Mercurial > repos > iuc > arriba_get_filters
changeset 0:125d20cb23d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
| author | iuc |
|---|---|
| date | Wed, 27 Jul 2022 11:25:14 +0000 |
| parents | |
| children | 1fe9d667447c |
| files | arriba_get_filters.xml macros.xml static/images/draw-fusions-example.png test-data/Aligned.out.bam test-data/Aligned.out.bam.bai test-data/Aligned.out.sam test-data/cytobands.tsv test-data/fusions.tsv test-data/genome.fasta.gz test-data/genome.gtf.gz test-data/protein_domains.gff3 tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 13 files changed, 588 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba_get_filters.xml Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,73 @@ +<tool id="arriba_get_filters" name="Arriba Get Filters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> + <description>to history</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + BASE_DIR=\$(dirname \$(dirname `which arriba`)) && + REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && + REF_DIR=\$(dirname \$REF_SCRIPT) && + REF_NAME=${arriba_reference_name.split('+')[0].replace('viral','')} && + echo \$REF_NAME && + cp `find \$REF_DIR -name 'blacklist_*' | grep -i \$REF_NAME` '$blacklist' && + cp `find \$REF_DIR -name 'known_fusions_*' | grep -i \$REF_NAME` '$known_fusions' && + cp `find \$REF_DIR -name 'protein_domains_*' | grep -i \$REF_NAME` '$protein_domains' && + cp `find \$REF_DIR -name 'cytobands_*' | grep -i \$REF_NAME` '$cytobands' + #* + cp "\$REF_DIR/blacklist_*${arriba_reference_name}*" '$blacklist' && + cp "\$REF_DIR/known_fusions_*${arriba_reference_name}*" '$known_fusions' && + cp "\$REF_DIR/protein_domains_*${arriba_reference_name}*" '$protein_domains' && + cp "\$REF_DIR/cytobands_*${arriba_reference_name}*" '$cytobands' + *# + ]]></command> + <inputs> + <param name="arriba_reference_name" type="text" label="Select reference"> + <help>GRCh38 GRCh37 hg38 hg19 GRCm38 mm10</help> + <option value="GRCh38">GRCh38</option> + <option value="GRCh37">GRCh37</option> + <option value="hg38">hg38</option> + <option value="hg19">hg19</option> + <option value="GRCm39">GRCm39</option> + <option value="GRCm38">GRCm38</option> + <option value="mm39">mm39</option> + <option value="mm10">mm10</option> + </param> + </inputs> + <outputs> + <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/> + <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/> + <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> + <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> + </outputs> + <tests> + <test> + <param name="arriba_reference_name" value="GRCh38"/> + <output name="cytobands"> + <assert_contents> + <has_text_matching expression="1\t1\t\d+\tp36.33\tgneg"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**Arriba Get Filters** + +Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. +It is based on chimeric alignments found by the STAR RNA-Seq aligner. + +The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history: + + - blacklist + - known_fusions + - protein_domains + - cytobands + + +.. _Arriba: https://arriba.readthedocs.io/en/latest/ +.. _input_files: https://arriba.readthedocs.io/en/latest/input-files/ + +]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,311 @@ +<macros> + <token name="@TOOL_VERSION@">2.3.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.257246.119</citation> + <yield /> + </citations> + </xml> + <xml name="version_command"> + <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command> + </xml> + <xml name="genome_source" token_assembly_optional="false" > + <conditional name="genome"> + <param name="genome_source" type="select" label="Genome assembly fasta (that was used for STAR alignment)"> + <option value="history">From your history</option> + <option value="cached">Use built-in Genome reference</option> + </param> + <when value="history"> + <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/> + </when> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="all_fasta"> + <validator type="no_options" message="No reference genomes are available" /> + </options> + </param> + </when> + </conditional> + </xml> + <xml name="gtf_source" token_assembly_optional="false" > + <conditional name="genome_gtf"> + <param name="gtf_source" type="select" label="Genome GTF annotation source"> + <option value="history">From your history</option> + <!-- <option value="cached">Use built-in Gtf annotation</option> --> + </param> + <when value="history"> + <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/> + </when> + </conditional> + </xml> + + <token name="@GENOME_SOURCE@"><![CDATA[ +#if str($genome.genome_source) == "history" + #if $genome.assembly + #set $genome_assembly = 'genome.fa' + ln -sf '$genome.assembly' $genome_assembly && + #end if +#elif str($genome.genome_source) == "cached" + #set $genome_assembly = $genome.ref_file.fields.fasta +#end if + ]]></token> + <token name="@GTF_SOURCE@"><![CDATA[ +#if str($genome_gtf.gtf_source) == "history" + #if $genome_gtf.annotation.is_of_type('gtf.gz') + #set $genome_annotation = 'genome.gtf.gz' + #else + #set $genome_annotation = 'genome.gtf' + #end if + ln -sf '$genome_gtf.annotation' $genome_annotation && +#end if + ]]></token> + + <xml name="visualization_options"> + <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> + <section name="options" expanded="false" title="Draw Fusion Options"> + <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/> + <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> + <help>By default the transcript isoform with the highest coverage is drawn. + Alternatively, the transcript isoform that is provided in the columns + transcript_id1 and transcript_id2 in the given fusions file can be drawn. + Selecting the isoform with the highest coverage usually produces nicer plots, + in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint. + However, the isoform with the highest coverage may not be the one that is involved in the fusion. + Often, genomic rearrangements lead to non-canonical isoforms being transcribed. + For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2, + which reflect the actual isoforms involved in a fusion. +\ As a third option, the transcripts that are annotated as canonical can be drawn. + Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical. + </help> + <option value="coverage">coverage</option> + <option value="provided">provided</option> + <option value="canonical">canonical</option> + </param> + <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection"> + <help>The