761 761 0 0
+IS 128 828 828 0 0
+IS 129 884 884 0 0
+IS 130 929 929 0 0
+IS 131 935 935 0 0
+IS 132 957 957 0 0
+IS 133 1008 1008 0 0
+IS 134 1091 1091 0 0
+IS 135 1138 1138 0 0
+IS 136 1183 1183 0 0
+IS 137 1285 1285 0 0
+IS 138 1387 1387 0 0
+IS 139 1430 1430 0 0
+IS 140 1500 1500 0 0
+IS 141 1630 1630 0 0
+IS 142 1701 1701 0 0
+IS 143 1848 1848 0 0
+IS 144 1908 1908 0 0
+IS 145 1969 1969 0 0
+IS 146 2217 2217 0 0
+IS 147 2223 2223 0 0
+IS 148 2284 2284 0 0
+IS 149 2464 2464 0 0
+IS 150 2580 2580 0 0
+IS 151 2545 2545 0 0
+IS 152 2644 2644 0 0
+IS 153 2605 2605 0 0
+IS 154 2592 2592 0 0
+IS 155 2759 2759 0 0
+IS 156 2770 2770 0 0
+IS 157 2732 2732 0 0
+IS 158 2781 2781 0 0
+IS 159 2796 2796 0 0
+IS 160 2897 2897 0 0
+IS 161 2839 2839 0 0
+IS 162 2795 2795 0 0
+IS 163 2726 2726 0 0
+IS 164 2790 2790 0 0
+IS 165 2868 2868 0 0
+IS 166 2815 2815 0 0
+IS 167 2874 2874 0 0
+IS 168 2908 2908 0 0
+IS 169 2826 2826 0 0
+IS 170 2856 2856 0 0
+IS 171 2827 2827 0 0
+IS 172 2857 2857 0 0
+IS 173 2864 2863 0 1
+IS 174 2785 2785 0 0
+IS 175 2695 2695 0 0
+IS 176 2713 2713 0 0
+IS 177 2594 2594 0 0
+IS 178 2525 2525 0 0
+IS 179 2584 2584 0 0
+IS 180 2505 2505 0 0
+IS 181 2379 2378 1 0
+IS 182 2330 2330 0 0
+IS 183 2195 2195 0 0
+IS 184 2121 2121 0 0
+IS 185 2002 2001 0 1
+IS 186 1921 1921 0 0
+IS 187 1839 1839 0 0
+IS 188 1891 1891 0 0
+IS 189 1711 1711 0 0
+IS 190 1618 1618 0 0
+IS 191 1489 1489 0 0
+IS 192 1489 1489 0 0
+IS 193 1363 1363 0 0
+IS 194 1295 1295 0 0
+IS 195 1181 1181 0 0
+IS 196 1156 1154 2 0
+IS 197 1020 1018 2 0
+IS 198 982 981 1 0
+IS 199 901 893 8 0
+IS 200 817 816 1 0
+IS 201 720 717 3 0
+IS 202 703 703 0 0
+IS 203 617 617 0 0
+IS 204 508 508 0 0
+IS 205 503 503 0 0
+IS 206 429 429 0 0
+IS 207 379 379 0 0
+IS 208 352 349 3 0
+IS 209 304 304 0 0
+IS 210 288 288 0 0
+IS 211 182 182 0 0
+IS 212 205 204 1 0
+IS 213 178 178 0 0
+IS 214 166 166 0 0
+IS 215 138 138 0 0
+IS 216 131 131 0 0
+IS 217 94 93 1 0
+IS 218 89 88 1 0
+IS 219 93 92 1 0
+IS 220 82 81 1 0
+IS 221 67 67 0 0
+IS 222 66 66 0 0
+IS 223 59 58 1 0
+IS 224 80 78 2 0
+IS 225 69 69 0 0
+IS 226 70 70 0 0
+IS 227 72 72 0 0
+IS 228 75 74 1 0
+IS 229 84 83 1 0
+IS 230 77 77 0 0
+IS 231 88 87 1 0
+IS 232 103 103 0 0
+IS 233 113 112 1 0
+IS 234 81 80 1 0
+IS 235 97 97 0 0
+IS 236 117 116 1 0
+IS 237 106 105 1 0
+IS 238 114 113 1 0
+IS 239 112 111 1 0
+IS 240 143 142 1 0
+IS 241 149 145 4 0
+IS 242 140 138 2 0
+IS 243 136 135 1 0
+IS 244 151 149 2 0
+IS 245 142 140 2 0
+IS 246 145 143 2 0
+IS 247 154 152 2 0
+IS 248 168 166 2 0
+IS 249 162 161 1 0
+IS 250 149 147 2 0
+IS 251 178 177 1 0
+IS 252 156 155 1 0
+IS 253 186 183 3 0
+IS 254 191 189 2 0
+IS 255 193 190 3 0
+IS 256 196 192 4 0
+IS 257 190 185 5 0
+IS 258 193 191 2 0
+IS 259 191 188 3 0
+IS 260 201 201 0 0
+IS 261 205 204 1 0
+IS 262 206 201 5 0
+IS 263 190 185 5 0
+IS 264 212 211 1 0
+IS 265 202 196 6 0
+IS 266 222 218 4 0
+IS 267 227 222 5 0
+IS 268 216 212 4 0
+IS 269 199 196 3 0
+IS 270 193 191 2 0
+IS 271 196 192 4 0
+IS 272 204 200 4 0
+IS 273 196 192 4 0
+IS 274 224 221 3 0
+IS 275 213 210 3 0
+IS 276 187 184 3 0
+IS 277 215 215 0 0
+IS 278 198 198 0 0
+IS 279 209 207 2 0
+IS 280 187 184 3 0
+IS 281 184 182 2 0
+IS 282 183 180 3 0
+IS 283 175 175 0 0
+IS 284 182 181 1 0
+IS 285 175 171 4 0
+IS 286 178 175 3 0
+IS 287 190 186 4 0
+IS 288 195 188 7 0
+IS 289 200 198 2 0
+IS 290 150 146 4 0
+IS 291 169 166 3 0
+IS 292 186 183 3 0
+IS 293 182 178 4 0
+IS 294 142 138 4 0
+IS 295 160 155 5 0
+IS 296 143 141 2 0
+IS 297 152 148 4 0
+IS 298 146 145 1 0
+IS 299 149 147 2 0
+IS 300 125 125 0 0
+IS 301 130 128 2 0
+IS 302 120 117 3 0
+IS 303 110 106 4 0
+IS 304 121 119 2 0
+IS 305 117 117 0 0
+IS 306 124 123 1 0
+IS 307 131 131 0 0
+IS 308 115 114 1 0
+IS 309 100 99 1 0
+IS 310 99 99 0 0
+IS 311 109 109 0 0
+IS 312 98 98 0 0
+IS 313 104 101 3 0
+IS 314 110 109 1 0
+IS 315 84 83 1 0
+IS 316 90 89 1 0
+IS 317 85 85 0 0
+IS 318 95 95 0 0
+IS 319 80 80 0 0
+IS 320 88 88 0 0
+IS 321 93 93 0 0
+IS 322 97 97 0 0
+IS 323 87 87 0 0
+IS 324 97 97 0 0
+IS 325 89 89 0 0
+IS 326 105 105 0 0
+IS 327 101 101 0 0
+IS 328 96 96 0 0
+IS 329 242 242 0 0
+IS 330 105 105 0 0
+IS 331 80 80 0 0
+IS 332 94 94 0 0
+IS 333 84 84 0 0
+IS 334 116 116 0 0
+IS 335 108 108 0 0
+IS 336 100 100 0 0
+IS 337 102 102 0 0
+IS 338 113 112 1 0
+IS 339 96 96 0 0
+IS 340 131 131 0 0
+IS 341 105 105 0 0
+IS 342 111 111 0 0
+IS 343 107 107 0 0
+IS 344 110 110 0 0
+IS 345 117 117 0 0
+IS 346 102 102 0 0
+IS 347 114 114 0 0
+IS 348 99 99 0 0
+IS 349 118 118 0 0
+IS 350 102 102 0 0
+IS 351 104 104 0 0
+IS 352 117 117 0 0
+IS 353 124 124 0 0
+IS 354 108 108 0 0
+IS 355 111 111 0 0
+IS 356 93 93 0 0
+IS 357 133 133 0 0
+IS 358 115 115 0 0
+IS 359 132 132 0 0
+IS 360 132 132 0 0
+IS 361 127 127 0 0
+IS 362 129 129 0 0
+IS 363 104 104 0 0
+IS 364 121 121 0 0
+IS 365 118 118 0 0
+IS 366 104 104 0 0
+IS 367 118 118 0 0
+IS 368 120 120 0 0
+IS 369 113 113 0 0
+IS 370 110 110 0 0
+IS 371 113 113 0 0
+IS 372 126 126 0 0
+IS 373 119 119 0 0
+IS 374 126 126 0 0
+IS 375 125 124 1 0
+IS 376 110 110 0 0
+IS 377 104 104 0 0
+IS 378 136 136 0 0
+IS 379 106 105 1 0
+IS 380 119 119 0 0
+IS 381 96 96 0 0
+IS 382 110 109 1 0
+IS 383 106 106 0 0
+IS 384 103 103 0 0
+IS 385 123 123 0 0
+IS 386 115 115 0 0
+IS 387 98 97 1 0
+IS 388 107 107 0 0
+IS 389 95 95 0 0
+IS 390 101 101 0 0
+IS 391 83 83 0 0
+IS 392 89 89 0 0
+IS 393 89 89 0 0
+IS 394 83 82 1 0
+IS 395 90 90 0 0
+IS 396 84 84 0 0
+IS 397 116 116 0 0
+IS 398 86 86 0 0
+IS 399 92 92 0 0
+IS 400 92 88 4 0
+IS 401 99 98 1 0
+IS 402 63 63 0 0
+IS 403 110 110 0 0
+IS 404 88 88 0 0
+IS 405 73 73 0 0
+IS 406 76 75 1 0
+IS 407 83 82 1 0
+IS 408 97 97 0 0
+IS 409 68 68 0 0
+IS 410 99 98 1 0
+IS 411 83 83 0 0
+IS 412 82 81 1 0
+IS 413 75 74 1 0
+IS 414 63 63 0 0
+IS 415 74 74 0 0
+IS 416 85 85 0 0
+IS 417 74 74 0 0
+IS 418 82 82 0 0
+IS 419 81 80 1 0
+IS 420 68 68 0 0
+IS 421 74 74 0 0
+IS 422 64 64 0 0
+IS 423 78 78 0 0
+IS 424 65 65 0 0
+IS 425 76 76 0 0
+IS 426 66 65 1 0
+IS 427 74 74 0 0
+IS 428 83 82 1 0
+IS 429 71 71 0 0
+IS 430 72 72 0 0
+IS 431 76 76 0 0
+IS 432 75 75 0 0
+IS 433 67 67 0 0
+IS 434 79 79 0 0
+IS 435 85 85 0 0
+IS 436 90 90 0 0
+IS 437 82 81 1 0
+IS 438 89 87 2 0
+IS 439 77 77 0 0
+IS 440 89 89 0 0
+IS 441 87 86 1 0
+IS 442 81 81 0 0
+IS 443 68 68 0 0
+IS 444 89 88 1 0
+IS 445 85 84 1 0
+IS 446 73 71 2 0
+IS 447 86 82 4 0
+IS 448 61 60 1 0
+IS 449 70 69 1 0
+IS 450 89 84 5 0
+IS 451 95 92 3 0
+IS 452 83 78 5 0
+IS 453 99 98 1 0
+IS 454 87 86 1 0
+IS 455 89 88 1 0
+IS 456 105 100 5 0
+IS 457 113 110 3 0
+IS 458 89 85 4 0
+IS 459 100 96 4 0
+IS 460 108 106 2 0
+IS 461 93 91 2 0
+IS 462 99 98 1 0
+IS 463 92 89 3 0
+IS 464 116 112 4 0
+IS 465 114 110 4 0
+IS 466 116 110 6 0
+IS 467 111 107 4 0
+IS 468 91 89 2 0
+IS 469 109 105 4 0
+IS 470 106 102 4 0
+IS 471 112 111 1 0
+IS 472 106 104 2 0
+IS 473 110 107 3 0
+IS 474 128 124 4 0
+IS 475 104 101 3 0
+IS 476 117 107 10 0
+IS 477 111 107 4 0
+IS 478 109 105 4 0
+IS 479 103 98 5 0
+IS 480 116 112 4 0
+IS 481 118 113 5 0
+IS 482 108 105 3 0
+IS 483 124 121 3 0
+IS 484 123 118 5 0
+IS 485 120 116 4 0
+IS 486 130 127 3 0
+IS 487 119 114 5 0
+IS 488 127 121 6 0
+IS 489 123 121 2 0
+IS 490 118 114 4 0
+IS 491 126 123 3 0
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+IS 7877 0 0 0 0
+IS 7878 1 1 0 0
+IS 7879 0 0 0 0
+IS 7880 0 0 0 0
+IS 7881 0 0 0 0
+IS 7882 0 0 0 0
+IS 7883 0 0 0 0
+IS 7884 0 0 0 0
+IS 7885 0 0 0 0
+IS 7886 0 0 0 0
+IS 7887 0 0 0 0
+IS 7888 0 0 0 0
+IS 7889 1 1 0 0
+IS 7890 0 0 0 0
+IS 7891 0 0 0 0
+IS 7892 1 1 0 0
+IS 7893 0 0 0 0
+IS 7894 1 1 0 0
+IS 7895 0 0 0 0
+IS 7896 1 1 0 0
+IS 7897 0 0 0 0
+IS 7898 1 1 0 0
+IS 7899 0 0 0 0
+IS 7900 0 0 0 0
+IS 7901 0 0 0 0
+IS 7902 0 0 0 0
+IS 7903 0 0 0 0
+IS 7904 1 1 0 0
+IS 7905 0 0 0 0
+IS 7906 0 0 0 0
+IS 7907 0 0 0 0
+IS 7908 0 0 0 0
+IS 7909 0 0 0 0
+IS 7910 0 0 0 0
+IS 7911 0 0 0 0
+IS 7912 0 0 0 0
+IS 7913 0 0 0 0
+IS 7914 0 0 0 0
+IS 7915 0 0 0 0
+IS 7916 0 0 0 0
+IS 7917 0 0 0 0
+IS 7918 0 0 0 0
+IS 7919 0 0 0 0
+IS 7920 0 0 0 0
+IS 7921 0 0 0 0
+IS 7922 0 0 0 0
+IS 7923 0 0 0 0
+IS 7924 0 0 0 0
+IS 7925 0 0 0 0
+IS 7926 0 0 0 0
+IS 7927 0 0 0 0
+IS 7928 0 0 0 0
+IS 7929 0 0 0 0
+IS 7930 0 0 0 0
+IS 7931 0 0 0 0
+IS 7932 0 0 0 0
+IS 7933 0 0 0 0
+IS 7934 0 0 0 0
+IS 7935 0 0 0 0
+IS 7936 0 0 0 0
+IS 7937 0 0 0 0
+IS 7938 0 0 0 0
+IS 7939 0 0 0 0
+IS 7940 0 0 0 0
+IS 7941 0 0 0 0
+IS 7942 0 0 0 0
+IS 7943 0 0 0 0
+IS 7944 1 1 0 0
+IS 7945 0 0 0 0
+IS 7946 0 0 0 0
+IS 7947 0 0 0 0
+IS 7948 0 0 0 0
+IS 7949 0 0 0 0
+IS 7950 0 0 0 0
+IS 7951 0 0 0 0
+IS 7952 0 0 0 0
+IS 7953 0 0 0 0
+IS 7954 0 0 0 0
+IS 7955 0 0 0 0
+IS 7956 0 0 0 0
+IS 7957 0 0 0 0
+IS 7958 0 0 0 0
+IS 7959 1 1 0 0
+IS 7960 1 1 0 0
+IS 7961 0 0 0 0
+IS 7962 0 0 0 0
+IS 7963 0 0 0 0
+IS 7964 0 0 0 0
+IS 7965 0 0 0 0
+IS 7966 0 0 0 0
+IS 7967 0 0 0 0
+IS 7968 0 0 0 0
+IS 7969 1 1 0 0
+IS 7970 0 0 0 0
+IS 7971 0 0 0 0
+IS 7972 0 0 0 0
+IS 7973 0 0 0 0
+IS 7974 0 0 0 0
+IS 7975 0 0 0 0
+IS 7976 0 0 0 0
+IS 7977 1 1 0 0
+IS 7978 0 0 0 0
+IS 7979 0 0 0 0
+IS 7980 0 0 0 0
+IS 7981 0 0 0 0
+IS 7982 0 0 0 0
+IS 7983 0 0 0 0
+IS 7984 0 0 0 0
+IS 7985 1 1 0 0
+IS 7986 0 0 0 0
+IS 7987 0 0 0 0
+IS 7988 1 1 0 0
+IS 7989 0 0 0 0
+IS 7990 0 0 0 0
+IS 7991 1 1 0 0
+IS 7992 0 0 0 0
+IS 7993 1 1 0 0
+IS 7994 1 1 0 0
+IS 7995 0 0 0 0
+IS 7996 0 0 0 0
+IS 7997 0 0 0 0
+IS 7998 2 2 0 0
+IS 7999 3573 3553 11 9
+# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
+RL 101 641821
+# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
+ID 1 4895 3362
+ID 2 826 512
+# 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 0 3 0 0
+IC 3 8 9 2 2
+IC 4 14 13 33 36
+IC 5 58 65 31 35
+IC 6 58 67 19 20
+IC 7 31 30 14 13
+IC 8 32 32 12 13
+IC 9 27 41 15 13
+IC 10 15 21 25 17
+IC 11 29 24 27 22
+IC 12 20 18 19 18
+IC 13 31 23 29 21
+IC 14 25 32 15 16
+IC 15 33 29 22 20
+IC 16 24 15 23 23
+IC 17 24 20 25 22
+IC 18 27 30 20 35
+IC 19 30 39 35 47
+IC 20 30 25 38 22
+IC 21 36 29 30 25
+IC 22 31 23 26 24
+IC 23 25 43 32 29
+IC 24 31 35 20 19
+IC 25 30 33 17 13
+IC 26 39 28 16 15
+IC 27 50 56 24 18
+IC 28 31 26 10 17
+IC 29 34 31 21 20
+IC 30 26 28 25 19
+IC 31 27 27 22 20
+IC 32 28 37 20 22
+IC 33 24 24 25 10
+IC 34 22 32 24 23
+IC 35 36 25 19 15
+IC 36 26 23 15 29
+IC 37 15 20 30 29
+IC 38 25 32 18 21
+IC 39 20 23 25 24
+IC 40 31 47 26 21
+IC 41 23 29 29 29
+IC 42 27 24 16 17
+IC 43 25 29 21 29
+IC 44 27 32 19 13
+IC 45 36 40 19 26
+IC 46 24 29 21 24
+IC 47 33 28 16 14
+IC 48 41 38 10 16
+IC 49 32 39 22 24
+IC 50 34 29 18 15
+IC 51 15 21 31 28
+IC 52 40 37 28 13
+IC 53 26 21 24 19
+IC 54 20 21 12 22
+IC 55 29 28 17 21
+IC 56 22 20 13 15
+IC 57 23 15 33 30
+IC 58 28 23 19 19
+IC 59 43 39 21 20
+IC 60 38 39 20 21
+IC 61 25 23 21 24
+IC 62 29 21 15 18
+IC 63 39 25 17 14
+IC 64 27 23 11 17
+IC 65 20 35 26 31
+IC 66 23 30 24 13
+IC 67 35 29 22 29
+IC 68 20 24 21 27
+IC 69 28 27 21 14
+IC 70 41 28 21 13
+IC 71 36 35 15 22
+IC 72 25 24 15 18
+IC 73 15 27 18 15
+IC 74 24 27 22 19
+IC 75 28 38 18 22
+IC 76 29 46 24 16
+IC 77 28 48 22 14
+IC 78 23 21 15 28
+IC 79 30 34 26 23
+IC 80 34 30 29 19
+IC 81 31 32 14 17
+IC 82 33 28 20 15
+IC 83 37 20 28 9
+IC 84 27 26 19 12
+IC 85 31 25 16 14
+IC 86 22 26 14 13
+IC 87 30 23 20 23
+IC 88 33 24 8 13
+IC 89 31 26 17 24
+IC 90 34 30 11 19
+IC 91 34 17 16 17
+IC 92 29 29 14 16
+IC 93 23 29 9 9
+IC 94 18 40 13 18
+IC 95 28 48 18 12
+IC 96 42 49 26 27
+IC 97 48 64 36 35
+IC 98 25 28 1 1
+IC 99 10 9 0 0
+# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
+COV [1-1] 1 639227
+COV [2-2] 2 385861
+COV [3-3] 3 200311
+COV [4-4] 4 140538
+COV [5-5] 5 100920
+COV [6-6] 6 78198
+COV [7-7] 7 63261
+COV [8-8] 8 53571
+COV [9-9] 9 45160
+COV [10-10] 10 40242
+COV [11-11] 11 35638
+COV [12-12] 12 32108
+COV [13-13] 13 28874
+COV [14-14] 14 26269
+COV [15-15] 15 24346
+COV [16-16] 16 22055
+COV [17-17] 17 19763
+COV [18-18] 18 18165
+COV [19-19] 19 17543
+COV [20-20] 20 16315
+COV [21-21] 21 16254
+COV [22-22] 22 14587
+COV [23-23] 23 13217
+COV [24-24] 24 12790
+COV [25-25] 25 12207
+COV [26-26] 26 11415
+COV [27-27] 27 10704
+COV [28-28] 28 9967
+COV [29-29] 29 9972
+COV [30-30] 30 9503
+COV [31-31] 31 9486
+COV [32-32] 32 8859
+COV [33-33] 33 8810
+COV [34-34] 34 8445
+COV [35-35] 35 7811
+COV [36-36] 36 7790
+COV [37-37] 37 7349
+COV [38-38] 38 7298
+COV [39-39] 39 6735
+COV [40-40] 40 6474
+COV [41-41] 41 6543
+COV [42-42] 42 6136
+COV [43-43] 43 6119
+COV [44-44] 44 5783
+COV [45-45] 45 5411
+COV [46-46] 46 5548
+COV [47-47] 47 5121
+COV [48-48] 48 5074
+COV [49-49] 49 4915
+COV [50-50] 50 4760
+COV [51-51] 51 4813
+COV [52-52] 52 4591
+COV [53-53] 53 4309
+COV [54-54] 54 3935
+COV [55-55] 55 4026
+COV [56-56] 56 3923
+COV [57-57] 57 3709
+COV [58-58] 58 3561
+COV [59-59] 59 3609
+COV [60-60] 60 3413
+COV [61-61] 61 3414
+COV [62-62] 62 3233
+COV [63-63] 63 3285
+COV [64-64] 64 3172
+COV [65-65] 65 3188
+COV [66-66] 66 2992
+COV [67-67] 67 2840
+COV [68-68] 68 3046
+COV [69-69] 69 2891
+COV [70-70] 70 2646
+COV [71-71] 71 2584
+COV [72-72] 72 2724
+COV [73-73] 73 2563
+COV [74-74] 74 2439
+COV [75-75] 75 2286
+COV [76-76] 76 2219
+COV [77-77] 77 2212
+COV [78-78] 78 2172
+COV [79-79] 79 2027
+COV [80-80] 80 1978
+COV [81-81] 81 2120
+COV [82-82] 82 2141
+COV [83-83] 83 1983
+COV [84-84] 84 2075
+COV [85-85] 85 1855
+COV [86-86] 86 1761
+COV [87-87] 87 1824
+COV [88-88] 88 1805
+COV [89-89] 89 1663
+COV [90-90] 90 1661
+COV [91-91] 91 1671
+COV [92-92] 92 1618
+COV [93-93] 93 1675
+COV [94-94] 94 1480
+COV [95-95] 95 1460
+COV [96-96] 96 1400
+COV [97-97] 97 1447
+COV [98-98] 98 1402
+COV [99-99] 99 1484
+COV [100-100] 100 1364
+COV [101-101] 101 1364
+COV [102-102] 102 1435
+COV [103-103] 103 1373
+COV [104-104] 104 1299
+COV [105-105] 105 1267
+COV [106-106] 106 1208
+COV [107-107] 107 1157
+COV [108-108] 108 1171
+COV [109-109] 109 1115
+COV [110-110] 110 1089
+COV [111-111] 111 1109
+COV [112-112] 112 1057
+COV [113-113] 113 1018
+COV [114-114] 114 1011
+COV [115-115] 115 976
+COV [116-116] 116 970
+COV [117-117] 117 887
+COV [118-118] 118 889
+COV [119-119] 119 876
+COV [120-120] 120 914
+COV [121-121] 121 835
+COV [122-122] 122 819
+COV [123-123] 123 751
+COV [124-124] 124 753
+COV [125-125] 125 766
+COV [126-126] 126 733
+COV [127-127] 127 650
+COV [128-128] 128 737
+COV [129-129] 129 745
+COV [130-130] 130 636
+COV [131-131] 131 643
+COV [132-132] 132 612
+COV [133-133] 133 668
+COV [134-134] 134 668
+COV [135-135] 135 645
+COV [136-136] 136 570
+COV [137-137] 137 587
+COV [138-138] 138 571
+COV [139-139] 139 616
+COV [140-140] 140 618
+COV [141-141] 141 571
+COV [142-142] 142 582
+COV [143-143] 143 535
+COV [144-144] 144 547
+COV [145-145] 145 519
+COV [146-146] 146 500
+COV [147-147] 147 500
+COV [148-148] 148 483
+COV [149-149] 149 463
+COV [150-150] 150 494
+COV [151-151] 151 474
+COV [152-152] 152 445
+COV [153-153] 153 477
+COV [154-154] 154 457
+COV [155-155] 155 427
+COV [156-156] 156 444
+COV [157-157] 157 436
+COV [158-158] 158 393
+COV [159-159] 159 382
+COV [160-160] 160 400
+COV [161-161] 161 436
+COV [162-162] 162 395
+COV [163-163] 163 387
+COV [164-164] 164 397
+COV [165-165] 165 419
+COV [166-166] 166 404
+COV [167-167] 167 393
+COV [168-168] 168 413
+COV [169-169] 169 415
+COV [170-170] 170 358
+COV [171-171] 171 335
+COV [172-172] 172 328
+COV [173-173] 173 334
+COV [174-174] 174 286
+COV [175-175] 175 315
+COV [176-176] 176 290
+COV [177-177] 177 305
+COV [178-178] 178 290
+COV [179-179] 179 285
+COV [180-180] 180 303
+COV [181-181] 181 251
+COV [182-182] 182 261
+COV [183-183] 183 265
+COV [184-184] 184 269
+COV [185-185] 185 242
+COV [186-186] 186 301
+COV [187-187] 187 284
+COV [188-188] 188 291
+COV [189-189] 189 293
+COV [190-190] 190 225
+COV [191-191] 191 255
+COV [192-192] 192 242
+COV [193-193] 193 247
+COV [194-194] 194 245
+COV [195-195] 195 205
+COV [196-196] 196 235
+COV [197-197] 197 236
+COV [198-198] 198 213
+COV [199-199] 199 217
+COV [200-200] 200 215
+COV [201-201] 201 175
+COV [202-202] 202 182
+COV [203-203] 203 206
+COV [204-204] 204 181
+COV [205-205] 205 212
+COV [206-206] 206 210
+COV [207-207] 207 212
+COV [208-208] 208 163
+COV [209-209] 209 216
+COV [210-210] 210 174
+COV [211-211] 211 195
+COV [212-212] 212 161
+COV [213-213] 213 182
+COV [214-214] 214 174
+COV [215-215] 215 147
+COV [216-216] 216 176
+COV [217-217] 217 185
+COV [218-218] 218 143
+COV [219-219] 219 154
+COV [220-220] 220 137
+COV [221-221] 221 159
+COV [222-222] 222 209
+COV [223-223] 223 168
+COV [224-224] 224 152
+COV [225-225] 225 161
+COV [226-226] 226 162
+COV [227-227] 227 177
+COV [228-228] 228 136
+COV [229-229] 229 127
+COV [230-230] 230 149
+COV [231-231] 231 151
+COV [232-232] 232 108
+COV [233-233] 233 139
+COV [234-234] 234 150
+COV [235-235] 235 153
+COV [236-236] 236 120
+COV [237-237] 237 128
+COV [238-238] 238 142
+COV [239-239] 239 113
+COV [240-240] 240 130
+COV [241-241] 241 112
+COV [242-242] 242 134
+COV [243-243] 243 145
+COV [244-244] 244 111
+COV [245-245] 245 174
+COV [246-246] 246 166
+COV [247-247] 247 144
+COV [248-248] 248 186
+COV [249-249] 249 130
+COV [250-250] 250 107
+COV [251-251] 251 153
+COV [252-252] 252 134
+COV [253-253] 253 135
+COV [254-254] 254 131
+COV [255-255] 255 110
+COV [256-256] 256 117
+COV [257-257] 257 113
+COV [258-258] 258 131
+COV [259-259] 259 107
+COV [260-260] 260 104
+COV [261-261] 261 131
+COV [262-262] 262 112
+COV [263-263] 263 128
+COV [264-264] 264 97
+COV [265-265] 265 129
+COV [266-266] 266 132
+COV [267-267] 267 95
+COV [268-268] 268 98
+COV [269-269] 269 115
+COV [270-270] 270 105
+COV [271-271] 271 121
+COV [272-272] 272 109
+COV [273-273] 273 115
+COV [274-274] 274 101
+COV [275-275] 275 97
+COV [276-276] 276 134
+COV [277-277] 277 112
+COV [278-278] 278 134
+COV [279-279] 279 133
+COV [280-280] 280 113
+COV [281-281] 281 104
+COV [282-282] 282 127
+COV [283-283] 283 126
+COV [284-284] 284 115
+COV [285-285] 285 115
+COV [286-286] 286 116
+COV [287-287] 287 99
+COV [288-288] 288 109
+COV [289-289] 289 107
+COV [290-290] 290 106
+COV [291-291] 291 96
+COV [292-292] 292 92
+COV [293-293] 293 93
+COV [294-294] 294 98
+COV [295-295] 295 95
+COV [296-296] 296 98
+COV [297-297] 297 116
+COV [298-298] 298 104
+COV [299-299] 299 108
+COV [300-300] 300 107
+COV [301-301] 301 106
+COV [302-302] 302 105
+COV [303-303] 303 114
+COV [304-304] 304 116
+COV [305-305] 305 91
+COV [306-306] 306 107
+COV [307-307] 307 114
+COV [308-308] 308 109
+COV [309-309] 309 111
+COV [310-310] 310 101
+COV [311-311] 311 132
+COV [312-312] 312 115
+COV [313-313] 313 120
+COV [314-314] 314 86
+COV [315-315] 315 109
+COV [316-316] 316 125
+COV [317-317] 317 126
+COV [318-318] 318 111
+COV [319-319] 319 106
+COV [320-320] 320 110
+COV [321-321] 321 107
+COV [322-322] 322 91
+COV [323-323] 323 100
+COV [324-324] 324 99
+COV [325-325] 325 100
+COV [326-326] 326 97
+COV [327-327] 327 122
+COV [328-328] 328 97
+COV [329-329] 329 142
+COV [330-330] 330 109
+COV [331-331] 331 114
+COV [332-332] 332 105
+COV [333-333] 333 109
+COV [334-334] 334 107
+COV [335-335] 335 97
+COV [336-336] 336 108
+COV [337-337] 337 86
+COV [338-338] 338 101
+COV [339-339] 339 95
+COV [340-340] 340 90
+COV [341-341] 341 93
+COV [342-342] 342 84
+COV [343-343] 343 92
+COV [344-344] 344 96
+COV [345-345] 345 105
+COV [346-346] 346 88
+COV [347-347] 347 90
+COV [348-348] 348 84
+COV [349-349] 349 85
+COV [350-350] 350 73
+COV [351-351] 351 99
+COV [352-352] 352 104
+COV [353-353] 353 95
+COV [354-354] 354 95
+COV [355-355] 355 95
+COV [356-356] 356 98
+COV [357-357] 357 125
+COV [358-358] 358 72
+COV [359-359] 359 71
+COV [360-360] 360 84
+COV [361-361] 361 84
+COV [362-362] 362 75
+COV [363-363] 363 95
+COV [364-364] 364 74
+COV [365-365] 365 78
+COV [366-366] 366 82
+COV [367-367] 367 81
+COV [368-368] 368 67
+COV [369-369] 369 79
+COV [370-370] 370 81
+COV [371-371] 371 74
+COV [372-372] 372 85
+COV [373-373] 373 72
+COV [374-374] 374 76
+COV [375-375] 375 62
+COV [376-376] 376 81
+COV [377-377] 377 82
+COV [378-378] 378 74
+COV [379-379] 379 55
+COV [380-380] 380 71
+COV [381-381] 381 80
+COV [382-382] 382 74
+COV [383-383] 383 69
+COV [384-384] 384 65