fusion of interest is drawn as a solid line in the circos plot. + To give an impression of the overall degree of rearrangement, + all other fusions are drawn as semi-transparent lines in the background. + This option determines which other fusions should be included in the circos plot. + Values specify the minimum confidence a fusion must have to be included. + It usually makes no sense to include low-confidence fusions in circos plots, + because they are abundant and unreliable, and would clutter up the circos plot. + Default: medium + </help> + <option value="none">none - only the fusion of interest is drawn</option> + <option value="low">low</option> + <option value="medium">medium</option> + <option value="high">high</option> + </param> + <param argument="--squishIntrons" type="select" optional="true" label="Squish introns"> + <help>Exons usually make up only a small fraction of a gene. + They may be hard to see in the plot. i + Since introns are in most situations of no interest in the context of gene fusions, + this switch can be used to shrink the size of introns to a fixed, negligible size. + It makes sense to disable this feature, if breakpoints in introns are of importance. + Default: TRUE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity"> + <help>This option only applies to intergenic breakpoints. + If it is set to a value greater than 0, then the script draws the genes + which are no more than the given distance away from an intergenic breakpoint. + The keywords closestGene and closestProteinCodingGene instruct the script + to dynamically determine the distance to the next (protein-coding) gene for each breakpoint. + Alternatively, instead of specifying a single distance + that is applied upstream and downstream of both breakpoints alike, + more fine-grained control over the region to be shown is possible by specifying four comma-separated values. + The first two values determine the region to the left and to the right of breakpoint 1; + the third and fourth values determine the region to the left and to the right of breakpoint 2. + Note that this option is incompatible with squishIntrons. + Default: 0 + </help> + <option value="closestGene">closestGene</option> + <option value="closestProteinCodingGene">closestProteinCodingGene</option> + <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator> + </param> + <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By"> + <help>Occasionally, domains are annotated redundantly. + For example, tyrosine kinase domains are frequently annotated as + Protein tyrosine kinase and Protein kinase domain. + In order to simplify the visualization, such domains can be merged into one, + given that they overlap by the given fraction. + The description of the larger domain is used. + Default: 0.9 + </help> + </param> + <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels"> + <help>By default the number of an exon is printed inside each exon, + which is taken from the attribute exon_number of the GTF annotation. + When a gene has many exons, the boxes may be too narrow to contain the labels, + resulting in unreadable exon labels. In these situations, i + it may be better to turn off exon labels. + Default: TRUE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect"> + <help>Whether light and shadow should be rendered to give objects a 3D effect. + Default: TRUE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors"> + <help>By default, the script colorizes domains according to the colors + specified in the file given in --annotation. + This way, coloring of domains is consistent across all proteins. + But since there are more distinct domains than colors, + this can lead to different domains having the same color. + If this option is set to TRUE, the colors are recomputed for each fusion separately. + This ensures that the colors have the maximum distance for each individual fusion, + but they are no longer consistent across different fusions. + Default: FALSE + </help> + <option value="TRUE">True</option> + <option value="FALSE">False</option> + </param> + <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/> + <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/> + <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches" + help="Default: 11.692"/> + <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches" + help="Default: 8.267"/> + <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text" + help="Default: 1.0"/> + <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots."> + <help>Default: Helvetica + </help> + <option value="serif">serif</option> + <option value="sans">sans</option> + <option value="mono">mono</option> + <option value="AvantGarde">AvantGarde</option> + <option value="Bookman">Bookman</option> + <option value="Courier">Courier</option> + <option value="Helvetica">Helvetica</option> + <option value="Helvetica-Narrow">Helvetica-Narrow</option> + <option value="NewCenturySchoolbook">NewCenturySchoolbook</option> + <option value="Palatino">Palatino</option> + <option value="Times">Times</option> + <option value="URWGothic">URWGothic</option> + <option value="URWBookman">URWBookman</option> + <option value="NimbusMon">NimbusMon</option> + <option value="NimbusSan">NimbusSan</option> + <option value="URWHelvetica">URWHelvetica</option> + <option value="NimbusSanCond">NimbusSanCond</option> + <option value="CenturySch">CenturySch</option> + <option value="URWPalladio">URWPalladio</option> + <option value="NimbusRom">NimbusRom</option> + <option value="URWTimes">URWTimes</option> + <option value="ArialMT">ArialMT</option> + <option value="Japan1">Japan1</option> + <option value="Japan1HeiMin">Japan1HeiMin</option> + <option value="Japan1GothicBBB">Japan1GothicBBB</option> + <option value="Japan1Ryumin">Japan1Ryumin</option> + <option value="Korea1">Korea1</option> + <option value="Korea1deb">Korea1deb</option> + <option value="CNS1">CNS1</option> + <option value="GB1">GB1</option> + </param> + <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions"> + <help>By default, transcripts are scaled automatically to fill the entire page. + This parameter enforces a fixed scale to be applied to all fusions, + which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable. + A common use case is the visualization of a gene that is found to be fused to multiple partners. + By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage + in a single plot one above the other with matching scales. + Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn, + or