+COV [385-385] 385 78
+COV [386-386] 386 80
+COV [387-387] 387 72
+COV [388-388] 388 67
+COV [389-389] 389 81
+COV [390-390] 390 71
+COV [391-391] 391 53
+COV [392-392] 392 67
+COV [393-393] 393 49
+COV [394-394] 394 78
+COV [395-395] 395 85
+COV [396-396] 396 65
+COV [397-397] 397 69
+COV [398-398] 398 62
+COV [399-399] 399 68
+COV [400-400] 400 68
+COV [401-401] 401 56
+COV [402-402] 402 64
+COV [403-403] 403 45
+COV [404-404] 404 64
+COV [405-405] 405 64
+COV [406-406] 406 76
+COV [407-407] 407 82
+COV [408-408] 408 76
+COV [409-409] 409 69
+COV [410-410] 410 63
+COV [411-411] 411 66
+COV [412-412] 412 79
+COV [413-413] 413 56
+COV [414-414] 414 62
+COV [415-415] 415 63
+COV [416-416] 416 75
+COV [417-417] 417 61
+COV [418-418] 418 53
+COV [419-419] 419 57
+COV [420-420] 420 59
+COV [421-421] 421 50
+COV [422-422] 422 63
+COV [423-423] 423 63
+COV [424-424] 424 41
+COV [425-425] 425 71
+COV [426-426] 426 70
+COV [427-427] 427 59
+COV [428-428] 428 54
+COV [429-429] 429 52
+COV [430-430] 430 54
+COV [431-431] 431 56
+COV [432-432] 432 58
+COV [433-433] 433 59
+COV [434-434] 434 55
+COV [435-435] 435 43
+COV [436-436] 436 52
+COV [437-437] 437 50
+COV [438-438] 438 57
+COV [439-439] 439 66
+COV [440-440] 440 70
+COV [441-441] 441 55
+COV [442-442] 442 68
+COV [443-443] 443 61
+COV [444-444] 444 63
+COV [445-445] 445 64
+COV [446-446] 446 73
+COV [447-447] 447 61
+COV [448-448] 448 54
+COV [449-449] 449 56
+COV [450-450] 450 46
+COV [451-451] 451 69
+COV [452-452] 452 64
+COV [453-453] 453 53
+COV [454-454] 454 68
+COV [455-455] 455 65
+COV [456-456] 456 52
+COV [457-457] 457 68
+COV [458-458] 458 70
+COV [459-459] 459 59
+COV [460-460] 460 52
+COV [461-461] 461 60
+COV [462-462] 462 37
+COV [463-463] 463 59
+COV [464-464] 464 42
+COV [465-465] 465 70
+COV [466-466] 466 59
+COV [467-467] 467 44
+COV [468-468] 468 42
+COV [469-469] 469 52
+COV [470-470] 470 57
+COV [471-471] 471 75
+COV [472-472] 472 58
+COV [473-473] 473 48
+COV [474-474] 474 65
+COV [475-475] 475 61
+COV [476-476] 476 47
+COV [477-477] 477 47
+COV [478-478] 478 52
+COV [479-479] 479 43
+COV [480-480] 480 57
+COV [481-481] 481 45
+COV [482-482] 482 58
+COV [483-483] 483 63
+COV [484-484] 484 62
+COV [485-485] 485 57
+COV [486-486] 486 67
+COV [487-487] 487 65
+COV [488-488] 488 63
+COV [489-489] 489 67
+COV [490-490] 490 63
+COV [491-491] 491 62
+COV [492-492] 492 72
+COV [493-493] 493 62
+COV [494-494] 494 60
+COV [495-495] 495 60
+COV [496-496] 496 61
+COV [497-497] 497 70
+COV [498-498] 498 57
+COV [499-499] 499 62
+COV [500-500] 500 59
+COV [501-501] 501 51
+COV [502-502] 502 55
+COV [503-503] 503 59
+COV [504-504] 504 61
+COV [505-505] 505 56
+COV [506-506] 506 57
+COV [507-507] 507 57
+COV [508-508] 508 45
+COV [509-509] 509 62
+COV [510-510] 510 65
+COV [511-511] 511 40
+COV [512-512] 512 69
+COV [513-513] 513 64
+COV [514-514] 514 37
+COV [515-515] 515 57
+COV [516-516] 516 47
+COV [517-517] 517 38
+COV [518-518] 518 69
+COV [519-519] 519 38
+COV [520-520] 520 58
+COV [521-521] 521 51
+COV [522-522] 522 40
+COV [523-523] 523 47
+COV [524-524] 524 40
+COV [525-525] 525 49
+COV [526-526] 526 47
+COV [527-527] 527 38
+COV [528-528] 528 44
+COV [529-529] 529 55
+COV [530-530] 530 44
+COV [531-531] 531 32
+COV [532-532] 532 43
+COV [533-533] 533 41
+COV [534-534] 534 36
+COV [535-535] 535 46
+COV [536-536] 536 41
+COV [537-537] 537 54
+COV [538-538] 538 39
+COV [539-539] 539 49
+COV [540-540] 540 36
+COV [541-541] 541 34
+COV [542-542] 542 39
+COV [543-543] 543 47
+COV [544-544] 544 33
+COV [545-545] 545 29
+COV [546-546] 546 34
+COV [547-547] 547 36
+COV [548-548] 548 29
+COV [549-549] 549 34
+COV [550-550] 550 33
+COV [551-551] 551 70
+COV [552-552] 552 32
+COV [553-553] 553 45
+COV [554-554] 554 38
+COV [555-555] 555 31
+COV [556-556] 556 43
+COV [557-557] 557 38
+COV [558-558] 558 42
+COV [559-559] 559 29
+COV [560-560] 560 26
+COV [561-561] 561 23
+COV [562-562] 562 35
+COV [563-563] 563 39
+COV [564-564] 564 28
+COV [565-565] 565 30
+COV [566-566] 566 29
+COV [567-567] 567 30
+COV [568-568] 568 42
+COV [569-569] 569 42
+COV [570-570] 570 30
+COV [571-571] 571 23
+COV [572-572] 572 26
+COV [573-573] 573 37
+COV [574-574] 574 34
+COV [575-575] 575 35
+COV [576-576] 576 39
+COV [577-577] 577 34
+COV [578-578] 578 32
+COV [579-579] 579 28
+COV [580-580] 580 29
+COV [581-581] 581 25
+COV [582-582] 582 29
+COV [583-583] 583 43
+COV [584-584] 584 30
+COV [585-585] 585 34
+COV [586-586] 586 29
+COV [587-587] 587 29
+COV [588-588] 588 35
+COV [589-589] 589 27
+COV [590-590] 590 26
+COV [591-591] 591 25
+COV [592-592] 592 34
+COV [593-593] 593 29
+COV [594-594] 594 21
+COV [595-595] 595 22
+COV [596-596] 596 28
+COV [597-597] 597 33
+COV [598-598] 598 40
+COV [599-599] 599 28
+COV [600-600] 600 29
+COV [601-601] 601 39
+COV [602-602] 602 36
+COV [603-603] 603 28
+COV [604-604] 604 27
+COV [605-605] 605 27
+COV [606-606] 606 32
+COV [607-607] 607 24
+COV [608-608] 608 40
+COV [609-609] 609 36
+COV [610-610] 610 37
+COV [611-611] 611 29
+COV [612-612] 612 35
+COV [613-613] 613 30
+COV [614-614] 614 41
+COV [615-615] 615 36
+COV [616-616] 616 42
+COV [617-617] 617 35
+COV [618-618] 618 27
+COV [619-619] 619 32
+COV [620-620] 620 33
+COV [621-621] 621 27
+COV [622-622] 622 43
+COV [623-623] 623 34
+COV [624-624] 624 39
+COV [625-625] 625 36
+COV [626-626] 626 31
+COV [627-627] 627 42
+COV [628-628] 628 29
+COV [629-629] 629 38
+COV [630-630] 630 32
+COV [631-631] 631 30
+COV [632-632] 632 38
+COV [633-633] 633 39
+COV [634-634] 634 26
+COV [635-635] 635 30
+COV [636-636] 636 23
+COV [637-637] 637 34
+COV [638-638] 638 23
+COV [639-639] 639 28
+COV [640-640] 640 36
+COV [641-641] 641 30
+COV [642-642] 642 43
+COV [643-643] 643 37
+COV [644-644] 644 36
+COV [645-645] 645 32
+COV [646-646] 646 39
+COV [647-647] 647 29
+COV [648-648] 648 37
+COV [649-649] 649 40
+COV [650-650] 650 31
+COV [651-651] 651 32
+COV [652-652] 652 24
+COV [653-653] 653 19
+COV [654-654] 654 28
+COV [655-655] 655 29
+COV [656-656] 656 27
+COV [657-657] 657 33
+COV [658-658] 658 28
+COV [659-659] 659 18
+COV [660-660] 660 25
+COV [661-661] 661 33
+COV [662-662] 662 29
+COV [663-663] 663 31
+COV [664-664] 664 26
+COV [665-665] 665 35
+COV [666-666] 666 21
+COV [667-667] 667 27
+COV [668-668] 668 26
+COV [669-669] 669 22
+COV [670-670] 670 30
+COV [671-671] 671 31
+COV [672-672] 672 21
+COV [673-673] 673 34
+COV [674-674] 674 40
+COV [675-675] 675 35
+COV [676-676] 676 36
+COV [677-677] 677 32
+COV [678-678] 678 40
+COV [679-679] 679 33
+COV [680-680] 680 32
+COV [681-681] 681 23
+COV [682-682] 682 32
+COV [683-683] 683 27
+COV [684-684] 684 32
+COV [685-685] 685 30
+COV [686-686] 686 31
+COV [687-687] 687 26
+COV [688-688] 688 28
+COV [689-689] 689 31
+COV [690-690] 690 22
+COV [691-691] 691 27
+COV [692-692] 692 22
+COV [693-693] 693 27
+COV [694-694] 694 27
+COV [695-695] 695 25
+COV [696-696] 696 25
+COV [697-697] 697 32
+COV [698-698] 698 25
+COV [699-699] 699 27
+COV [700-700] 700 27
+COV [701-701] 701 27
+COV [702-702] 702 24
+COV [703-703] 703 29
+COV [704-704] 704 22
+COV [705-705] 705 26
+COV [706-706] 706 16
+COV [707-707] 707 23
+COV [708-708] 708 23
+COV [709-709] 709 23
+COV [710-710] 710 28
+COV [711-711] 711 26
+COV [712-712] 712 28
+COV [713-713] 713 39
+COV [714-714] 714 22
+COV [715-715] 715 29
+COV [716-716] 716 16
+COV [717-717] 717 18
+COV [718-718] 718 26
+COV [719-719] 719 22
+COV [720-720] 720 21
+COV [721-721] 721 20
+COV [722-722] 722 30
+COV [723-723] 723 26
+COV [724-724] 724 25
+COV [725-725] 725 22
+COV [726-726] 726 24
+COV [727-727] 727 30
+COV [728-728] 728 21
+COV [729-729] 729 26
+COV [730-730] 730 20
+COV [731-731] 731 30
+COV [732-732] 732 27
+COV [733-733] 733 28
+COV [734-734] 734 25
+COV [735-735] 735 22
+COV [736-736] 736 32
+COV [737-737] 737 36
+COV [738-738] 738 32
+COV [739-739] 739 26
+COV [740-740] 740 22
+COV [741-741] 741 21
+COV [742-742] 742 18
+COV [743-743] 743 28
+COV [744-744] 744 28
+COV [745-745] 745 21
+COV [746-746] 746 16
+COV [747-747] 747 30
+COV [748-748] 748 28
+COV [749-749] 749 22
+COV [750-750] 750 21
+COV [751-751] 751 30
+COV [752-752] 752 12
+COV [753-753] 753 24
+COV [754-754] 754 28
+COV [755-755] 755 19
+COV [756-756] 756 36
+COV [757-757] 757 27
+COV [758-758] 758 26
+COV [759-759] 759 29
+COV [760-760] 760 26
+COV [761-761] 761 24
+COV [762-762] 762 21
+COV [763-763] 763 18
+COV [764-764] 764 19
+COV [765-765] 765 26
+COV [766-766] 766 21
+COV [767-767] 767 17
+COV [768-768] 768 26
+COV [769-769] 769 18
+COV [770-770] 770 14
+COV [771-771] 771 18
+COV [772-772] 772 20
+COV [773-773] 773 21
+COV [774-774] 774 20
+COV [775-775] 775 16
+COV [776-776] 776 17
+COV [777-777] 777 24
+COV [778-778] 778 12
+COV [779-779] 779 19
+COV [780-780] 780 14
+COV [781-781] 781 25
+COV [782-782] 782 21
+COV [783-783] 783 27
+COV [784-784] 784 21
+COV [785-785] 785 19
+COV [786-786] 786 23
+COV [787-787] 787 19
+COV [788-788] 788 24
+COV [789-789] 789 15
+COV [790-790] 790 17
+COV [791-791] 791 16
+COV [792-792] 792 23
+COV [793-793] 793 19
+COV [794-794] 794 17
+COV [795-795] 795 13
+COV [796-796] 796 18
+COV [797-797] 797 23
+COV [798-798] 798 22
+COV [799-799] 799 22
+COV [800-800] 800 13
+COV [801-801] 801 13
+COV [802-802] 802 13
+COV [803-803] 803 13
+COV [804-804] 804 23
+COV [805-805] 805 20
+COV [806-806] 806 17
+COV [807-807] 807 16
+COV [808-808] 808 11
+COV [809-809] 809 23
+COV [810-810] 810 17
+COV [811-811] 811 10
+COV [812-812] 812 17
+COV [813-813] 813 12
+COV [814-814] 814 14
+COV [815-815] 815 14
+COV [816-816] 816 14
+COV [817-817] 817 24
+COV [818-818] 818 17
+COV [819-819] 819 21
+COV [820-820] 820 21
+COV [821-821] 821 10
+COV [822-822] 822 20
+COV [823-823] 823 19
+COV [824-824] 824 17
+COV [825-825] 825 18
+COV [826-826] 826 21
+COV [827-827] 827 24
+COV [828-828] 828 14
+COV [829-829] 829 21
+COV [830-830] 830 25
+COV [831-831] 831 18
+COV [832-832] 832 23
+COV [833-833] 833 19
+COV [834-834] 834 17
+COV [835-835] 835 19
+COV [836-836] 836 19
+COV [837-837] 837 20
+COV [838-838] 838 24
+COV [839-839] 839 20
+COV [840-840] 840 16