else dynamic scaling is applied, because display errors would occur otherwise. + The default value is 0, which means that no fixed scale should be used + and that the scale should be adapted dynamically for each fusion. Default: 0 + </help> + </param> + <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot"> + <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes. + The plots can be cropped at a fixed level by passing a non-zero value to this parameter. + When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level. + When two comma-separated values are given, the cutoffs can be specified independently for the two plots. + A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage) + and that the coverage plots of both genes should be on the same scale. This is the default behavior. + A value of 0,0 also indicates that no cropping should be applied, + but the coverage plots of the two genes have different scales: + each one is scaled individually to the peak coverage of the respective gene. + Default: 0 + </help> + <validator type="regex" message="">^\d+(,\d+)?$</validator> + </param> + </section> + </xml> + <token name="@DRAW_FUSIONS@"> +draw_fusions.R + --fusions='$fusions' + --alignments='Aligned.sortedByCoord.out.bam' + --annotation='$genome_gtf.annotation' + --output=fusions.pdf + #if $visualization.cytobands + --cytobands='$visualization.cytobands' + #end if + #if $protein_domains + --proteinDomains='$protein_domains' + #end if + ## Visualization Options + #if $visualization.options.transcriptSelection + --transcriptSelection=$visualization.options.transcriptSelection + #end if + #if $visualization.options.minConfidenceForCircosPlot + --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot + #end if + #if $visualization.options.squishIntrons + --squishIntrons=$visualization.options.squishIntrons + #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity + --showIntergenicVicinity='$visualization.options.showIntergenicVicinity' + #end if + #end if + #if $visualization.options.mergeDomainsOverlappingBy + --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy + #end if + #if $visualization.options.sampleName + --sampleName='$visualization.options.sampleName' + #end if + #if $visualization.options.printExonLabels + --printExonLabels=$visualization.options.printExonLabels + #end if + #if $visualization.options.coverageRange + --coverageRange='$visualization.options.coverageRange' + #end if + #if $visualization.options.render3dEffect + --render3dEffect=$visualization.options.render3dEffect + #end if + #if $visualization.options.optimizeDomainColors + --optimizeDomainColors=$visualization.options.optimizeDomainColors + #end if + #if $visualization.options.color1 + --color1='$visualization.options.color1' + #end if + #if $visualization.options.color2 + --color2='$visualization.options.color2' + #end if + #if str($visualization.options.pdfWidth) + --pdfWidth=$visualization.options.pdfWidth + #end if + #if str($visualization.options.pdfHeight) + --pdfHeight=$visualization.options.pdfHeight + #end if + # fontFamily + #if $visualization.options.fontFamily + --fontFamily=$visualization.options.fontFamily + #end if + #if str($visualization.options.fontSize) + --fontSize=$visualization.options.fontSize + #end if +</token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Aligned.out.sam Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,89 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:22 LN:269079 +@SQ SN:9 LN:515509 +@PG ID:STAR PN:STAR VN:2.7.8a CL:STAR --runThreadN 12 --genomeDir tempstargenomedir --genomeLoad NoSharedMemory --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --limitBAMsortRAM 122880000000 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM ch --outSAMunmapped Within --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --outSAMattrIHstart 1 --winAnchorMultimapNmax 50 --chimSegmentMin 12 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --twopassMode Basic +@CO user command line: STAR --runThreadN 12 --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outSAMunmapped Within --chimSegmentMin 12 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 122880000000 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1 +BCR-ABL1-46 163 22 225687 60 71M2994N7M1344N72M = 225737 5255 AACTGGAGGCAGTGCCCAACATCCCCCTGGTGCCCGATGAGGAGCTGGACGCTTTGAACATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTG CCCGGGGGG=GGGJJJGGJJJGGJJJJCJJGGJJGCJGCGGGC8J8JGGJJJJJGJJC(JGCCG=GGJJGCCCGC8GCCGGGGGG=GGCGGG1GG=GC1G=CJCJJCCCGGCGG1CGG1GGGGGGGG=GGGGGCCGCGGG8GGGCGG=GG NH:i:1 HI:i:1 AS:i:285 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-72 163 22 225696 60 62M2994N7M1344N81M = 228752 5264 CAGTGCCCAACATCCCCCTGGTGCCCGATGAGGAGCTGCACGCTTTGAAGATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCA CCCCGGGGGGGGGGJGJCCCJ1GJJJJGCGGGCJJJ=C1JJGGJGG8JGC=CCGJ1JGG8GGGGGJCGJCCGGGCG=CGGGGGGCGG=GGCGGG=8CCGCGGJJJ=JGGGCGGGGGCCGCCGGGGGGGGC=CCGCG8GGGGGC1GGGGCC NH:i:1 HI:i:1 AS:i:290 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-46 83 22 225737 60 21M2994N7M1344N105M717N17M = 225687 -5255 GCTTTGAAGATCAAGATCTCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGG =GGCGGGGGGG=GGGCCCGCCCGGGGGGGGGGCCGGGGCGG8CGCGGG1JGGCCGG(C=GCCCGGGGGGCGGGGGCGCGGCGGJCGGGJJGJGGGJJCGGGJJJGJJJJJJJGJJJJGGGJJJJJGGJJJJJGCJJJCGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:285 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-72 83 22 228752 60 3S7M1344N105M717N35M = 225696 -5264 TCCAAGAAGTGTTTCAGAAGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAAT =GGGGGG==GGGGCCCC=GGGGG=GGGGCGGGCGGGGGGG=CGGCCGCCJGGCGGGGG=GGG8GGGCGGC=G=CCJGGGGGGCGJJGJJCGGGGGGJJJGCJCCGJG=JJJGJGJJCJJJJGJJJJJJJ=GCJGJGCGGG=GGGGGGCC= NH:i:1 HI:i:1 AS:i:290 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-4 99 22 230111 60 97M717N53M = 230176 889 AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCC C==GGGGGGGGGGJJJJ1JJJGGJJGGJGGJJGJJCJGJGJJCGGCJGCJJJJCGJGGGGJGGGGGGCCGG8JGGCGCGG=GGGGGGGGGGGGGG=GCCGJGGGCCGGGGGG1GGGGGGCGCGGCGGGGGG=GGGGGGGGGCCGCGGGCC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 XS:A:+ NM:i:0 +BCR-ABL1-18 99 22 230118 60 90M717N60M = 230165 882 CCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGTAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCAATCAGCCACTGGAT CCCGGGCGGGCGGJGJJJJJJJJJ=GCJJCJJJJJGJJJGJJGJJJCGGJJGGJCGJC=GG8GCGJGCGCG==GGGCGGGGG1CCCGCGGGGGCGGCCGGC=GCGGG=GGGGCGGGGCGCGGGGGGG=GGGCGGGG(GGGCGGGCGCCGG NH:i:1 HI:i:1 AS:i:266 nM:i:2 XS:A:+ NM:i:2 +BCR-ABL1-12 163 22 230132 60 76M717N74M = 230923 868 GAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCA CCCGGGGGGGGGGJGGJJJJJCCJJCJJGJJGJJGGCJJJCJCGGGJJ=CGJGJJJJGGCGGGJJJ==GG(GGC=GGGGGGCGCGG(GGGGC1C8GCC=GG=C=CCJGGGGGG8CGGCCCGCGGGGGGGGCGGGG=GGGGGCGGGG=GGC NH:i:1 HI:i:1 AS:i:227 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-18 147 22 230165 60 43M717N75M32S = 230118 -882 CTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTT =GCGGGGG(GGGGGGGGGGGCC=GGC=GGCGGCCGGGGCGGG8JJJJ=GCGGGGG1GGGCCGGGCCGGGCGGCGGGJGC8GCCGCGGCG=GJCGJJGC8GC1JGG=GJJCJC1JGJGGJJJGJGCJJJ=1JJJJ=JGGCG=GGCGGGCCC NH:i:1 HI:i:1 AS:i:266 nM:i:2 XS:A:+ NM:i:0 +BCR-ABL1-4 147 22 230176 60 32M717N75M43S = 230111 -889 CCACAGCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGG CGGCGGGGGCGGCGCCG=GCGCGGGG8GCG881CGG=C=GCCGJJCJCCCGGG8GGCGG=GGGCCCGGCGGCCCCGGCGGGG=GGCGCJJGCGGJG1JGJJJ8JGJJCJJJ(JJGJGJJJGGJJGJCC1JJCGGJGG=GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 XS:A:+ NM:i:0 SA:Z:9,275100,-,107H43M,60,0; +BCR-ABL1-12 83 22 230923 60 19S77M54S = 230132 -868 CGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAG 8CCCGGCCGGCCGGGGGCGG1CCG=GGCGGGGGC1GGGGCCGCGGGGCCJGG=CGGCGGGGCGCGCGGGCGGCGGJG==GGCGCJGCGGGCJGGGGGGGCJGJGGJJJGJGGGGCJJJGJJJGGJGJJJGJJCCJJGGG1GGGGGGG=CC NH:i:1 HI:i:1 AS:i:227 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-60 2145 22 230961 60 39M111H 9 275110 0 TCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA =CCGGCGGGGG=GJJGJGGGCJJCJJGJCGJG(J(JJJG NH:i:1 HI:i:1 AS:i:38 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,39S111M,60,0; +BCR-ABL1-76 2145 22 230973 60 27M123H 9 275139 0 CAGCCACTGGATTTAAGCAGAGTTCAA CCCGGGGCGGGCGJJJJJGJJJGJJJJ NH:i:1 HI:i:1 AS:i:26 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,27S123M,60,0; +BCR-ABL1-28 2209 22 230978 60 22M128H 9 275128 0 ACTGGATTTAAGCAGAGTTCAA CCCGCGGGGGGGGGJ=GJCGJJ NH:i:1 HI:i:1 AS:i:21 nM:i:0 ch:A:1 NM:i:0 SA:Z:9,275100,+,22S128M,60,1; +BCR-ABL1-64 99 9 275097 60 6S144M = 275140 756 AGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGG CCCGGGGGCGGGGGJJJGJJJGGJJJJJCJJJJGGJJJGJJGJGJG=GGJG=JJJJCGCCC==JGGCGGGCJG1CCCCGG8CGGGGGGGGCCGC=CGCGGJGGGGCGCGGGGGGGGCCGCGGGG=GCGGGGGGG=GGGGCGGGGGGCCGG NH:i:1 HI:i:1 AS:i:290 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-54 99 9 275097 60 61S89M = 275097 140 CCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTGAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTC CCCGGGGGGGGGGGJJJJJGJ=JJJJJJGJJJGGJJJJJJJCJJG8JJJGJJGJ=GG=JJJGGCGGCGGJGC(GGGGGCGC8CGGCGCCGGC=GGGCGGGJG1GGGGGG1CG=GGGGC=1G1CGGGGGCCGGGGCGG=CC=C=CGGGGG8 NH:i:1 HI:i:1 AS:i:219 nM:i:4 NM:i:2 +BCR-ABL1-54 147 9 275097 60 10S140M = 275097 -140 AAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACGTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTT =GGGGGGGCCCCGCCGGG=G(GGGG=CGCGGCGCCGG=GGGGGCJJJ=GC8C1GGGGGCG8GCCGC=GGG1GCCGGJC8GCGGCGCGJGJJJG1CGJGG=CJJJGGGGJG=CJGJJJJCJCJJGGJJJJJGGJGGJJCGGGGGGGGG=CC NH:i:1 HI:i:1 AS:i:219 nM:i:4 NM:i:2 +BCR-ABL1-48 163 9 275097 60 3S147M = 275137 753 GTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCA CCCGGGCGGGGGGGJ1JJJJJJJCJJJCGJJCGGJCJJGJGGJJJGGGCGJJ=GJJJG=JCG=GJGGGC8=GCG=G=GCCGGG1CG1GC=GGG8GGGGG1GCJJCJJCCGGCGCCG=CGCGGGCGG=GCGGG1CGC1CGC=CGGGCGGGG NH:i:1 HI:i:1 AS:i:295 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-2 99 9 275097 60 62S88M = 275097 134 TCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCCTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCT CCCGGGGGGGGGGGJ1JJJJJJ=JGGGGJJJCGCJJJCJJJJGGCJGGGJCJGGJJGJCGJGG1GCG=CGG(G=CGGG1GGCCGGGGGGGCGGGG=GCCGJGGCGCGGGGCCCG1GGGCCGGG8GGCGGCGG=CC(G=GC1GGCCGGGCG NH:i:1 HI:i:1 AS:i:214 nM:i:3 NM:i:2 +BCR-ABL1-2 147 9 275097 60 16S134M = 275097 -134 GGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTAT CGGGC=GGGGG=GGGGGGCCCCG=GG8=8CCGCGGGGGCGCGCJJCJ=CCCCC81GGGGC=GGGC8C8GGCGCGJCCGG8JCCGCC1GGCGGCJGGGJJJGGJJJJJCGGJGCJJJJJJG=JGJGJJJJGJJJGGJGCGCGGGGGGGCCC NH:i:1 HI:i:1 AS:i:214 nM:i:3 NM:i:1 +BCR-ABL1-76 99 9 275100 60 27S123M = 275139 752 CAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTG CCCGGGGCGGGCGJJJJJGJJJGJJJJJJJJJGJ1JCJJGJGGJJJGJJGGJJJ8GGJJGGGJJ=GGCGGGGGG=GGCCGGG8GC=GGGG=GCGGCGGGGJGG=GGGG=GGGGGGGGCGGGGCCGGGCG=GG(G=GCGCCG1CCGGCGGG NH:i:1 HI:i:1 AS:i:273 nM:i:0 ch:A:1 XS:A:+ NM:i:0 SA:Z:22,230973,+,27M123H,60,0; +BCR-ABL1-68 99 9 275100 60 1S149M = 275125 175 AAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGA CC1=GC=GGGGGGJJJJGJJJJJGGJJJJJJJGJJJJJ=(GJGGG8CCGJJ=GJGGGGJGJGJ=GGGCCGCGGCG1CGCGGGGGGGCGCCGCGGCGGGGGJGCC8GCGGGGCGGC=GGGGG=GGGCCC=GCGGGGGGCGCGGGCGGCGCG NH:i:1 HI:i:1 AS:i:291 nM:i:3 NM:i:0 +BCR-ABL1-60 99 9 275100 60 39S111M = 275110 160 TCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCA =CCGGCGGGGG=GJJGJGGGCJJCJJGJCGJG(J(JJJGGCGGGJJJGCJGGG1G=JGGJJGCJCCGGJ(JJCCGCC=GCGGGCGGGGG1GGGGCGCGG(JCGCGGGGGGGGGGGGCCGGCGCGCGGGGGGGCGGGGCGG1GGGGGGCGC NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 NM:i:0 SA:Z:22,230961,+,39M111H,60,0; +BCR-ABL1-28 163 9 275100 60 22S128M = 275128 741 ACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCCCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTG CCCGCGGGGGGGGGJ=GJCGJJJ1JCJJJJGJJJJJCCJJJJG8JJCC=CGGCGGJGGC(JGGG=GCCGCGCJ8CGGG=GGGCGGGGGCGGCCGGCCGGGCCJ=JC=CGCGCGC1G8GCCGGGGGC=GCGGGCGGGGGGGGGGGGGCGCC NH:i:1 HI:i:1 AS:i:274 nM:i:2 ch:A:1 XS:A:+ NM:i:1 SA:Z:22,230978,+,22M128H,60,0; +BCR-ABL1-4 2193 9 275100 60 107H43M 22 230111 0 AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGG CJJJ(JJGJGJJJGGJJGJCC1JJCGGJGG=GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:42 nM:i:0 ch:A:1 NM:i:0 SA:Z:22,230176,-,32M717N75M43S,60,0; +BCR-ABL1-60 147 9 275110 60 150M = 275100 -160 GCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCT GCGGCCCGCGG=GG8GGCGGGGCCGCC=GCGCGGCG1GGCGG1JCJJ8CCCG=GGGGGGCG=GCGGGG18CCGCG=GGGG1CGG8C=GGGGCGGCJGJGJGJGJJGGJGJJJGJGJJJGGJC(JJJGJJJGJCJJGCGGGGGCGGGGCC= NH:i:1 HI:i:1 AS:i:259 nM:i:0 ch:A:1 NM:i:0 +BCR-ABL1-68 147 9 275125 60 150M = 275100 -175 TGACTTTGAGCCTCAGGGTCTAAGTGAAGCCGCTCGTAGGAACTCCAAGGAAAACCTTCTCGGTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGG G=CGGCGGGCCGCGCGGCCGG8GCCGCC(GGC=8=GGG=GGGCJ1=JJCCGGGCGGGGGGGG=GCGGGGCGCG==GGCGGGGGJGCCJJGGCCG=GCCCGGJCGGJJJJJ=GJJJJGJCJ=GCJGJGJJJC1GGJJJGGG=GG1GGGCCC NH:i:1 HI:i:1 AS:i:291 nM:i:3 NM:i:3 +BCR-ABL1-50 99 9 275125 60 150M = 275169 757 TGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGG CC1GGCGCGGGG=JGCJJJJJGJJJGJJGGJJGJJ8JGCGJJJJJJ8CJJGJJCGJGGGGJJCCG=CGGGGGCCCG=CGGCCGCGGGGGCGG=GGGGGGGCCGGG==GGGGGCCGG=GGGGCCG=GGGGGCCC=GGCGGGGCCGGCCGGG NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-28 83 9 275128 60 146M563N4M = 275100 -741 CTTTGAGCCTCAAGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGA GGGGGCGGGG=C1=8GGCGCGGGCGCGGGGG=GC=GGGGCG1CCCGCGGCCGGGC=GG=GGGGGCCGGGGCGGGCGJJGGGGCGGJ1JGGGGCGGJGJGGJJJCGGCJJCGJ=GJGCGGJJJJGGJJG1JJJGG1JJ=GGCGCGGG1CCC NH:i:1 HI:i:1 AS:i:274 nM:i:2 ch:A:1 XS:A:+ NM:i:1 +BCR-ABL1-48 83 9 275137 60 137M563N13M = 275097 -753 TCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCG GGGCGGCGCGGGG8GGGGGCGGCGGGCG1GCGCGG8GCGGCGC1G8CCGCGCGGCCGGGGGCGCCGCC1=CCCCGCCJCGGGGGGJJGJC=CCJ8JJC=JJCGCJJJGJJJJJJJJJJGJJGGGCJJJJJJJGJGJGCGGCGGGCGC=C1 NH:i:1 HI:i:1 AS:i:295 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-76 147 9 275139 60 135M563N15M = 275100 -752 AGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGG CGGCGGGGCGGGGGGCGCCGCGCGGGGC=GGCGCCGCGCGGGCJJCJC1GGGGG=GCGGGGG=GGGGGGGGGGGGGCGGCGGGGGGJGJCGJGGJGJCJGJJJJJG8JJCJGG1JJJJJJJG8(JJJJJGJJJGJJJGGGGGGGG1GCCC NH:i:1 HI:i:1 AS:i:273 nM:i:0 ch:A:1 XS:A:+ NM:i:0 +BCR-ABL1-64 147 9 275140 60 134M563N16M = 275097 -756 GGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTGTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGT C=GGGGGCGGCGGGGGGC=GGGGC1CG=1=GGGCCC=GGGCGCCCCJJGCGCGGGGCGGCGCGCCGCCGCGGGGGCGC1GGGGG=GG1CGJGJJJ(CCGGJJGCGJGJGJJJGGGCGJGJJJJJJJJJGJGJGJJJCGCGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:290 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-14 99 9 275146 60 128M563N22M = 275170 737 GAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGG CC=GGGGGGGGGGJGJJCJGJJJGG1JJGJ=JGGGJJJJGGJJJGCJJCGJJGC=GCJGGJGGCGGGCCGGGCGGCGCGGGGGGGGGGGGCC8GGGGCGCJCGGGCCCGCG8GGGGCGGGCGGCGGGGGGCGGGGGCGGG=GGGGGGCCG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-78 99 9 275151 60 123M563N27M = 275200 762 AAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATA CC=1G=GGGGCGGJJJJGJJGG8JJCJGJGJJ8JJJJGJCGJGJJ=JGGGCGJCJCGGG=JJJJGGG=JGC=GGGCGGGGGGCGGCG=GCCGGGGGGCGGJCGCCGCGGGGGGGCCGGGGCGCCGGG=GGGCGCGGGGCGGGCCGGGGGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-62 163 9 275157 60 117M563N33M = 275215 771 CTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACA CCCCGGGGGGGGCJGGGJJGJJJJJJJ=GJJCJJGJCJGJCGCGCGGGCCJGJCGJ81JC1GGGGGCG8GGCGGGGCG1C1GGGGCGGCGCCCGGG=GC=CGCJJJJGGGGGCGGCGC=8GCCGGGGGGGG=GCG=1GGGCGGGCGG1CG NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-50 147 9 275169 60 105M563N45M = 275125 -757 CCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGT CCGCCCGGGGGCGGGG1GCGGGGGGC8CGG=CGGCCC=CGGGCCJ(JJ=GGCGCGGGGCGGGGGCC8GCCCGGCGCGGGJ8GGGGCC1JJGJCGGJJJGJG8JJGJJJJCJJJGGJGGGCJGGJJJJGGGJJJ=CJCGG=GCGGGGG=CC NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-14 147 9 275170 60 104M563N46M = 275146 -737 CAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTG 1CGGGGGCGGCCGG1CG=GGGGGGGCGGGGGCCGGG1CGCGCCJJJJJCG1CGGGCCGCGGGGGGGGGGGGCGGGGGGGCCGGGCGJJGG=JJ(J18GJCJGJ8JJGGJ=JJGJJGGGJJJ=JJJJCJJJJJJJJJGGGGGGG1GGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-20 163 9 275172 60 102M563N48M = 275219 760 AGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTG CC=GGGGGGGGGGJJGJJJJJJCJJ=JJJJGGGGJCJJGCGCGJGGCCCJJJGJJJJCGGJG=GGJGGGGGJGJGCCGGGGCCG=GG=C=G=GGCCGGGCGCCCC=JG11GGCCGCCCGCGCC8CGGGGCC1CGCGGG=GG=CCC1GGCG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-26 163 9 275174 60 100M563N50M = 275216 755 GAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGCAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAA C1CGGGCGGGGGGJJJ=JJGGCGGGJJGJJGGJGGJJGJCJGJJ=GGCJJGJJGGCGCGCGGG=JGGG8GGGGCGGGGGCGCCCGGGCGGGCCCCCG=GGGCJ(JCJ=GGCCGGGGGGGGGGGGGCCGCGGGCCGGGGGCGCGGGGGGGG NH:i:1 HI:i:1 AS:i:298 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-34 99 9 275183 60 91M563N59M = 275223 753 CTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCCCTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACC CCCGGGGGGGGGGJJJJJGJGJJGG=JJJJJJGJJJGJGJC1JGGGJGGJJGGGJJGG=GCGJGGJCGGGGGGCG=GGCGG1CGGGG=CGGCCGGGCGGGJ88=CGCG=GGGGGC=GGCGGGGG1GGCCGGGG1GGGCGGGGCCCGCGGC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-80 99 9 275199 60 75M563N75M = 275250 764 AAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAACTGGCCAAGGCT CC=GGGGGGGGGGJJJJCJCJJJJJJGGGJJJCJGCCJJJJJ=JCGJJJ=J8JGJGJ=J=JGG=CJCCGG1GG=CGGG=8GG=GCGCCGGCGCGGGG8GGJG1CGCGCCGCCGCGG=GGGGCGCGGGGGG=G==GGCC(GGCGGGGCGCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-8 163 9 275199 60 75M563N75M = 275246 760 AAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCT =C=GG(1GGGGGGJGGJGCCJJCJJJJJJ=GJGGJJGJ=JJGCGCGJJJJJGGJ1GGJJG8C8GGG=GCCG8GGGG1=CGG88CG=GG8GG=GGGCGG8GGCJ18CJ=CGGCGGGG1CC=GCCGCGGG=GGGCGGCGCC8GCCGCGCCGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-78 147 9 275200 60 74M563N76M = 275151 -762 AAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTG GGGGGCG8GGGGGGGCCGCGG=GCCGCGCGCGGGGGGGC=GCGJ88JJ=CGCGGGG=CGGGGG(GG=G(CCGCGGCJGJGGGCCGGCCJJGGJJJGJJGG1G(JJJGCGJJG=J=GJJJGJJJJJ=CGJJJGJGGJJGGCGGCGGGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-42 163 9 275204 60 70M563N80M = 275245 754 GACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTC CC=GGGGGGGGGGGGJJJGGJJJ=JJJGGGJJGJGCJJJJ(GJGJJCCJGGGJCGJGGJJJGG=G1C8GCGGGG18GCC=GGGGGCCCGC1GGGGCGGCGG=CCJCCGGG==GGGGGGGG1G(GGG=C=GGGG88=CC=GGCGGGGCGGG NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-62 83 9 275215 60 59M563N91M = 275157 -771 TTTCGTTGCACTGTATGATTTTGTGGCCGGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTA GCCC1CCCCCGCGCCC=GGGGGGCCGGC8CGGC1GGC=CGGGGCCCGGC8GCC=GCGGGCGGGGGGGCCGJGGGGGGGGGJGG=GJGCGJGGJ=JJGJGJCG=JJJJGJJJJGJJJGJJGCGJCJ=JJJJJGJGGJJGGGGCGGGGGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-26 83 9 275216 60 58M563N92M = 275174 -755 TTCGTTGTACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTAC CGGGGGC(GGGCGGCGCCGGGCGGCGCCGGGCGCGGGGCGGC==GGCCG=1GCCGGCGGCGGGCCCGGG=GGGCGCCCCJJGCCC1GJJCJGGGJJJG8JGG=GJJ=GGJJJJCJGCCGJJJJJJGJJJJJGGJGJJGGGGGGGCGCCCC NH:i:1 HI:i:1 AS:i:298 nM:i:2 XS:A:+ NM:i:1 +BCR-ABL1-44 163 9 275217 60 57M563N93M = 275260 756 TCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACA C=CGGGGGGCGGGJJJJJGJGJJJJJ1JJJJJJ1JJJGCGGG=JGJGJGGJGGCGGCGJGCJG=JJGGCJCGCCCGGGGCCCGGGC=GG=CGGGGGGGGGGGCJJJJGC=GGGGCGGCGGC=CCGG8GGGCGCGGCCCGGCG=GGCGGGC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-40 99 9 275219 60 55M563N94M1S = 275838 769 GTTGCACTGTATGATTTTGTGGCCCGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATG CCCCGGGGGGCGGJJJJGGJCJJJ(GJJ=JJJJJCJJJGGGGJJJGGGJJCJJJGJCJCCJJ(CJ=CGGGJ=GGGCJCGGGGCGGGCGGGGGCGGCGGGGCCGGCGCCGGGGGGCCGCGGGGGGGG=GGGCGG=GGGGGCGGG8G=CGG1 NH:i:1 HI:i:1 AS:i:297 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-20 83 9 275219 60 55M563N95M = 275172 -760 GTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATC GCG=GGGCC8GCCGCGGGGGGG=GGCCGGCGGGGCCGGGCGG8CGGCGGJGCGGCGGGGGGCGG=GGG1GCGGGGGGGGGC==JJGG=GGGCCJGGGGGGJJJJJGCCGJJGGJGJCJJCJJJJJGGJJJJGJJJJ1GGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-34 147 9 275223 60 51M563N99M = 275183 -753 CACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGC CGGG8GCC=GGGCGGGGGGCGGGGG=GGGGGGGCGGCGCGGGGJJJJCCCGC1GGGGG8GGCC=GGGGGGGGGGGCCGGCCCG=GCJJJGGGGGG81J8=CGJGGGGJGJJCJGGJGGJGCCJJGJJJJJCJJJJGJGGGCGGGG=GCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-22 99 9 275237 60 37M563N113M = 275864 777 GTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTG CC1GGGGGCGGGGGGCJJGCGJCJJJJJJJJGJJJJGJJGGG1JGCJJCJJGJJJJJGGGGJGJJCGJJGCC8CGGCGCGGCGCCG1GGCCCCGC=GG=GJCGGGGCGCG=GGGGGCGGC=CGGGGGGGGGCGGCCCGGG(G8GGGGGGG NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-42 83 9 275245 60 29M563N121M = 275204 -754 TGGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACA GGGCGGGCGCCGGGGGCGGGGGG=CGGGGC1CGCGGGCG=GGCG=GGCCCGGGGCGCGGCGGCCGGGGGGG(GG=GGG=GGGCCGGJJGJJ=GGGGGJJGCGJGGJJJJJJGCJGJGG(GGJJJGJJJJJJJ8GJJJCGGGGCGG1G1CC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-8 83 9 275246 60 28M563N122M = 275199 -760 GGAGATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACAC G=GGCGGGGG=GGGGGGGCCGCCGCGCGGCCGGCGGGCCGGCGGCGGGGJGG=GGGGGGGC=GCGGGCCCG=JGCG=GGGJGGGJGJGGGJCGCGCGGJGGJJJJJJGJGJGJJJG1JJJJJJJJGJCGGJJJJJJCGGGGGGGGCGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-80 147 9 275250 60 24M563N126M = 275199 -764 ATAACACTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCT CCCCCGGCC8GCG=CGCGCGGG(GGGGGGGGC=GGG=GG=CGCJJJJJGGGGC==G8CGGG=GCGGC1GGGC(GG=G=GGCGJC8GCGJGJCGCJGJGCGJGJJJGGJJGJGJCJJJJGJGJJJGGJJJJJJGJJJJ8GGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-30 163 9 275254 60 20M563N130M = 275867 763 CACTCTAAGCATAACTAAAGGTGAAAAGCACCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTA CCCGG1GGGGGGGJGJCJGJGJJJ(JGJJ(JGJGC=GJJJGJJGGJGGJJJJGGJGGCCCCJG8CG=GCJCGGGJ=GCGJ1CGGGGCCGCG8CG=GGCGGC(CJJC=CGGCGG(CGGGGGGCGCCGG=GC1GCGG=G1CGGCCCCG===8 NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-52 99 9 275256 60 18M563N132M = 275877 771 CTCTAAGCATAACTAAAGGTGAAAAGCTCCGGGTCCTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACC CCCGGGGGGGGGGGJJGCGJGG8GJJJGJJGJG=G=JJGGCJGGGGGJGGJJGJJGJGGGCJ=GJGGGCGJCGGGGGGG8CGGGGGGC=GGCGGGGCGCGJCGCGCCCCGCG11GGGGGGGGGGGGGGCCCGGGGCCGGCGGGGGCGGCG NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:1 +BCR-ABL1-44 83 9 275260 60 14M563N136M = 275217 -756 AAGCATAACTAAAGGTGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGG CGGGCGCGGGGCGCGGGGGCGGGGGGGGGCGGGGGGGG=G1GGGCGCGGCGCGGGGGGGCGGCGCCGCGGC==GGG=1GGG=CJJGCGJGJJJCGCJJ8GJJGGGJJGGJJJGJJGJJJGJJJJJJCJGJ=GGJJ=JGGGGGCGGCGCCC NH:i:1 HI:i:1 AS:i:302 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-40 147 9 275838 60 150M = 275219 -769 TGAAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAA =GCCGGGGCGGGG=GG1G8G=G(GGCGGGGGGGGC1C=GCGG=J8JJ1GGGGGGGGGGGGGGGGGC=1G8CGGCJ8GC1GGCGCCGJG1GGJGGJGJ8JJCJJJGJ8GGJJJ=JGJJG=CGG=JJJJJJJ8JJ=JJGGGGGGGGGCGC=C NH:i:1 HI:i:1 AS:i:297 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-16 163 9 275840 60 150M = 275888 198 AAAAGCTCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCACCAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATG CC8GGG1CCGGGCCJJGJG(JJJJJ(JGJCJGJJJJJJJJGGJGJGJJCCJJJGJGGGGCGGG=C=JGJJG=C8GGGCGGGGGC(GGCGCGCGGCG(CGG=1(C=JCGGGCCGGGGGCGCGGGCGGCGGGCGGCCGGGGGGGG8GGGCGC NH:i:1 HI:i:1 AS:i:296 nM:i:1 NM:i:1 +BCR-ABL1-6 99 9 275846 60 150M = 275903 207 TCCGGGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTG CCCGGGGGGCGGGGJJGJGJ=JJJJJJJJJJGJGGJJJGGJC=GGGGJ=GGCJJJGCGJGJGJJGJGCGJGGJGJCGCGGGGGGGGGG8GC8GC8G=GGGJ=GCGGGGGCCGCCGGGGGGGG1G1=GCGC81CGGGGGCCCGGGGGCGGG NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-32 99 9 275850 60 150M = 275894 194 GGTCTTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTA CCCGGGGGGGGGGJJGGJJJ=JJGJ8JGJ=JGJG=GGGJGCCJJJC=J8JJ=GCCJC8JC=GGGJGG(GGCJGGGG1GC=GJ=GCCGGCCGGG=GGGGGGJGCGGCGG=CGGCGCG=GGC=CGGGGCCGGGGGGCCCCGCCGGGCCGGGG NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-38 163 9 275854 60 150M = 275900 196 TTAGGCTATAATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTG CCCGCGGGGGGGG=GGJGJGJJJ1=GGCJJJCGJ=GJJJGGCJGGCGJGGJJCGJCGJGGG=GGGGJCGGGGGGJGGGGGGGGG8C=G=GCGG==CG8GCG=JCJJCCGG8CGGCGGCCGGGCCGCGGCGGG=GCGGCGG=8CGGCGCG= NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-22 147 9 275864 60 150M = 275237 -777 ATCACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCG GGG1C8GGG=C=GGGCGCGG=GG=GCGGGGCGGGCGCGGGCGGJ1CCJCCC8GCC=GGCGGGGGGGCGCGCGGGCCGJGCGJGJGGJGCJGGGGGCGGGJ(JCGGGJJJJJJG=1GGJJJGJJJGGJJJJJJGJ1JJGG=GGGGGCGCCC NH:i:1 HI:i:1 AS:i:300 nM:i:0 XS:A:+ NM:i:0 +BCR-ABL1-30 83 9 275867 60 150M = 275254 -763 ACAATGGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGA CG8GC==GCGCCGGGGGGG8=CGGGGGC=CGGCGGGGGCG=GGGC=GCCJGGGGCGGCGCGGGGCGCGGGCCCGJGGG8(8GC8GCGCGCJGGGGGGJGGGJGJJJJJGJJJJCGGJJGJJJ=JJJJGGJ=JJJJGGGGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-36 99 9 275872 60 150M = 275919 197 GGGGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAAT CCCGGGGGGGGGGJJJGGJJ=JJJJGJJJJJ=GGJJJCJ=JGGGJGGJGJJGGGGCGCG=JGCCGJGCJGCGGGJGGCGCG1GJGC=8GGCCCCGG8CCGJCCGGGCGGGCGGGGGCG1GCCGGCGGGGGCCCGGCCCG(G8GC8=CCGC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-70 163 9 275874 60 150M = 275911 187 GGAATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGG CCCGGG==GGGGGJJJJJJJJJJJ=GJ8J=GJGJGJGGJCCJJJCGG1=GJGJG18JG=GGGC1GGGJ8GCCC1=CCGCGGG(GC1GCG1GCCGC8GG1GG=JJCJ1GGCGCCGCG(CGGCGGGGGG(GGGGGGCGCCGGGGCGCGCCG= NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-52 147 9 275877 60 150M = 275256 -771 ATGGTGTGAAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAG CG=GGGGC(CGGGGGGGCCGCGCCGGGGG=GGCC8CGGCCCCCCJ=CJ=GGGGGGGGCG=GGGGCG(GC1GGGC=GJCCCGJ=88GJGGJGJGCJGGJJGGJJJGJJJJGCGJJGGJ(GJGGJCJJJCJJJJJ=(JJGGGGGGGGGCCCC NH:i:1 HI:i:1 AS:i:298 nM:i:1 XS:A:+ NM:i:0 +BCR-ABL1-56 99 9 275885 60 150M = 275928 193 AAGCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGG =CCGC=GGGGGG1JJJGJGJJJCJJCGJJJJJJJJJJCGJJJJJJGGCCJ1JGCGGCGJ8GG(CJGJGJCGGCGG1CC=CG=GCC=GGGGG=GGCGCCG1CGGGGGGG1GGGGGCGGGCGCGGCGG811G8CCGGGGCGGGGGCCG=CGC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-16 83 9 275888 60 150M = 275840 -198 CCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGC CGGGGGG=GGCGGGCGGGGGGGCGGGGCGGGGCCCG=CGGGGGCGGGCCCGG8GCCCGG8GCGGC=GCCCGGGGGGCGGGCGGJGGGCCGGJCGGJJGJGGGGGJJJJGJJGGJJGG=JGGJJGGJ=JGJJJJJJGJC1GGGG=GGG1C1 NH:i:1 HI:i:1 AS:i:296 nM:i:1 NM:i:0 +BCR-ABL1-32 147 9 275894 60 150M = 275850 -194 CCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGA 8GCCCCGGCGCGC1GGGGCGGCCGGGGCG1(GG=GG=GCGGCGJCJJCGG8=GGGCCGCGGGCGGGGGC=GC1=GGGGGJGGCCGJJCGGGJJJCGGG8CCGGGCJGJGJJGCCGCJJJJJJJJJJGCGJJJGJJGJGGGGGCGGGG=CC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-38 83 9 275900 60 150M = 275854 -196 ATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGA GCGCCGCGGGCGGGGGGGCGGCGCG8CGCGGGG8GGCGGGCCCCG8CC=JGCGGGGGGCGGGGCGCCGC=GCCCGGJGGGCGGGCJGCCJJGJG=GGCJJJGGJCGJCGCGJJJC=JJGJCJGJGJJGJJJ=JJJ1GGGGGGGGGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-6 147 9 275903 60 150M = 275846 -207 GCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCA CG8GCGGGCCCCGGCGCGGGGCCGGGCGG8CG=G=GCCGCGG=1CJ8JCCGCGGGGGCGGGGGGCGG=G=8GCGJG=GGGGGGJGCCGGJJGG=G=CJ8=JJJJGG=JJJJJGJJGJGJJGJJJJJCCCJJJGGJJJG1GGG1GGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-70 83 9 275911 60 150M = 275874 -187 TGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGC CGGGCGGGCGGGCCGGGG=GGG8GCGGG8GGCGGGCGGCGGGCGGGGG=JGGGGGCGCGGGGGCGGGGCGCG1GGGGCJC8GG=JGGJJCCCJJGGGGJGJGJGGJJGGJJJJJGCJJJJGGJJGJJGJJJGGGJJJGGGGCGGGGG=CC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-36 147 9 275919 60 150M = 275872 -197 AAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTC C=GGGGGGCCGGGGGGGGG=GGCCGCGGGC1GCGC1GCGGCCGJJ(CCG8GCCGGGCCGGGC=CC1CG=CGCCGGG=CGGGGGGGGCGGGGGJ==JJJJJ1CJJJGJGGJCGCJGJGJGJJJJ=GG1CJJCGJG1GC=GGGCGCGGGCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-56 147 9 275928 60 150M = 275885 -193 CATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTCCATCTCGCT CCGGGCGCGCGGGCG=CCCGGCGCGGGGC=CGGCGGCCGCGGGJJJJCCGCCG(GCCCCCGGCCGGG=G8GGGGGGCC=C=CGGJGJJJGC=JGGJJJGJGJ1JJJGC=JJJG=JCJJJJJJJ=JJGGGJJJCGJJJGGGGGCGG=GCCC NH:i:1 HI:i:1 AS:i:298 nM:i:0 NM:i:0 +BCR-ABL1-74 77 * 0 0 * * 0 0 TCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTC CC11GGGGGGGGGGCCJJJGCGJJGJJJJJGGGGGGJJJGGJG==GCJCJ=GGJJGGJJGGCJGG=GGGGGJGGJGC=GC=GGGCGGGCGGGGCCGCGGGJCGC=GGC8CGCGCGGGGGGCGCC1GGCGCC=GCCGCGGC8GCGGGCCCG NH:i:0 HI:i:0 AS:i:155 nM:i:2 uT:A:1 +BCR-ABL1-74 141 * 0 0 * * 0 0 CATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAGGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG CCCGGGGGGCGCGJGGJJGGJGJJJGJGGJJGGJGJJ1=JCJJGGGJJJJGGGJGCCJGGJGG=J1JG8JGCGGGJG=GC1CGCCGGCG(GGCGGCGGGGGCJC1CCGC==CCGGGGCGGCGGGCCGGCGCGC8CCCCGGG=GGGC=GGG NH:i:0 HI:i:0 AS:i:155 nM:i:2 uT:A:1 +BCR-ABL1-66 77 * 0 0 * * 0 0 TCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAAACCCATAGAG CCC=GGGGCGGGGJJJJJGJJJJ=JJJGJJ1GJJGJJJJJGJJJJJGGGGCGJJGGGJJJGGCGGGGJGCGG1JCGGG=GCCGCG=GC=G=GCCGGGGG8JGGGGGGGGGGGG=GGCGGC8GGCCGGGC=GGGGGGGGG=CGG=8GGCCG NH:i:0 HI:i:0 AS:i:159 nM:i:0 uT:A:1 +BCR-ABL1-66 141 * 0 0 * * 0 0 CATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG CCCGGGGGGGGGGGGJ=JGJJJJJJJGGJJCCCJGJJ1JJJGCJGGGGJJJJ=GGGJGJGC(GGGGJGGGJG1=GGGGGGGG=G=C=GG8CC8GGGGGCCCCJCCCJGCG=GGCCGGCGGCGGCG==1GCCGGC1GGGGGCGGGGGGCGG NH:i:0 HI:i:0 AS:i:159 nM:i:0 uT:A:1 +BCR-ABL1-58 77 * 0 0 * * 0 0 ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGG CCCGGCGGGGGGGGJJJJJGJJGJGJGJGJJJJJJJJJCJGJJJJGCG=8GGGJGJGGCGGJGCGJJJCJGGG=CGCCGGCCGGGCGCGGGCGCG1GGGCCCGGGGCG8GCCC=C8CGCGG=CCCGCCCCGGG=CCGGCGGGCGGGGGCG NH:i:0 HI:i:0 AS:i:185 nM:i:3 uT:A:1 +BCR-ABL1-58 141 * 0 0 * * 0 0 TTGGGGTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATTCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATG CCCGGGGGGGGGGJJJJJJGJGJJJGGJ=JJJJJJJJGC=GJJGGJJGJJGG1GCJGGGG=JGGG8C=GCCGC==GGGCGGGGGG=GGG=(G=CCGCCGGGGCJJJJGGGC8GCGCGCG8CGGCCGGGCGCGCGG8CCGG8CGGGGGGGG NH:i:0 HI:i:0 AS:i:185 nM:i:3 uT:A:1 +BCR-ABL1-24 77 * 0 0 * * 0 0 CGCAGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGGCTGAGTGAAG CC11GCGGGGGGGJCGJGJJCCJJJJGJJJJGJJGGJJJCJJJG8JJJ1GJ=JGGGGJJJCG=8GGCGCCGGGCCGGGCGGGGCGGGGCCGCGGCCGGG=J1GCCC1(CCGGCGGGCCGCGGGCGGGGC=GGCGCCGCC1GCGGGGGCGG NH:i:0 HI:i:0 AS:i:154 nM:i:3 uT:A:1 +BCR-ABL1-24 141 * 0 0 * * 0 0 TTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAA C=CCGGGGGGGGCJ1GGJJJJ1JJJJJGJJ=GJJG8GGJ=GJGJJGJJGGGCGJGCGGGCGGG8GG=GJJGCG1GCGGJGCCGGCGGGCCGGGCG8GGGGG8C1==CGGCCCGCGGGGC8GCGGG8GGGCGCCGCCGCGGGCGGGGGGCG NH:i:0 HI:i:0 AS:i:154 nM:i:3 uT:A:1 +BCR-ABL1-10 77 * 0 0 * * 0 0 AGGTTGGGGTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACG CC=GGGGGGGGGG1GJJJJJCJJJJJJJJJJJGJ=GJJJGCJJJJCJGJGCJGJJJGGJJJGGCCGGJGC=GGJ1C8GGGGGGCGCCGGGGGGCGGGCGCCCG1GGCGCGCGGGCC8GCGCGCGC8CCCGCGCGGGGGCGGGGGCGGCGG NH:i:0 HI:i:0 AS:i:181 nM:i:2 uT:A:1 +BCR-ABL1-10 141 * 0 0 * * 0 0 ATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGA 1CCGGCGGGGGG1GGJJJGCC1JJJJCCG=JGGJJGJJJ=GGGGGJJGGGGGGC1J=CJGCGGGGCGC(CGGGGG=GGGGG(G=CGGCGGGGCCCGC=CCCCJJCC8G1GGGGCGGGGGGCGCGGGGGGGCG=GGCCGCCGCC1G=GGGG NH:i:0 HI:i:0 AS:i:181 nM:i:2 uT:A:1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cytobands.tsv Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,5 @@ +contig start end name giemsa +22 1 40586 q11.22 gpos25 +22 40586 269079 q11.23 gneg +9 1 21036 q34.11 gneg +9 21036 515509 q34.12 gpos25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fusions.tsv Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,2 @@ +#gene1 gene2 strand1(gene/fusion) strand2(gene/fusion) breakpoint1 breakpoint2 site1 site2 type split_reads1 split_reads2 discordant_mates coverage1 coverage2 confidence reading_frame tags retained_protein_domains closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1 gene_id2 transcript_id1 transcript_id2 direction1 direction2 filters fusion_transcript peptide_sequence read_identifiers +BCR ABL1 +/+ +/+ 22:230999 9:275100 CDS/splice-site CDS/splice-site translocation 1 3 0 3 8 low in-frame . Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%) . . ENSG00000186716 ENSG00000097007 ENST00000305877 ENST00000372348 downstream upstream . AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR BCR-ABL1-4,BCR-ABL1-28,BCR-ABL1-60,BCR-ABL1-76