+COV [841-841] 841 21
+COV [842-842] 842 20
+COV [843-843] 843 17
+COV [844-844] 844 18
+COV [845-845] 845 14
+COV [846-846] 846 16
+COV [847-847] 847 11
+COV [848-848] 848 17
+COV [849-849] 849 12
+COV [850-850] 850 18
+COV [851-851] 851 22
+COV [852-852] 852 15
+COV [853-853] 853 17
+COV [854-854] 854 16
+COV [855-855] 855 18
+COV [856-856] 856 11
+COV [857-857] 857 7
+COV [858-858] 858 6
+COV [859-859] 859 23
+COV [860-860] 860 14
+COV [861-861] 861 10
+COV [862-862] 862 19
+COV [863-863] 863 8
+COV [864-864] 864 14
+COV [865-865] 865 10
+COV [866-866] 866 9
+COV [867-867] 867 11
+COV [868-868] 868 16
+COV [869-869] 869 8
+COV [870-870] 870 9
+COV [871-871] 871 9
+COV [872-872] 872 13
+COV [873-873] 873 6
+COV [874-874] 874 15
+COV [875-875] 875 5
+COV [876-876] 876 6
+COV [877-877] 877 8
+COV [878-878] 878 8
+COV [879-879] 879 14
+COV [880-880] 880 8
+COV [881-881] 881 20
+COV [882-882] 882 15
+COV [883-883] 883 12
+COV [884-884] 884 14
+COV [885-885] 885 14
+COV [886-886] 886 12
+COV [887-887] 887 11
+COV [888-888] 888 13
+COV [889-889] 889 11
+COV [890-890] 890 6
+COV [891-891] 891 11
+COV [892-892] 892 9
+COV [893-893] 893 9
+COV [894-894] 894 12
+COV [895-895] 895 16
+COV [896-896] 896 10
+COV [897-897] 897 8
+COV [898-898] 898 8
+COV [899-899] 899 11
+COV [900-900] 900 7
+COV [901-901] 901 15
+COV [902-902] 902 13
+COV [903-903] 903 17
+COV [904-904] 904 9
+COV [905-905] 905 8
+COV [906-906] 906 13
+COV [907-907] 907 10
+COV [908-908] 908 8
+COV [909-909] 909 13
+COV [910-910] 910 7
+COV [911-911] 911 9
+COV [912-912] 912 8
+COV [913-913] 913 9
+COV [914-914] 914 8
+COV [915-915] 915 9
+COV [916-916] 916 6
+COV [917-917] 917 9
+COV [918-918] 918 7
+COV [919-919] 919 9
+COV [920-920] 920 8
+COV [921-921] 921 13
+COV [922-922] 922 5
+COV [923-923] 923 5
+COV [924-924] 924 5
+COV [925-925] 925 7
+COV [926-926] 926 10
+COV [927-927] 927 6
+COV [928-928] 928 21
+COV [929-929] 929 10
+COV [930-930] 930 10
+COV [931-931] 931 7
+COV [932-932] 932 12
+COV [933-933] 933 14
+COV [934-934] 934 14
+COV [935-935] 935 7
+COV [936-936] 936 12
+COV [937-937] 937 13
+COV [938-938] 938 10
+COV [939-939] 939 12
+COV [940-940] 940 18
+COV [941-941] 941 11
+COV [942-942] 942 10
+COV [943-943] 943 6
+COV [944-944] 944 12
+COV [945-945] 945 12
+COV [946-946] 946 8
+COV [947-947] 947 12
+COV [948-948] 948 10
+COV [949-949] 949 5
+COV [950-950] 950 9
+COV [951-951] 951 16
+COV [952-952] 952 13
+COV [953-953] 953 15
+COV [954-954] 954 15
+COV [955-955] 955 8
+COV [956-956] 956 15
+COV [957-957] 957 18
+COV [958-958] 958 9
+COV [959-959] 959 21
+COV [960-960] 960 14
+COV [961-961] 961 17
+COV [962-962] 962 9
+COV [963-963] 963 14
+COV [964-964] 964 6
+COV [965-965] 965 5
+COV [966-966] 966 13
+COV [967-967] 967 12
+COV [968-968] 968 13
+COV [969-969] 969 10
+COV [970-970] 970 13
+COV [971-971] 971 8
+COV [972-972] 972 13
+COV [973-973] 973 12
+COV [974-974] 974 14
+COV [975-975] 975 9
+COV [976-976] 976 12
+COV [977-977] 977 4
+COV [978-978] 978 14
+COV [979-979] 979 6
+COV [980-980] 980 12
+COV [981-981] 981 5
+COV [982-982] 982 8
+COV [983-983] 983 4
+COV [984-984] 984 9
+COV [985-985] 985 9
+COV [986-986] 986 10
+COV [987-987] 987 8
+COV [988-988] 988 4
+COV [989-989] 989 6
+COV [990-990] 990 3
+COV [991-991] 991 5
+COV [992-992] 992 2
+COV [993-993] 993 6
+COV [994-994] 994 6
+COV [995-995] 995 7
+COV [996-996] 996 14
+COV [997-997] 997 12
+COV [998-998] 998 7
+COV [999-999] 999 8
+COV [1000-1000] 1000 8
+COV [1000<] 1000 5025
+# 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 0.554 0.000 0.000 0.000 0.000 0.000
+GCD 0.5 0.831 0.525 0.525 0.525 0.525 0.525
+GCD 36.0 1.385 0.954 0.954 0.954 1.490 1.490
+GCD 37.0 2.216 2.495 2.495 4.146 6.560 6.560
+GCD 38.0 5.263 0.247 0.454 3.520 5.868 9.883
+GCD 39.0 9.141 0.177 0.303 2.161 8.777 12.812
+GCD 40.0 12.188 0.020 1.192 9.060 22.018 27.371
+GCD 41.0 16.343 0.035 0.550 2.702 11.469 12.908
+GCD 42.0 21.884 0.010 0.172 2.121 5.621 17.094
+GCD 43.0 28.255 0.010 0.328 1.449 4.277 10.166
+GCD 44.0 36.288 0.162 0.394 5.484 15.145 50.490
+GCD 45.0 42.105 0.020 0.131 1.252 7.009 17.811
+GCD 46.0 49.861 0.015 0.121 0.636 1.939 37.506
+GCD 47.0 56.510 0.030 0.141 1.015 4.500 6.338
+GCD 48.0 64.543 0.010 0.091 2.565 7.287 21.872
+GCD 49.0 68.975 0.010 0.333 0.672 10.751 27.129
+GCD 50.0 73.407 0.010 0.121 1.358 3.883 6.615
+GCD 51.0 77.008 0.121 0.576 1.576 4.363 13.923
+GCD 52.0 81.994 0.010 0.086 1.560 4.414 109.383
+GCD 53.0 84.488 0.040 0.071 0.500 3.025 31.234
+GCD 54.0 86.704 0.020 0.313 9.332 39.683 203.959
+GCD 55.0 89.197 0.005 0.051 1.268 5.045 23.578
+GCD 56.0 91.136 0.071 0.192 1.566 9.994 33.315
+GCD 57.0 94.460 0.040 0.348 1.167 5.050 11.660
+GCD 58.0 95.845 0.131 0.131 1.899 2.742 4.929
+GCD 59.0 96.399 3.313 3.313 3.313 3.666 3.666
+GCD 60.0 97.507 0.995 0.995 5.176 6.954 33.234
+GCD 61.0 98.338 1.591 1.591 1.788 4.848 4.848
+GCD 62.0 98.892 3.171 3.171 3.171 7.343 7.343
+GCD 63.0 99.446 0.530 0.530 0.530 6.403 6.403
+GCD 64.0 100.000 1.025 1.025 1.025 4.585 4.585
diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_stats_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample bases_trimmed error_rate insert_size_standard_deviation non-primary_alignments maximum_length reads_MQ0_percent reads_mapped_and_paired sequences average_quality insert_size_average reads_mapped reads_unmapped reads_QC_failed reads_duplicated_percent reads_paired 1st_fragments reads_MQ0 average_length reads_mapped_and_paired_percent bases_mapped total_length bases_mapped_(cigar) bases_duplicated pairs_with_other_orientation mismatches reads_properly_paired inward_oriented_pairs filtered_sequences outward_oriented_pairs reads_unmapped_percent reads_QC_failed_percent reads_properly_paired_percent reads_paired_percent reads_mapped_percent raw_total_sequences pairs_on_different_chromosomes last_fragments is_sorted reads_duplicated
+samtools_stats 0.0 0.004248509 1223.0 12111.0 101.0 0.0109064676911 638746.0 641821.0 26.0 719.7 641821.0 0.0 0.0 0.0 641821.0 320981.0 70.0 101.0 99.520894455 64823921.0 64823921.0 64823921.0 0.0 30.0 275405.0 635626.0 317512.0 0.0 1294.0 0.0 0.0 99.0347776093 100.0 100.0 641821.0 0.0 320840.0 1.0 0.0
diff -r 000000000000 -r 3bad335ccea9 test-data/snpeff.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snpeff.csv Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,588 @@
+
+# Summary table
+
+Name , Value
+Genome , GRCh37.75
+Date , 2016-02-24 19:23
+SnpEff_version , SnpEff 4.1a (build 2015-01-14), by Pablo Cingolani
+Command_line_arguments , SnpEff -csvStats -stats /scratch/108820/ANALYSIS/P4107/piper_ngi/07_variant_calls/Sample1.clean.dedup.recal.bam.recalibrated.indel.annotated.vcf.gz.snpEff.summary.csv GRCh37.75 /scratch/108820/ANALYSIS/P4107/piper_ngi/07_variant_calls/Sample1.clean.dedup.recal.bam.recalibrated.indel.vcf.gz
+Warnings , 1214759
+Number_of_lines_in_input_file, 917355
+Number_of_variants_before_filter, 972155
+Number_of_not_variants , 0
+Number_of_variants_processed , 972155
+Number_of_known_variants (i.e. non-empty ID) , 764271, 78.616167%
+Number_of_effects , 5499894
+Genome_total_length ,32036512383
+Genome_effective_length ,3101536026
+Change_rate , 3190
+
+# Change rate by chromosome
+
+Chromosome , Length , Changes , Change_rate
+1 , 249250621 , 76982 , 3237
+2 , 243199373 , 77562 , 3135
+3 , 198022430 , 63396 , 3123
+4 , 191154276 , 65298 , 2927
+5 , 180915260 , 56287 , 3214
+6 , 171115067 , 59086 , 2896
+7 , 159138663 , 55505 , 2867
+8 , 146364022 , 44876 , 3261
+9 , 141213431 , 40484 , 3488
+10 , 135534747 , 48468 , 2796
+11 , 135006516 , 45528 , 2965
+12 , 133851895 , 45727 , 2927
+13 , 115169878 , 36006 , 3198
+14 , 107349540 , 30507 , 3518
+15 , 102531392 , 29009 , 3534
+16 , 90354753 , 29320 , 3081
+17 , 81195210 , 30895 , 2628
+18 , 78077248 , 26998 , 2891
+19 , 59128983 , 25980 , 2275
+20 , 63025520 , 20817 , 3027
+21 , 48129895 , 16197 , 2971
+22 , 51304566 , 13805 , 3716
+GL000191.1 , 106433 , 24 , 4434
+GL000192.1 , 547496 , 131 , 4179
+GL000193.1 , 189789 , 133 , 1426
+GL000194.1 , 191469 , 159 , 1204
+GL000195.1 , 182896 , 269 , 679
+GL000197.1 , 37175 , 1 , 37175
+GL000198.1 , 90085 , 146 , 617
+GL000199.1 , 169874 , 54 , 3145
+GL000201.1 , 36148 , 1 , 36148
+GL000202.1 , 40103 , 9 , 4455
+GL000203.1 , 37498 , 78 , 480
+GL000204.1 , 81310 , 15 , 5420
+GL000205.1 , 174588 , 229 , 762
+GL000206.1 , 41001 , 1 , 41001
+GL000208.1 , 92689 , 66 , 1404
+GL000209.1 , 159169 , 4 , 39792
+GL000210.1 , 27682 , 1 , 27682
+GL000211.1 , 166566 , 161 , 1034
+GL000212.1 , 186858 , 123 , 1519
+GL000213.1 , 164239 , 14 , 11731
+GL000214.1 , 137718 , 169 , 814
+GL000215.1 , 172545 , 12 , 14378
+GL000216.1 , 172294 , 636 , 270
+GL000217.1 , 172149 , 227 , 758
+GL000218.1 , 161147 , 141 , 1142
+GL000219.1 , 179198 , 384 , 466
+GL000220.1 , 161802 , 294 , 550
+GL000221.1 , 155397 , 90 , 1726
+GL000222.1 , 186861 , 175 , 1067
+GL000223.1 , 180455 , 2 , 90227
+GL000224.1 , 179693 , 324 , 554
+GL000225.1 , 211173 , 537 , 393
+GL000226.1 , 15008 , 2 , 7504
+GL000227.1 , 128374 , 5 , 25674
+GL000228.1 , 129120 , 65 , 1986
+GL000229.1 , 19913 , 157 , 126
+GL000230.1 , 43691 , 40 , 1092
+GL000231.1 , 27386 , 114 , 240
+GL000232.1 , 40652 , 175 , 232
+GL000233.1 , 45941 , 54 , 850
+GL000234.1 , 40531 , 165 , 245
+GL000235.1 , 34474 , 80 , 430
+GL000236.1 , 41934 , 12 , 3494
+GL000237.1 , 45867 , 50 , 917
+GL000238.1 , 39939 , 3 , 13313
+GL000239.1 , 33824 , 11 , 3074
+GL000240.1 , 41933 , 37 , 1133
+GL000241.1 , 42152 , 138 , 305
+GL000242.1 , 43523 , 4 , 10880
+GL000243.1 , 43341 , 28 , 1547
+GL000244.1 , 39929 , 8 , 4991
+GL000245.1 , 36651 , 12 , 3054
+GL000246.1 , 38154 , 9 , 4239
+GL000247.1 , 36422 , 12 , 3035
+GL000248.1 , 39786 , 6 , 6631
+MT , 16569 , 3 , 5523
+X , 155270560 , 24853 , 6247
+Y , 59373566 , 2769 , 21442
+
+# Effects by impact
+
+Type , Count , Percent
+HIGH , 1367 , 0.024855%
+LOW , 2178258 , 39.605454%
+MODERATE , 3322 , 0.060401%
+MODIFIER , 3316947 , 60.30929%
+
+# Effects by functional class
+
+Type , Count , Percent
+
+Missense_Silent_ratio, ?
+
+# Count by effects
+
+Type , Count , Percent
+3_prime_UTR_variant , 15811 , 0.287478%
+5_prime_UTR_truncation+exon_loss_variant , 2 , 0.000036%
+5_prime_UTR_variant , 3350 , 0.06091%
+TF_binding_site_variant , 986 , 0.017928%
+disruptive_inframe_deletion , 408 , 0.007418%
+disruptive_inframe_deletion+splice_region_variant , 2 , 0.000036%
+disruptive_inframe_insertion , 277 , 0.005036%
+downstream_gene_variant , 339790 , 6.178119%
+frameshift_variant , 800 , 0.014546%
+frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018%
+frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant , 2 , 0.000036%
+frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant , 6 , 0.000109%
+frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant , 3 , 0.000055%
+frameshift_variant+splice_region_variant , 77 , 0.0014%
+frameshift_variant+start_lost , 8 , 0.000145%
+frameshift_variant+start_lost+splice_region_variant , 1 , 0.000018%
+frameshift_variant+stop_gained , 21 , 0.000382%
+frameshift_variant+stop_lost , 3 , 0.000055%
+inframe_deletion , 159 , 0.002891%
+inframe_deletion+splice_region_variant , 10 , 0.000182%
+inframe_insertion , 266 , 0.004836%
+inframe_insertion+splice_region_variant , 2 , 0.000036%
+intergenic_region , 461247 , 8.386471%
+intragenic_variant , 267 , 0.004855%
+intron_variant , 2126738 , 38.668709%
+non_coding_exon_variant , 15320 , 0.278551%
+sequence_feature , 2174428 , 39.535817%
+splice_acceptor_variant+5_prime_UTR_variant+intron_variant , 2 , 0.000036%
+splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018%
+splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018%
+splice_acceptor_variant+intron_variant , 224 , 0.004073%
+splice_acceptor_variant+splice_donor_variant+intron_variant , 61 , 0.001109%
+splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 2 , 0.000036%
+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 1 , 0.000018%
+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant , 3 , 0.000055%
+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 5 , 0.000091%
+splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 7 , 0.000127%
+splice_acceptor_variant+splice_region_variant+intron_variant , 32 , 0.000582%
+splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 5 , 0.000091%
+splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 2 , 0.000036%
+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018%
+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 13 , 0.000236%
+splice_donor_variant+5_prime_UTR_variant+intron_variant , 2 , 0.000036%
+splice_donor_variant+intron_variant , 41 , 0.000745%
+splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 1 , 0.000018%
+splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant , 1 , 0.000018%
+splice_donor_variant+splice_region_variant+intron_variant , 15 , 0.000273%
+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 5 , 0.000091%
+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 1 , 0.000018%
+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant , 3 , 0.000055%
+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 12 , 0.000218%
+splice_region_variant , 187 , 0.0034%
+splice_region_variant+intron_variant , 4390 , 0.07982%
+splice_region_variant+non_coding_exon_variant , 462 , 0.0084%
+splice_region_variant+splice_region_variant , 1 , 0.000018%
+start_lost+disruptive_inframe_insertion , 1 , 0.000018%
+stop_gained+inframe_insertion , 3 , 0.000055%
+transcript , 77 , 0.0014%
+upstream_gene_variant , 354347 , 6.442797%
+
+# Count by genomic region
+
+Type , Count , Percent
+DOWNSTREAM , 339790 , 6.178119%
+EXON , 17369 , 0.315806%
+INTERGENIC , 461247 , 8.386471%
+INTRON , 2126738 , 38.668709%
+MOTIF , 986 , 0.017928%
+NONE , 2174772 , 39.542071%
+SPLICE_SITE_ACCEPTOR , 360 , 0.006546%
+SPLICE_SITE_DONOR , 81 , 0.001473%
+SPLICE_SITE_REGION , 5040 , 0.091638%
+TRANSCRIPT , 1 , 0.000018%
+UPSTREAM , 354347 , 6.442797%
+UTR_3_PRIME , 15811 , 0.287478%
+UTR_5_PRIME , 3352 , 0.060947%
+
+# Quality
+
+Values , 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+Count , 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215,184,188,190,174,154,213,190,199,233,218,205,222,188,167,183,172,186,197,195,183,188,196,197,210,176,197,207,229,264,304,310,217,225,166,182,167,184,200,183,194,195,293,740,248,209,188,217,145,177,159,141,160,164,167,156,151,137,166,192,167,176,171,181,162,161,171,138,176,174,220,241,228,256,233,274,266,250,211,193,165,227,216,212,212,189,168,331,869,238,179,153,127,125,133,147,149,124,143,139,155,148,141,162,159,178,187,192,177,196,183,192,219,192,200,189,200,183,206,223,266,320,291,238,224,210,160,157,141,132,155,176,234,854,215,163,134,122,132,129,166,135,183,149,165,160,158,158,158,152,192,172,211,184,209,180,175,192,187,207,160,218,201,177,210,237,265,196,183,143,153,135,158,151,139,149,174,236,940,212,155,118,134,124,140,140,171,164,157,162,156,174,170,192,176,226,213,193,157,169,134,131,151,118,139,117,136,172,172,211,238,224,195,185,153,146,146,146,153,134,138,165,241,1008,229,148,175,146,155,144,134,170,163,251,193,161,154,157,113,120,120,139,158,123,144,136,121,143,131,155,121,133,155,173,193,241,250,197,153,133,147,155,138,162,163,140,187,262,984,234,138,155,153,137,201,95,127,117,100,74,120,102,100,121,110,131,125,109,114,120,127,109,116,131,131,149,140,164,167,185,246,241,210,173,159,150,129,132,148,156,115,181,242,932,240,121,112,88,100,87,95,87,111,102,96,97,95,99,106,110,106,120,153,132,130,129,131,130,143,136,125,163,167,165,208,291,245,219,149,164,125,108,124,108,144,102,121,221,953,172,91,88,65,77,98,77,82,106,104,99,80,94,101,94,104,105,136,145,136,121,132,132,133,145,139,104,141,148,147,172,217,204,189,155,127,132,86,113,138,80,86,105,182,877,127,69,89,71,97,84,84,78,94,91,95,99,97,92,98,106,123,101,138,125,119,95,89,99,92,94,96,118,119,135,146,233,200,152,133,89,96,87,104,90,97,94,122,158,867,126,80,82,69,75,81,86,75,110,104,90,71,84,71,60,73,84,83,117,109,83,87,98,89,93,107,105,124,141,133,143,187,191,136,109,102,86,90,83,103,92,96,82,168,839,117,81,77,68,77,90,64,67,75,79,67,80,64,71,84,77,72,106,101,96,101,80,100,92,82,98,77,85,94,106,128,172,149,126,74,80,69,86,85,91,69,52,69,126,761,105,80,44,56,59,50,61,56,73,73,66,74,70,63,68,69,72,116,102,98,90,76,63,68,79,75,67,75,94,114,108,152,174,122,80,61,74,53,71,84,56,48,72,108,578,107,51,64,49,42,62,64,43,69,55,51,57,58,77,52,49,71,80,86,71,75,75,75,55,62,63,57,78,92,105,104,127,107,102,68,48,59,53,63,59,54,52,52,100,605,73,48,41,40,38,49,51,33,70,69,48,56,45,49,47,53,69,47,69,79,49,43,52,49,53,50,44,57,71,73,84,121,143,100,61,43,45,55,58,61,43,44,66,91,546,64,31,41,45,51,30,34,41,49,37,33,43,46,40,35,41,53,60,51,50,46,43,47,50,59,50,51,58,64,79,83,110,107,88,50,55,52,44,38,43,49,35,43,92,452,58,31,27,34,19,24,34,24,37,45,29,20,28,28,38,29,41,46,49,44,41,29,24,36,46,41,37,44,58,74,70,82,80,66,49,31,36,48,37,52,41,27,42,72,363,38,23,14,32,25,31,29,35,34,36,32,30,30,29,30,34,40,39,42,37,32,35,29,38,39,37,34,32,58,49,66,90,79,58,37,41,30,28,32,35,24,28,38,63,324,42,25,16,15,14,20,27,21,30,22,31,23,29,23,22,16,23,32,40,23,32,33,21,26,27,20,23,37,39,40,45,58,62,45,31,28,26,15,30,26,19,15,32,58,257,28,15,16,16,16,21,19,17,26,31,26,18,27,23,18,21,20,27,21,25,27,26,20,29,31,17,23,21,27,27,29,49,40,32,18,9,21,26,16,25,19,15,18,48,205,26,19,16,20,12,13,14,15,23,17,22,6,17,20,23,12,23,19,31,25,13,10,15,16,13,16,21,24,23,23,33,29,39,26,14,18,18,14,15,28,14,12,15,26,157,25,16,9,8,12,13,11,11,16,18,16,12,14,12,11,18,17,14,12,13,13,8,14,17,17,19,14,21,19,24,25,35,33,15,24,8,19,11,10,12,10,11,12,27,128,15,9,14,7,11,8,4,11,10,8,11,13,7,10,9,9,12,19,17,15,17,6,10,12,15,17,11,15,15,13,17,23,25,21,15,9,15,13,15,13,11,13,15,23,94,10,8,8,3,4,5,7,15,5,9,5,6,8,9,11,7,16,13,10,11,10,16,15,7,10,8,13,12,12,8,15,30,20,19,7,13,10,8,12,13,9,12,6,16,66,6,6,10,5,7,6,6,5,8,13,4,5,8,8,8,14,4,5,8,15,9,13,6,8,9,6,3,13,11,15,6,10,12,11,5,7,9,8,5,7,11,6,7,13,54,3,1,5,6,6,7,6,7,5,6,3,5,5,7,6,6,7,6,9,9,10,3,2,6,8,6,4,8,5,17,8,11,15,7,6,8,3,6,7,5,9,5,11,13,38,2,2,4,4,6,6,6,4,8,4,1,5,9,6,4,5,2,8,8,7,7,1,2,3,4,5,5,6,7,7,11,11,4,7,7,4,5,6,3,7,4,7,2,7,39,6,2,1,7,5,1,5,1,2,4,4,7,2,3,4,3,5,1,4,3,2,2,4,2,10,2,5,3,5,6,5,8,8,7,2,5,4,4,2,2,9,3,2,5,19,2,4,4,4,4,4,1,5,9,3,6,4,2,5,3,5,2,4,1,5,8,2,4,5,1,4,5,2,6,1,6,4,4,5,6,2,4,5,1,3,5,5,2,3,21,2,2,3,3,3,2,3,3,3,2,3,1,3,3,1,2,4,3,2,3,4,3,2,1,3,3,2,6,3,7,4,7,1,4,6,2,4,2,7,4,3,3,4,5,12,2,3,3,3,2,2,4,2,1,4,3,3,3,4,1,1,2,4,6,2,3,2,4,5,2,1,3,1,5,3,2,4,6,2,2,4,2,3,1,5,2,1,2,5,5,4,3,2,1,1,1,6,2,5,2,5,2,1,2,1,3,2,5,2,2,3,4,1,2,2,1,7,6,4,1,2,3,3,3,4,6,4,5,2,2,3,3,3,3,6,2,4,2,3,4,3,1,1,1,4,3,2,1,2,2,3,1,4,2,1,3,1,2,1,1,5,1,3,3,1,1,2,4,5,2,2,6,1,6,3,2,1,2,1,2,2,1,1,2,2,5,5,1,2,5,1,2,1,3,2,4,3,4,2,3,2,3,1,2,1,4,3,1,3,3,1,1,1,1,2,3,1,1,1,2,2,1,1,2,4,2,4,1,1,4,1,2,2,1,2,2,3,1,2,2,4,1,1,3,2,4,1,1,5,1,2,2,2,2,2,1,1,1,1,1,1,3,1,6,3,6,2,1,1,4,3,1,3,2,3,2,1,1,1,1,2,2,1,3,2,2,1,3,5,4,1,2,1,1,2,1,1,2,1,3,1,1,3,1,3,1,1,3,2,2,3,2,2,3,4,1,1,1,1,1,1,3,1,1,2,3,2,2,1,2,1,1,3,2,2,1,2,1,2,1,1,1,2,2,1,1,1,1,6,1,1,1,2,1,2,1,1,1,1,1,2,3,1,1,1,1,1,5,1,2,1,2,1,2,1,2,1,1,2,1,1,4,1,2,3,1,2,1,1,1,1,2,2,1,2,1,1,1,3,3,1,1,2,1,1,1,1,1,1,2,4,1,1,3,3,1,1,3,1,2,1,2,1,1,1,2,1,1,1,2,1,1,3,3,1,3,2,2,2,1,1,1,1,1,1,1,4,1,1,4,1,2,3,1,1,1,1,3,1,2,2,3,1,4,3,3,1,2,2,2,2,1,1,3,2,1,1,1,2,2,1,1,2,1,1,4,2,1,3,1,3,1,2,1,2,2,1,1,4,1,3,1,1,1,1,3,4,3,1,3,2,1,1,1,3,1,1,1,2,3,6,2,2,1,2,1,3,2,1,1,1,2,1,1,1,1,2,2,6,2,1,1,2,1,4,1,2,1,2,3,1,1,1,2,1,2,1,1,1,1,2,2,3,1,1,1,5,4,2,2,2,1,3,1,2,3,2,1,2,1,1,2,1,1,1,1,2,4,1,3,2,1,1,3,1,2,1,1,2,2,2,1,3,2,2,1,1,1,1,1,2,1,1,2,4,1,2,1,1,2,1,3,2,1,2,2,1,3,1,1,1,1,1,1,2,1,1,3,2,1,3,2,2,3,3,2,1,3,1,2,1,1,1,2,1,2,1,1,1,1,2,3,1,1,2,1,1,1,4,1,4,2,2,1,2,1,2,1,1,1,1,1,3,3,1,1,1,2,1,2,1,1,3,1,1,1,1,2,2,2,2,1,1,1,3,1,1,2,2,2,1,1,1,2,2,3,2,1,1,2,1,2,1,1,4,1,1,1,1,2,1,2,2,1,2,1,1,1,1,2,2,2,1,1,1,1,1,1,1,2,1,1,1,2,1,2,1,2,2,1,1,1,1,3,1,2,2,2,1,1,1,1,1,1,2,2,1,1,1,2,3,2,2,1,1,2,1,1,1,4,2,1,1,3,1,1,2,5,1,1,2,2,1,1,1,2,1,1,1,3,1,1,1,2,2,1,2,2,2,1,1,1,3,1,1,2,2,2,3,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,2,3,1,1,2,2,1,1,2,1,1,1,1,1,1,1,1,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,2,1,1,2,1,2,1,1,1,1,1,2,1,2,1,2,1,1,1,1,1,2,1,3,2,3,2,1,2,2,1,1,1,1,1,1,1,1,1,1,1,2,1,3,1,1,2,1,1,1,2,1,1,1,1,2,2,2,1,1,1,2,1,2,1,2,1,1,1,1,2,1,1,1,1,1,1,1,2,2,1,1,1,1,2,1,3,1,1,1,1,1,1,2,2,1,3,3,2,1,1,3,2,1,2,1,1,1,2,1,1,2,2,2,1,3,2,1,1,1,1,1,2,2,2,1,1,2,1,2,1,1,1,2,1,2,2,1,1,1,1,1,1,2,2,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,2,1,1,1,1,1,1,2,1,3,3,2,2,1,1,3,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,2,2,2,2,2,1,1,1,2,1,1,1,1,1,2,1,2,1,2,1,1,1,2,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,4,1,1,2,1,1,1,1,1,2,2,1,2,1,1,1,1,1,1,2,1,1,1,1,1,1,2,1,1,1,2,1,1,1,1,1,1,1,1,1,2,1,1,1,2,2,2,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,2,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,3,1,1,1,1,2,2,1,1,1,1,1,1,1,1,1,2,2,1,1,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,2,2,1,1,1,1,1,2,1,1,1,1,2,1,1,2,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,2,2,1,3,1,1,1,1,1,1,1,2,1,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,2,1,1,2,1,1,1,2,2,1,1,2,1,1,1,1,2,1,1,1,1,1,2,2,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,3,1,2,1,1,2,1,1,1,1,1,1,1,1,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,3,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+
+# InDel lengths
+
+Values , 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,182,183,184,185,186,187,188,191,193,194,195,196,197,198,199,200,201,202,203,205,209,212,215,219,220,223,226,227,228,229,234,239,240,241,242,247,248,250,257,259,263,264,269,272,273,283,301,310,316,329,333,337,345,349,357,365,371,376,385,415,431,465,468
+Count , 224126,581518,30481,45770,12815,14371,4393,12389,3495,6543,2136,6605,1548,2877,1892,3247,913,1778,721,2174,651,966,487,1226,528,641,389,722,264,539,242,440,216,278,220,311,164,217,137,244,114,153,102,120,97,111,82,140,85,109,64,92,82,103,58,74,53,58,51,79,54,72,36,68,40,63,30,47,26,44,25,50,30,31,33,42,21,26,24,28,26,21,10,28,15,25,22,17,15,25,10,16,17,12,22,33,10,17,15,14,5,10,9,14,6,14,6,9,10,14,8,16,5,6,11,9,8,7,5,4,6,11,9,8,9,5,1,2,8,7,6,4,13,6,10,5,7,3,7,2,4,1,6,1,2,2,1,2,8,3,3,1,3,1,3,3,9,1,1,1,1,2,2,3,6,1,1,4,3,2,3,5,3,2,4,2,4,1,2,1,2,1,1,1,2,2,3,1,1,2,3,2,2,1,1,2,3,2,1,1,2,1,1,1,3,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+
+# Base changes
+
+base , A , C , G , T
+ A , 0 , 0 , 0 , 0
+ C , 0 , 0 , 0 , 0
+ G , 0 , 0 , 0 , 0
+ T , 0 , 0 , 0 , 0
+
+# Ts/Tv summary
+
+Transitions , 0
+Transversions , 0
+Ts_Tv_ratio , 0
+
+# Ts/Tv : All variants
+
+No results available (empty input?)