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein_domains.gff3 Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,83 @@ +9 pfam protein_domain 33502 33541 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 33992 34063 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 35324 35381 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 37391 37409 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 37479 37553 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 38833 38931 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 41390 41413 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 41489 41494 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 43744 43846 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 44647 44729 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 47496 47541 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 51664 51812 0 + . Name=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013 +9 pfam protein_domain 102331 102396 0 + . Name=Zinc finger%2C C2H2 type;color=#80FF00;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF00096 +9 pfam protein_domain 102412 102480 0 + . Name=C2H2-type zinc finger;color=#80FF80;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF13894 +9 pfam protein_domain 114903 114949 0 + . Name=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382 +9 pfam protein_domain 116528 116596 0 + . Name=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382 +9 pfam protein_domain 121951 121971 0 + . Name=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985 +9 pfam protein_domain 123179 123300 0 + . Name=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985 +9 pfam protein_domain 275219 275273 0 + . Name=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018 +9 pfam protein_domain 275837 275922 0 + . Name=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018 +9 pfam protein_domain 275962 276132 0 + . Name=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017 +9 pfam protein_domain 283799 283855 0 + . Name=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017 +9 pfam protein_domain 283973 284071 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 293165 293249 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 293896 294073 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 295904 296088 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 299451 299603 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 301104 301156 0 + . Name=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069 +9 pfam protein_domain 306405 306716 0 + . Name=F-actin binding;color=#800000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF08919 +9 pfam protein_domain 314470 314862 0 - . Name=Orexigenic neuropeptide Qrfp/P518 ;color=#808000;gene_id=ENSG00000188710;gene_name=QRFP;protein_domain_id=PF11109 +9 pfam protein_domain 325106 325108 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 325118 325359 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 326270 326449 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 332828 332924 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 344780 344908 0 - . Name=Fibrinogen beta and gamma chains%2C C-terminal globular domain;color=#808000;gene_id=ENSG00000130720;gene_name=FIBCD1;protein_domain_id=PF00147 +9 pfam protein_domain 430353 430623 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055 +9 pfam protein_domain 447321 447625 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055 +9 pfam protein_domain 453081 453209 0 + . Name=Laminin N-terminal (Domain VI);color=#000080;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00055 +9 pfam protein_domain 457203 457334 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 459902 460054 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 460070 460088 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 460167 460282 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 462677 462771 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 466560 466608 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 470157 470166 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 473527 473719 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 473886 474001 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 477965 478038 0 + . Name=Laminin B (Domain IV);color=#FFFF80;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00052 +9 pfam protein_domain 478042 478107 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 478144 478183 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 482071 482168 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 482175 482259 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 487996 488060 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 488076 488222 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 489116 489262 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 489945 490067 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +9 pfam protein_domain 490710 490856 0 + . Name=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053 +22 pfam protein_domain 2420 2524 0 - . Name=Armadillo/beta-catenin-like repeat;color=#000080;gene_id=ENSG00000100218;gene_name=RSPH14;protein_domain_id=PF00514 +22 pfam protein_domain 36321 37004 0 + . Name=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503 +22 pfam protein_domain 63673 63981 0 + . Name=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503 +22 pfam protein_domain 90736 90740 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 93060 93112 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 93619 93720 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 96554 96622 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 98578 98629 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 99484 99565 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 99749 99839 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 101465 101502 0 + . Name=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071 +22 pfam protein_domain 121553 121771 0 + . Name=Bcr-Abl oncoprotein oligomerisation domain;color=#FF0000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF09036 +22 pfam protein_domain 201581 201640 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 201941 202126 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 208994 209101 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 212118 212178 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 213667 213719 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 214220 214312 0 + . Name=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621 +22 pfam protein_domain 230954 230999 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 233127 233224 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 235610 235741 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 250010 250018 0 + . Name=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168 +22 pfam protein_domain 252302 252422 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620 +22 pfam protein_domain 253473 253607 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620 +22 pfam protein_domain 254554 254659 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620 +22 pfam protein_domain 255138 255228 0 + . Name=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Jul 27 11:25:14 2022 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>