+
+# Ts/Tv : Known variants
+
+No results available (empty input?)
+
+# Allele frequency
+
+# Allele frequency : All variants
+
+Values , 50,100
+Count , 524875,392480
+
+# Allele Count
+
+Values , 1,2
+Count , 524875,392480
+
+# Hom/Het table
+
+Sample_names , Sample1
+Reference , 0
+Het , 524875
+Hom , 392480
+Missing , 0
+
+
+# Codon change table
+
+codons , - , AAA , AAC , AAG , AAT , ACA , ACC , ACG , ACT , AGA , AGC , AGG , AGT , ATA , ATC , ATG , ATT , CAA , CAC , CAG , CAT , CCA , CCC , CCG , CCT , CGA , CGC , CGG , CGT , CTA , CTC , CTG , CTT , GAA , GAC , GAG , GAT , GCA , GCC , GCG , GCT , GGA , GGC , GGG , GGT , GTA , GTC , GTG , GTT , TAA , TAC , TAG , TAT , TCA , TCC , TCG , TCT , TGA , TGC , TGG , TGT , TTA , TTC , TTG , TTT
+ - , 0 , 27 , 16 , 45 , 14 , 22 , 43 , 15 , 7 , 26 , 82 , 21 , 27 , 9 , 15 , 27 , 0 , 32 , 45 , 401 , 17 , 20 , 87 , 51 , 65 , 5 , 14 , 18 , 12 , 18 , 17 , 57 , 12 , 34 , 50 , 123 , 50 , 17 , 59 , 30 , 52 , 37 , 182 , 67 , 47 , 25 , 12 , 34 , 14 , 8 , 5 , 6 , 13 , 22 , 68 , 6 , 26 , 3 , 18 , 21 , 32 , 7 , 38 , 8 , 39
+ AAA , 52 , 6 , 0 , 5 , 4 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 3 , 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 , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 2 , 0 , 0
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+ TGT , 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 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 2 , 0 , 0 , 0 , 1 , 0 , 2 , 1 , 1 , 0 , 0 , 1 , 1
+ TTA , 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 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 4 , 2 , 0 , 0 , 0
+ TTC , 33 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 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 , 1 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 1 , 1 , 1 , 0 , 3
+ TTG , 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 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 1 , 3
+ TTT , 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 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 1 , 0 , 0 , 2 , 1
+
+# Amino acid change table
+
+aa , * , - , ? , A , C , D , E , F , G , H , I , K , L , M , N , P , Q , R , S , T , V , W , Y
+ * , 0 , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0
+ - , 17 , 0 , 467 , 158 , 50 , 100 , 157 , 77 , 333 , 62 , 24 , 72 , 119 , 27 , 30 , 223 , 433 , 96 , 231 , 87 , 85 , 21 , 18
+ ? , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0
+ A , 0 , 224 , 0 , 81 , 1 , 2 , 2 , 0 , 23 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 1 , 2 , 1 , 4 , 0 , 0
+ C , 0 , 70 , 0 , 1 , 5 , 0 , 0 , 2 , 2 , 0 , 0 , 0 , 5 , 1 , 0 , 0 , 0 , 0 , 2 , 0 , 0 , 4 , 2
+ D , 0 , 133 , 0 , 6 , 0 , 29 , 30 , 0 , 33 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 2 , 5 , 0 , 0
+ E , 0 , 211 , 0 , 3 , 0 , 17 , 60 , 0 , 18 , 0 , 0 , 0 , 1 , 0 , 2 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0
+ F , 0 , 48 , 0 , 0 , 2 , 0 , 0 , 5 , 0 , 0 , 3 , 0 , 3 , 0 , 0 , 0 , 0 , 0 , 2 , 0 , 1 , 0 , 1
+ G , 0 , 290 , 0 , 26 , 0 , 4 , 24 , 1 , 91 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 4 , 4 , 0 , 7 , 3 , 0
+ H , 0 , 51 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 4 , 0 , 0 , 0 , 0 , 0 , 2 , 3 , 1 , 1 , 0 , 0 , 0 , 0
+ I , 1 , 43 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 6 , 1 , 0 , 0 , 2 , 0 , 0 , 0 , 6 , 14 , 1 , 0 , 0
+ K , 0 , 112 , 0 , 2 , 0 , 0 , 8 , 2 , 0 , 0 , 3 , 29 , 3 , 0 , 16 , 0 , 2 , 4 , 5 , 0 , 0 , 0 , 0
+ L , 0 , 167 , 0 , 0 , 4 , 0 , 0 , 4 , 0 , 3 , 0 , 0 , 40 , 0 , 0 , 17 , 0 , 0 , 5 , 2 , 0 , 0 , 2
+ M , 0 , 32 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 5 , 0 , 0 , 2 , 2 , 0 , 0 , 0 , 2 , 8 , 0 , 0 , 0
+ N , 0 , 46 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 2 , 5 , 0 , 0 , 9 , 0 , 0 , 2 , 2 , 0 , 0 , 0 , 0
+ P , 0 , 319 , 0 , 6 , 0 , 0 , 0 , 0 , 0 , 3 , 0 , 0 , 5 , 0 , 0 , 83 , 32 , 6 , 6 , 1 , 0 , 0 , 0
+ Q , 0 , 189 , 0 , 3 , 0 , 0 , 0 , 0 , 1 , 5 , 0 , 0 , 0 , 0 , 0 , 12 , 110 , 23 , 0 , 2 , 0 , 0 , 0
+ R , 0 , 135 , 0 , 3 , 0 , 0 , 0 , 0 , 0 , 7 , 0 , 8 , 3 , 0 , 0 , 17 , 10 , 33 , 14 , 3 , 0 , 0 , 0
+ S , 0 , 321 , 0 , 0 , 2 , 0 , 0 , 5 , 0 , 0 , 22 , 1 , 4 , 0 , 4 , 2 , 0 , 9 , 57 , 3 , 0 , 1 , 3
+ T , 0 , 248 , 0 , 2 , 0 , 0 , 1 , 0 , 0 , 1 , 1 , 7 , 0 , 3 , 4 , 1 , 0 , 6 , 19 , 37 , 0 , 0 , 0
+ V , 0 , 117 , 0 , 4 , 1 , 0 , 3 , 0 , 15 , 0 , 0 , 0 , 3 , 3 , 0 , 0 , 4 , 0 , 0 , 0 , 18 , 0 , 0
+ W , 3 , 19 , 0 , 0 , 2 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 3 , 0 , 0 , 0 , 0 , 1 , 2 , 0 , 0 , 1 , 0
+ Y , 3 , 18 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 1 , 0 , 0 , 0 , 4
+
+# Chromosome change table
+
+1, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000,172000000,173000000,174000000,175000000,176000000,177000000,178000000,179000000,180000000,181000000,182000000,183000000,184000000,185000000,186000000,187000000,188000000,189000000,190000000,191000000,192000000,193000000,194000000,195000000,196000000,197000000,198000000,199000000,200000000,201000000,202000000,203000000,204000000,205000000,206000000,207000000,208000000,209000000,210000000,211000000,212000000,213000000,214000000,215000000,216000000,217000000,218000000,219000000,220000000,221000000,222000000,223000000,224000000,225000000,226000000,227000000,228000000,229000000,230000000,231000000,232000000,233000000,234000000,235000000,236000000,237000000,238000000,239000000,240000000,241000000,242000000,243000000,244000000,245000000,246000000,247000000,248000000,249000000
+1,Count,223,417,271,272,399,352,417,379,475,423,369,380,347,187,399,493,554,534,372,300,311,469,461,325,457,275,371,242,159,228,253,490,171,357,277,200,287,301,333,447,361,416,324,342,351,329,493,262,237,156,190,168,247,365,333,345,291,309,258,286,232,327,489,378,325,336,315,393,273,233,258,265,333,428,286,236,371,305,236,280,347,255,334,352,252,405,338,314,305,272,236,367,273,357,251,378,319,216,289,309,352,365,384,360,300,441,305,333,298,354,260,313,281,398,349,329,354,245,247,261,277,135,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,461,389,310,537,266,250,330,407,509,443,244,333,367,322,384,283,394,306,381,481,372,329,335,473,249,366,303,229,294,270,212,206,101,269,339,311,296,473,390,243,316,376,296,240,417,322,468,416,358,335,311,285,352,387,300,281,182,442,442,413,400,380,380,397,221,298,283,316,404,294,423,302,374,320,297,323,320,300,339,325,340,284,512,286,407,506,186,222,256,338,311,322,387,323,526,515,401,323,517,451,507,273,390,422,396,531,484,25
+
+2, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000,172000000,173000000,174000000,175000000,176000000,177000000,178000000,179000000,180000000,181000000,182000000,183000000,184000000,185000000,186000000,187000000,188000000,189000000,190000000,191000000,192000000,193000000,194000000,195000000,196000000,197000000,198000000,199000000,200000000,201000000,202000000,203000000,204000000,205000000,206000000,207000000,208000000,209000000,210000000,211000000,212000000,213000000,214000000,215000000,216000000,217000000,218000000,219000000,220000000,221000000,222000000,223000000,224000000,225000000,226000000,227000000,228000000,229000000,230000000,231000000,232000000,233000000,234000000,235000000,236000000,237000000,238000000,239000000,240000000,241000000,242000000,243000000
+2,Count,307,398,307,400,408,280,303,350,323,264,479,395,343,387,309,341,313,268,277,296,265,272,267,293,495,354,421,374,325,427,333,231,288,393,428,388,327,428,454,347,300,357,522,307,343,265,372,331,203,238,318,295,305,201,363,470,266,346,205,217,309,246,249,224,235,486,276,399,366,195,267,355,212,192,165,248,319,449,304,292,238,157,332,370,222,363,345,326,257,136,197,449,298,0,0,104,219,250,208,160,358,335,416,252,226,274,471,305,276,368,216,192,277,347,356,353,352,315,357,260,243,305,226,331,324,299,391,279,455,326,234,201,583,690,287,249,145,362,284,335,367,522,483,255,282,264,280,253,251,229,266,315,358,418,272,308,277,324,254,370,463,249,269,117,148,230,354,338,267,399,511,475,492,293,305,319,232,283,325,291,345,384,192,294,323,255,350,320,288,266,318,396,341,326,259,273,281,392,253,371,277,302,415,354,347,237,414,392,435,323,354,337,416,412,359,418,447,305,275,271,419,329,289,391,407,473,307,290,536,383,372,297,286,411,294,365,383,363,309,367,253,300,321,36
+
+3, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000,172000000,173000000,174000000,175000000,176000000,177000000,178000000,179000000,180000000,181000000,182000000,183000000,184000000,185000000,186000000,187000000,188000000,189000000,190000000,191000000,192000000,193000000,194000000,195000000,196000000,197000000,198000000
+3,Count,298,345,390,389,335,373,306,400,341,324,330,452,441,389,305,293,394,246,250,174,356,404,328,414,321,271,235,290,211,277,335,203,465,203,357,265,255,283,252,388,203,443,356,255,225,320,328,444,296,380,228,241,156,367,292,291,458,490,312,284,394,363,317,338,302,347,272,335,326,364,222,409,310,423,274,624,393,418,319,243,373,280,261,235,311,258,280,323,389,200,81,0,0,76,374,384,217,129,409,262,323,395,272,404,294,364,352,270,408,393,337,343,357,207,218,279,396,325,327,311,174,336,380,265,430,532,310,298,326,311,240,369,290,248,278,239,423,278,248,217,316,452,360,289,276,346,339,283,314,280,321,451,429,336,238,258,207,269,248,208,318,342,672,356,232,302,331,227,194,299,312,361,275,274,451,301,418,324,273,396,174,265,268,440,408,349,372,324,390,478,403,389,308,308,427,639,446,271,0
+
+4, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000,172000000,173000000,174000000,175000000,176000000,177000000,178000000,179000000,180000000,181000000,182000000,183000000,184000000,185000000,186000000,187000000,188000000,189000000,190000000,191000000
+4,Count,337,304,371,451,378,367,367,376,329,427,422,299,283,255,336,256,355,416,258,328,396,418,286,384,380,421,393,368,493,277,323,296,468,201,289,230,362,430,329,585,614,344,373,332,297,340,260,305,390,837,0,0,95,292,346,330,522,460,349,316,372,331,323,416,431,311,390,328,470,356,459,340,296,336,242,282,435,366,291,310,284,315,234,506,319,219,276,284,351,298,256,251,266,194,288,306,289,213,179,345,308,301,313,232,130,179,282,272,273,430,235,347,287,280,302,296,307,359,264,427,462,306,375,187,355,259,310,373,209,356,319,374,364,381,217,278,291,366,375,362,507,295,303,305,339,245,281,200,341,320,151,371,319,282,378,333,361,260,279,348,403,432,386,395,356,374,285,338,338,423,400,331,301,367,325,378,362,426,375,377,469,457,431,407,496,476,524,460,434,530,857,20
+
+5, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000,172000000,173000000,174000000,175000000,176000000,177000000,178000000,179000000,180000000
+5,Count,261,440,390,487,308,319,396,365,427,320,424,339,387,355,318,256,364,438,494,429,390,488,319,233,375,398,342,345,387,510,300,559,391,291,469,307,314,257,310,345,435,228,265,307,277,92,62,0,0,136,321,290,343,412,393,363,318,283,339,192,320,262,302,157,243,220,240,293,440,82,194,228,304,271,166,312,328,386,348,461,301,268,319,231,509,382,220,171,208,253,294,186,196,185,275,300,362,243,254,357,399,369,323,420,272,356,314,299,191,210,322,196,373,370,296,264,363,296,272,347,275,162,383,247,344,458,293,248,293,203,212,354,364,256,176,196,283,369,216,207,320,435,192,225,297,269,260,266,275,344,226,241,274,376,313,232,287,313,261,372,320,348,382,300,320,372,383,391,279,274,395,351,430,355,370,404,388,477,471,462,272
+
+6, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000,160000000,161000000,162000000,163000000,164000000,165000000,166000000,167000000,168000000,169000000,170000000,171000000
+6,Count,321,344,341,302,402,295,450,513,514,342,417,366,388,393,365,456,292,434,431,419,457,412,425,468,473,387,483,461,514,553,541,748,1702,334,494,379,351,430,308,275,247,357,398,294,386,322,240,441,408,308,283,314,367,332,401,354,264,1311,122,0,0,18,195,332,182,218,391,440,342,325,400,248,388,340,501,220,289,349,117,210,262,414,270,280,191,419,311,356,351,255,281,328,330,333,342,264,329,213,323,343,348,350,294,419,397,264,308,380,235,187,185,369,203,398,344,417,243,311,330,311,380,390,249,327,246,265,146,194,194,270,383,319,279,201,377,267,189,344,287,435,188,387,177,258,258,198,211,215,401,269,253,365,245,487,415,376,369,201,515,466,379,377,394,353,353,353,470,396,270,396,218,9
+
+7, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000,156000000,157000000,158000000,159000000
+7,Count,351,371,419,427,434,665,359,339,238,405,349,277,444,311,309,395,359,266,271,233,407,402,357,371,247,295,266,347,383,389,177,317,571,349,279,319,383,384,413,301,304,266,301,360,341,363,268,338,294,340,334,349,342,301,398,350,579,1025,9,0,0,468,216,499,561,520,397,638,518,239,536,529,162,441,117,471,340,304,384,248,328,262,224,392,274,396,268,125,326,389,293,111,164,232,262,306,358,408,430,121,651,569,405,292,380,385,271,296,282,360,285,170,318,259,258,206,277,234,285,169,247,411,308,286,378,333,298,309,507,529,420,428,272,325,449,418,401,312,319,263,417,250,621,228,330,259,362,428,449,371,367,366,590,376,361,434,471,411,462,89
+
+8, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000
+8,Count,257,400,485,551,457,472,512,198,374,415,330,366,499,647,397,498,326,414,386,318,254,292,351,360,322,440,468,427,350,353,373,383,325,285,211,212,180,281,362,312,381,339,279,189,0,0,32,140,138,170,336,301,368,235,234,318,333,265,250,342,212,325,187,243,189,246,328,175,266,277,354,314,205,339,344,298,360,317,299,107,207,344,305,305,306,285,193,376,221,219,316,148,286,229,198,407,340,305,261,234,146,356,260,333,386,348,217,332,332,248,212,178,345,322,359,141,312,337,254,329,344,369,254,260,311,462,275,365,347,320,304,323,308,289,398,297,281,428,490,369,325,349,195,398,411,219,75
+
+9, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000
+9,Count,491,255,295,302,433,269,443,299,432,318,406,292,420,283,368,346,407,347,254,395,264,228,259,280,291,387,284,331,404,409,232,351,329,598,548,322,426,297,318,152,196,85,153,210,255,215,156,43,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,58,455,305,677,568,162,491,271,377,437,188,329,292,367,328,256,248,288,391,270,302,379,255,203,284,433,263,188,345,304,227,274,393,255,190,386,300,305,268,296,380,317,464,286,212,334,328,314,435,435,448,259,333,414,378,297,333,291,289,378,281,322,264,334,319,342,372,769,415,349,381,453,226,393,347,211,95
+
+10, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000
+10,Count,279,456,465,516,376,506,659,500,505,362,352,379,568,512,437,437,334,425,357,385,430,229,202,256,221,341,525,522,422,556,504,209,545,285,340,428,333,352,795,280,0,0,807,454,235,232,155,224,139,192,337,225,291,360,402,532,470,405,367,461,303,458,279,283,398,447,312,382,302,254,504,373,443,268,268,223,287,275,376,376,244,289,323,314,284,284,322,226,279,320,251,302,265,300,447,411,252,356,293,355,348,470,309,322,509,334,299,368,343,356,305,298,330,311,374,331,370,334,379,353,423,416,399,455,271,327,470,290,310,429,293,279,331,361,319,251
+
+11, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000
+11,Count,401,392,287,365,298,539,337,320,401,556,296,347,325,326,293,288,291,339,439,297,418,441,311,507,476,501,486,343,315,302,320,280,297,404,442,243,371,320,356,388,324,415,358,373,375,244,259,372,517,464,287,113,0,0,45,364,409,368,300,183,308,345,435,376,355,358,257,401,476,350,349,321,287,220,375,267,343,398,273,268,315,354,364,308,221,267,406,250,399,279,456,254,187,358,268,368,219,311,443,475,324,363,329,455,386,325,322,442,287,229,364,289,387,320,356,290,396,302,489,438,209,317,485,432,343,322,351,313,334,277,273,314,225,246,302,0
+
+12, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000
+12,Count,409,445,290,360,390,314,449,437,505,437,504,696,504,337,466,310,274,331,253,472,454,490,271,269,392,492,448,314,247,343,458,490,501,197,267,0,0,93,385,233,424,373,473,290,300,261,239,344,355,231,283,383,305,478,419,223,390,387,312,270,248,322,322,345,422,290,371,267,333,468,388,288,132,354,241,179,325,388,323,190,266,308,382,250,410,194,395,303,280,212,328,340,352,378,366,494,455,355,374,259,360,223,220,242,468,373,299,337,344,236,140,61,82,255,398,404,391,404,307,372,359,479,422,479,346,408,325,415,459,468,432,451,296,308
+
+13, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000
+13,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,554,520,646,415,522,469,476,381,484,505,420,420,376,355,246,278,262,390,301,485,243,351,402,401,346,381,303,359,383,303,267,447,285,194,298,292,438,423,298,324,402,324,464,357,471,406,316,355,324,235,510,432,393,285,371,344,329,398,324,361,393,300,282,438,373,301,361,393,324,322,322,483,352,353,372,337,501,389,222,380,471,473,341,403,381,271,387,416,365,393,460,357,393,307,349,357,40
+
+14, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000
+14,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,350,391,459,533,462,347,394,326,379,292,264,193,342,327,331,364,440,199,299,313,136,345,435,279,316,335,148,373,374,321,209,541,412,375,319,315,206,258,310,370,338,177,353,302,245,349,388,190,127,236,372,317,372,315,402,537,284,317,581,565,284,324,308,250,391,298,324,547,262,256,322,422,400,536,376,292,368,368,282,279,312,368,281,236,460,375,302,781,354
+
+15, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000
+15,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,806,287,607,365,406,291,401,353,325,260,202,378,290,477,592,265,386,378,376,352,438,293,232,128,188,395,310,272,197,246,306,257,283,360,343,370,407,392,372,371,359,388,346,386,369,454,443,349,425,328,293,331,328,288,213,187,379,356,427,345,321,281,241,210,272,442,391,322,221,415,548,402,280,527,403,324,322,322,430,414,402,385,183
+
+16, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000
+16,Count,356,326,308,326,361,382,576,535,539,469,433,400,535,425,251,345,433,404,432,416,326,295,253,529,410,461,367,323,359,310,237,275,705,985,191,28,0,0,0,0,0,0,0,0,0,0,312,101,282,219,416,305,322,227,332,336,399,377,396,271,389,258,374,367,303,302,264,79,319,311,331,370,199,414,445,407,339,407,488,310,230,517,335,388,567,416,337,411,365,386,91
+
+17, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000
+17,Count,416,584,384,438,524,481,434,504,501,457,344,341,428,358,410,292,378,393,345,375,481,866,56,0,0,484,270,331,260,240,333,248,280,319,230,367,366,375,298,380,315,450,428,530,712,433,482,410,455,369,412,363,272,218,239,395,329,420,141,353,405,294,278,477,467,446,475,333,425,362,410,428,448,525,384,440,493,343,433,312,390,30
+
+18, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000
+18,Count,610,358,471,423,363,282,338,273,334,446,324,335,465,336,400,299,0,0,96,360,415,385,262,236,330,272,315,399,279,349,242,312,344,375,228,345,314,292,281,330,358,334,237,330,288,304,286,440,393,325,402,435,302,299,299,498,441,405,256,292,388,313,432,415,400,444,417,402,386,423,396,400,358,389,474,459,388,370,2
+
+19, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000
+19,Count,377,405,535,510,494,493,583,611,687,566,451,353,337,418,507,694,493,554,396,319,478,806,462,679,262,0,0,119,351,337,345,240,228,345,406,468,409,500,458,388,331,422,201,240,501,512,594,455,659,524,324,514,454,453,698,467,601,517,406,43
+
+20, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000
+20,Count,372,315,423,438,437,469,321,305,295,274,378,375,282,304,338,364,269,368,433,239,223,244,241,192,197,545,494,0,0,632,377,409,358,473,110,337,314,351,289,134,283,194,419,266,401,350,355,481,358,385,478,327,540,318,296,409,241,250,200,357,403,285,302,0
+
+21, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000
+21,Count,0,0,0,0,0,0,0,0,0,486,1182,545,0,0,289,366,276,327,578,412,413,439,512,389,452,425,389,616,424,475,399,297,446,372,442,410,272,372,555,360,437,408,422,362,408,360,357,471,52
+
+22, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000
+22,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,333,514,448,298,323,349,470,320,342,490,342,424,201,442,334,495,292,382,408,499,261,302,343,499,322,447,331,509,396,504,265,390,363,545,523,99
+
+GL000191.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000
+GL000191.1,Count,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,1,0,0,0,0,1,2,1,0,0,0,0,2,0,0,0,0,0,0,0,0,1,0,1,0,0,0,2,1,0,0,0,0,0,0,0,0,0,0,1,0,3,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
+
+GL000192.1, Position,0,10000,20000,30000,40000,50000,60000,70000,80000,90000,100000,110000,120000,130000,140000,150000,160000,170000,180000,190000,200000,210000,220000,230000,240000,250000,260000,270000,280000,290000,300000,310000,320000,330000,340000,350000,360000,370000,380000,390000,400000,410000,420000,430000,440000,450000,460000,470000,480000,490000,500000,510000,520000,530000,540000
+GL000192.1,Count,0,0,0,0,0,0,0,0,0,3,1,0,1,3,5,0,5,6,3,3,1,1,1,4,4,0,2,4,1,3,2,1,1,0,2,3,0,3,4,0,0,2,2,0,2,1,1,3,14,3,9,4,13,7,3
+
+GL000193.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000,173000,174000,175000,176000,177000,178000,179000,180000,181000,182000,183000,184000,185000,186000,187000,188000,189000
+GL000193.1,Count,0,0,0,0,0,2,0,0,0,1,2,1,2,2,1,0,2,0,1,0,0,0,1,2,0,0,1,3,0,3,2,0,4,1,4,2,1,1,0,1,0,2,0,2,0,0,0,2,0,0,0,0,1,1,0,0,0,1,1,0,0,1,2,1,0,0,0,0,2,0,0,1,1,0,0,1,0,0,1,2,1,5,2,0,1,3,0,2,1,0,1,0,1,0,0,3,0,0,0,0,2,0,0,0,2,0,1,1,0,1,0,0,0,0,0,1,0,1,0,1,0,1,2,1,0,1,0,1,0,1,0,1,0,1,1,0,0,2,2,1,0,1,2,3,0,1,2,0,0,0,0,0,6,1,2,0,0,0,0,0,3,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,1
+
+GL000194.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000,173000,174000,175000,176000,177000,178000,179000,180000,181000,182000,183000,184000,185000,186000,187000,188000,189000,190000,191000
+GL000194.1,Count,0,1,1,1,1,2,1,5,3,2,1,1,0,1,0,1,0,0,1,1,0,1,3,3,5,4,3,2,3,2,1,1,0,0,0,0,0,0,0,3,0,0,0,0,1,1,0,0,0,0,2,1,0,1,1,0,1,0,0,0,0,0,0,4,1,1,0,2,0,2,0,0,1,1,2,0,0,0,0,0,0,0,3,0,0,0,0,0,0,1,2,1,5,1,0,5,0,1,1,1,1,0,2,0,0,0,3,3,1,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,3,1,0,0,0,1,0,0,1,1,0,0,3,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,2,0,0,0,1,0,2,0,0,0,0,2,0,0,5,1,2,4,1,4,3,3,4,2,0
+
+GL000195.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000,173000,174000,175000,176000,177000,178000,179000,180000,181000,182000
+GL000195.1,Count,1,2,0,0,1,0,0,0,1,1,1,1,1,0,0,0,2,1,0,0,9,2,3,1,2,0,2,0,1,0,1,0,0,0,1,3,2,2,1,1,3,4,5,2,1,1,0,4,2,0,1,2,7,4,9,3,5,2,1,2,2,1,2,0,1,0,2,1,3,0,2,6,1,1,6,3,6,2,1,0,0,0,6,0,1,5,3,5,0,4,1,0,0,1,1,1,0,3,2,2,1,3,0,2,3,1,2,0,0,2,0,0,0,0,0,2,2,4,1,3,1,2,0,2,1,2,2,0,3,0,1,0,0,0,2,2,3,1,0,1,1,1,2,5,2,1,4,3,2,2,1,0,2,2,2,0,0,2,0,2,0,0,0,0,0,1,0,1,5,0,0,0,0,0,0,1,1,0,0,0,1,0,0
+
+GL000197.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000
+GL000197.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
+
+GL000198.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000
+GL000198.1,Count,1,7,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,5,3,2,4,3,7,9,6,4,1,1,5,2,3,3,3,3,4,6,1,10,2,9,1,4,2,3,0,7,7,1,8,4,2,1,0
+
+GL000199.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000
+GL000199.1,Count,0,0,1,0,1,0,0,0,5,1,0,0,0,0,1,0,1,0,0,0,3,0,0,0,0,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,2,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,2,0,0,0,0,0,0,0,2,1,0,0,0,0,0,0,0,1,1,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,1,0,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,5,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,2,0,2,0,0,0,1
+
+GL000201.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000
+GL000201.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0
+
+GL000202.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000
+GL000202.1,Count,0,0,0,0,0,0,0,0,0,0,2,0,1,0,0,0,0,1,2,0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+
+GL000203.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000
+GL000203.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,8,0,2,4,1,4,4,0,0,0,0,0,3,7,4,9,13,4,3,7,1
+
+GL000204.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000
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+GL000216.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000
+GL000216.1,Count,1,3,3,9,1,1,8,1,2,2,2,2,2,2,0,5,1,0,3,0,0,3,1,2,1,5,1,5,5,10,10,3,9,0,2,4,5,6,11,5,8,7,2,5,0,0,1,4,1,4,3,4,4,4,5,6,11,7,14,11,7,9,6,9,4,13,16,12,8,18,9,0,9,8,3,6,3,1,11,9,2,9,5,6,4,4,2,0,8,7,3,10,3,1,0,2,6,6,5,0,1,2,7,3,1,8,1,3,1,3,2,2,1,0,2,1,11,1,1,1,1,8,3,7,2,2,7,1,3,1,2,1,4,1,1,0,0,0,2,0,6,0,1,0,1,0,0,0,0,2,0,0,1,1,2,0,14,4,0,0,2,0,4,0,3,1,7,5,0,0,0,3,0
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+GL000217.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000
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+GL000218.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000
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+GL000219.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000,173000,174000,175000,176000,177000,178000,179000
+GL000219.1,Count,0,0,0,0,0,0,3,0,0,0,1,1,0,1,0,1,0,0,0,2,1,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,4,2,3,6,1,5,3,12,3,7,4,6,7,5,6,8,0,4,7,3,2,6,11,3,4,0,1,0,5,8,4,1,2,1,3,2,4,1,5,0,1,2,1,3,0,9,2,2,1,3,1,2,1,6,1,4,0,2,6,4,1,1,5,4,5,9,0,1,3,1,1,0,0,4,3,8,0,0,3,1,1,1,2,2,5,2,2,2,3,4,7,3,3,3,0,0,1,0,5,3,2,3,6,2,2,2,1,0,1,2,0,2,4,4,2,0,0,3,1,5,0,1,0,0,0,2,2,0,0,2,1,1,2,1,0,0,2,0,1
+
+GL000220.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000
+GL000220.1,Count,1,0,0,5,0,1,0,2,4,1,0,0,0,3,2,0,0,0,1,0,3,0,1,2,0,3,4,0,1,0,2,0,1,3,3,1,0,1,0,0,2,1,2,2,1,1,3,1,0,0,2,2,0,0,2,0,0,0,1,0,1,0,3,1,0,1,0,1,4,1,2,2,1,1,0,0,0,0,1,2,8,5,0,1,0,0,0,0,2,1,0,3,0,7,9,6,0,9,8,11,7,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,6,4,5,1,4,6,7,3,11,10,6,5,6,14,3,1,4,11,0,2,1,0,0,3,0,2,1,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+
+GL000221.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000
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+
+GL000222.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000,173000,174000,175000,176000,177000,178000,179000,180000,181000,182000,183000,184000,185000,186000
+GL000222.1,Count,0,0,0,0,0,0,1,0,2,0,0,0,0,0,0,1,0,1,0,0,1,0,2,1,0,6,2,0,4,2,0,0,0,2,0,0,0,4,0,0,0,0,0,1,0,0,0,2,5,4,11,0,4,6,1,2,5,6,0,3,3,8,5,8,5,7,3,5,0,3,0,0,0,0,0,4,0,0,0,1,6,0,0,0,0,8,2,0,0,0,0,1,0,0,0,3,0,0,0,0,0,0,1,5,2,5,3,1,1,0,1,0,0,0,0,2,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+
+GL000223.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000,130000,131000,132000,133000,134000,135000,136000,137000,138000,139000,140000,141000,142000,143000,144000,145000,146000,147000,148000,149000,150000,151000,152000,153000,154000,155000,156000,157000,158000,159000,160000,161000,162000,163000,164000,165000,166000,167000,168000,169000,170000,171000,172000,173000,174000,175000,176000,177000,178000,179000,180000
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+
+GL000227.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000
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+
+GL000228.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000,46000,47000,48000,49000,50000,51000,52000,53000,54000,55000,56000,57000,58000,59000,60000,61000,62000,63000,64000,65000,66000,67000,68000,69000,70000,71000,72000,73000,74000,75000,76000,77000,78000,79000,80000,81000,82000,83000,84000,85000,86000,87000,88000,89000,90000,91000,92000,93000,94000,95000,96000,97000,98000,99000,100000,101000,102000,103000,104000,105000,106000,107000,108000,109000,110000,111000,112000,113000,114000,115000,116000,117000,118000,119000,120000,121000,122000,123000,124000,125000,126000,127000,128000,129000
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+
+GL000230.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000
+GL000230.1,Count,3,2,2,4,2,0,1,1,1,0,2,2,1,2,2,3,3,2,2,0,3,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+
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+GL000231.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,5,0,0,4,1,0,0,0,0,0,0,1,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,2,0,0,0,0,3,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0,1,0,0,0,1,1,1,2,0,0,0,0,3,3,1,0,0,1,0,1,0,0,0,1,0,0,1,4,0,0,0,0,0,1,1,0,0,1,2,0,0,1,0,0,0,0,2,1,0,0,0,0,0,0,0,3,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,3,4,1,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,3,2,2,0,0,0,0,0,0,1,2,1,0,1,0,0,0,0,1,0,1,0,0,1,0,0,0,0,6,1,0,2,1,0,0,0,0,1,0,1,1,2,0,0,0,0,0,1,0,0,0,0,2,0,1,0,0,1,0,0,0,1,2,0,0,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+
+GL000232.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000
+GL000232.1,Count,5,10,3,7,5,9,6,5,1,2,4,2,0,2,2,6,6,5,5,4,2,5,6,7,5,4,7,2,10,2,4,2,0,7,2,6,2,2,6,5,0
+
+GL000233.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000
+GL000233.1,Count,0,4,0,2,0,3,1,4,0,3,3,1,1,4,1,1,3,2,3,1,5,4,3,2,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+
+GL000234.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000
+GL000234.1,Count,0,0,1,4,2,6,7,5,2,1,8,5,4,4,0,2,3,0,1,2,6,4,1,7,10,5,7,5,2,2,4,5,2,2,12,4,7,14,6,3,0
+
+GL000235.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000
+GL000235.1,Count,3,5,7,2,1,0,2,0,4,4,0,1,4,6,2,1,4,4,2,0,2,5,0,0,2,2,4,1,0,2,4,0,2,4,0
+
+GL000236.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000
+GL000236.1,Count,0,0,2,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,4,0,0,0,0,0,0,0,1
+
+GL000237.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000
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+
+GL000238.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000
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+
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+GL000244.1,Count,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0
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+GL000247.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000
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+
+GL000248.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000
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+MT,Count,0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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+X,Count,1053,986,644,282,170,296,159,83,204,207,64,72,234,178,111,238,97,119,153,70,71,87,166,242,165,92,22,90,69,194,145,154,158,158,111,198,95,68,162,139,256,108,105,124,176,126,222,219,192,89,133,97,73,196,112,145,223,103,34,0,0,33,38,48,62,98,95,178,143,166,145,146,103,145,139,143,141,145,162,168,131,68,147,159,127,170,263,174,242,119,147,167,161,154,109,167,172,147,83,207,210,77,170,177,187,65,140,70,112,86,98,100,181,143,159,163,119,136,315,179,92,204,186,195,215,159,133,186,185,116,106,118,170,96,144,191,165,135,158,205,134,222,128,283,189,146,140,146,148,145,251,129,140,137,113,205
+
+Y, Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000
+Y,Count,0,0,24,47,47,53,44,49,59,277,245,0,0,733,73,51,63,82,69,47,13,53,83,70,23,7,15,20,104,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,258,160
+
diff -r 000000000000 -r 3bad335ccea9 test-data/sortmerna.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,83 @@
+ Tue Jan 31 17:04:24 2017
+
+ Command: /home/lina/sortmerna/sortmerna --ref /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/home/lina/sortmerna/index/silva-bac-16s-db:/home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/home/lina/sortmerna/index/silva-bac-23s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/home/lina/sortmerna/index/silva-arc-16s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/home/lina/sortmerna/index/silva-arc-23s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/home/lina/sortmerna/index/silva-euk-18s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/home/lina/sortmerna/index/silva-euk-28s:/home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5s-db:/home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5.8s-db --reads 25839_merged.fastq --num_alignments 1 --fastx --aligned Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_reads --other Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_free_reads.fastq fastq tq --log -v --blast 1
+ Process pid = 27736
+ Parameters summary:
+ Index: /home/lina/sortmerna/index/silva-bac-16s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.602725
+ Gumbel K = 0.329559
+ Minimal SW score based on E-value = 57
+ Index: /home/lina/sortmerna/index/silva-bac-23s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.602436
+ Gumbel K = 0.335011
+ Minimal SW score based on E-value = 57
+ Index: /home/lina/sortmerna/index/silva-arc-16s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.596286
+ Gumbel K = 0.322254
+ Minimal SW score based on E-value = 55
+ Index: /home/lina/sortmerna/index/silva-arc-23s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.597507
+ Gumbel K = 0.331576
+ Minimal SW score based on E-value = 53
+ Index: /home/lina/sortmerna/index/silva-euk-18s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.612551
+ Gumbel K = 0.339810
+ Minimal SW score based on E-value = 56
+ Index: /home/lina/sortmerna/index/silva-euk-28s
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.612082
+ Gumbel K = 0.345772
+ Minimal SW score based on E-value = 56
+ Index: /home/lina/sortmerna/index/rfam-5s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.616694
+ Gumbel K = 0.342032
+ Minimal SW score based on E-value = 54
+ Index: /home/lina/sortmerna/index/rfam-5.8s-db
+ Seed length = 18
+ Pass 1 = 18, Pass 2 = 9, Pass 3 = 3
+ Gumbel lambda = 0.617555
+ Gumbel K = 0.343861
+ Minimal SW score based on E-value = 52
+ Number of seeds = 2
+ Edges = 4 (as integer)
+ SW match = 2
+ SW mismatch = -3
+ SW gap open penalty = 5
+ SW gap extend penalty = 2
+ SW ambiguous nucleotide = -3
+ SQ tags are not output
+ Number of threads = 20
+ Reads file = 25839_merged.fastq
+
+ Results:
+ Total reads = 4443556
+ Total reads passing E-value threshold = 48848 (1.10%)
+ Total reads failing E-value threshold = 4394708 (98.90%)
+ Minimum read length = 35
+ Maximum read length = 76
+ Mean read length = 74
+ By database:
+ /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta 0.59%
+ /home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta 0.24%
+ /home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta 0.00%
+ /home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta 0.00%
+ /home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta 0.25%
+ /home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta 0.01%
+ /home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta 0.00%
+ /home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta 0.00%
+
+ Tue Jan 31 17:08:40 2017
+
diff -r 000000000000 -r 3bad335ccea9 test-data/sortmerna_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortmerna_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample silva-arc-16s-id95_count silva-euk-28s-id98_pct non_rRNA silva-bac-23s-id98_pct silva-euk-18s-id95_pct silva-bac-23s-id98_count rRNA_pct silva-arc-23s-id98_count rfam-5s-database-id98_pct silva-arc-16s-id95_pct rfam-5s-database-id98_count non_rRNA_pct silva-euk-28s-id98_count rfam-5.8s-database-id98_pct rRNA silva-bac-16s-id90_pct silva-euk-18s-id95_count silva-bac-16s-id90_count total rfam-5.8s-database-id98_count silva-arc-23s-id98_pct
+25839_merged 0.0 0.01 4394708 0.24 0.25 10664.5344 1.09929975002 0.0 0.0 0.0 0.0 98.90070025 444.3556 0.0 48848 0.59 11108.89 26216.9804 4443556 0.0 0.0
diff -r 000000000000 -r 3bad335ccea9 test-data/star_counts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/star_counts.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,5 @@
+N_unmapped 0 0 0
+N_multimapping 1 1 1
+N_noFeature 0 51 48
+N_ambiguous 0 0 0
+GENE1 99 48 51
diff -r 000000000000 -r 3bad335ccea9 test-data/star_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/star_log.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,34 @@
+ Started job on | Mar 01 15:53:05
+ Started mapping on | Mar 01 15:53:08
+ Finished on | Mar 01 15:53:08
+ Mapping speed, Million of reads per hour | inf
+
+ Number of input reads | 100
+ Average input read length | 75
+ UNIQUE READS:
+ Uniquely mapped reads number | 89
+ Uniquely mapped reads % | 89.00%
+ Average mapped length | 74.80
+ Number of splices: Total | 47
+ Number of splices: Annotated (sjdb) | 0
+ Number of splices: GT/AG | 47
+ Number of splices: GC/AG | 0
+ Number of splices: AT/AC | 0
+ Number of splices: Non-canonical | 0
+ Mismatch rate per base, % | 1.73%
+ Deletion rate per base | 0.00%
+ Deletion average length | 0.00
+ Insertion rate per base | 0.00%
+ Insertion average length | 0.00
+ MULTI-MAPPING READS:
+ Number of reads mapped to multiple loci | 1
+ % of reads mapped to multiple loci | 1.00%
+ Number of reads mapped to too many loci | 0
+ % of reads mapped to too many loci | 0.00%
+ UNMAPPED READS:
+ % of reads unmapped: too many mismatches | 0.00%
+ % of reads unmapped: too short | 10.00%
+ % of reads unmapped: other | 0.00%
+ CHIMERIC READS:
+ Number of chimeric reads | 0
+ % of chimeric reads | 0.00%
diff -r 000000000000 -r 3bad335ccea9 test-data/star_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/star_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample uniquely_mapped_percent num_splices num_GCAG_splices insertion_length deletion_length unmapped_tooshort_percent avg_mapped_read_length deletion_rate mismatch_rate avg_input_read_length num_ATAC_splices num_annotated_splices num_GTAG_splices uniquely_mapped multimapped_toomany unmapped_mismatches unmapped_mismatches_percent total_reads unmapped_other insertion_rate unmapped_other_percent multimapped_percent multimapped num_noncanonical_splices unmapped_tooshort multimapped_toomany_percent
+star_log 89.0 47.0 0.0 0.0 0.0 10.0 74.8 0.0 1.73 75.0 0.0 0.0 47.0 89.0 0.0 0 0.0 100.0 0 0.0 0.0 1.0 1.0 0.0 10 0.0
diff -r 000000000000 -r 3bad335ccea9 test-data/tophat.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,14 @@
+Left reads:
+ Input : 316390
+ Mapped : 314921 (99.5% of input)
+ of these: 5715 ( 1.8%) have multiple alignments (0 have >20)
+Right reads:
+ Input : 316390
+ Mapped : 314789 (99.5% of input)
+ of these: 5707 ( 1.8%) have multiple alignments (0 have >20)
+99.5% overall read mapping rate.
+
+Aligned pairs: 313405
+ of these: 5638 ( 1.8%) have multiple alignments
+ 34 ( 0.0%) are discordant alignments
+99.0% concordant pair alignment rate.
diff -r 000000000000 -r 3bad335ccea9 test-data/tophat_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample unaligned_total aligned_total aligned_not_multimapped_discordant overall_aligned_percent aligned_multimap aligned_discordant total_reads concordant_aligned_percent
+tophat_align 2985.0 313405.0 307733.0 99.5 5638.0 34.0 316390.0 99.0
diff -r 000000000000 -r 3bad335ccea9 test-data/trimmomatic.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,6 @@
+TrimmomaticSE: Started with arguments: -threads 52 -phred64 -trimlog C2.log.txt C2.fastq.gz C2.Processed ILLUMINACLIP:./Trimmomatic-0.32/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:24 MINLEN:21
+Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
+Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
+ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
+Input Reads: 39733090 Surviving: 32590558 (82.02%) Dropped: 7142532 (17.98%)
+TrimmomaticSE: Completed successfully
\ No newline at end of file
diff -r 000000000000 -r 3bad335ccea9 test-data/trimmomatic_stats.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_stats.tabular Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,2 @@
+Sample input_reads surviving_pct dropped surviving dropped_pct
+C2 39733090.0 82.02 7142532.0 32590558.0 17.98
diff -r 000000000000 -r 3bad335ccea9 test-data/vcftools.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcftools.txt Tue Oct 24 06:29:59 2017 -0400
@@ -0,0 +1,1000 @@
+QUAL_THRESHOLD N_Ts_LT_QUAL_THRESHOLD N_Tv_LT_QUAL_THRESHOLD Ts/Tv_LT_QUAL_THRESHOLD N_Ts_GT_QUAL_THRESHOLD N_Tv_GT_QUAL_THRESHOLD Ts/Tv_GT_QUAL_THRESHOLD
+3.01037 0 0 -nan 1.5337e+07 6.70583e+06 2.28711
+3.01039 1 0 inf 1.5337e+07 6.70583e+06 2.28711
+3.01041 2 0 inf 1.5337e+07 6.70583e+06 2.28711
+3.01042 3 0 inf 1.5337e+07 6.70583e+06 2.28711
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+3.01058 6 3 2 1.5337e+07 6.70583e+06 2.28711
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