@sjcrh/proteinpaint-server 2.30.4 → 2.31.0

package/cards/featuredDatasets.json

@@ -1,84 +0,0 @@
-{
-    "datasets": [
-        {
-            "name": "Pediatric Cancer Mutation",
-            "id": 1000,
-            "intro": "The Pediatric dataset consists of somatic variants and tumor RNA-seq data shown in the protein view. The dataset is comprised of the GRCh37/hg19 genome as well as data from the Pediatric Cancer Genome Project <a href='https://permalinks.stjude.cloud/permalinks/pcgp' target='_blank'>(PCGP)</a>, NCI Target cohort, the Pan-TARGET study <a href='https://pubmed.ncbi.nlm.nih.gov/29489755/' target='_blank'>(PMID: 29489755)</a>, and the Shanghai Children's Medical Center T-ALL cohort <a href='https://pubmed.ncbi.nlm.nih.gov/32632335/' target='_blank'>(PMID: 32632335)</a>. A liftover of genomic variants and gene internals created the GRCh/hg38 dataset.<br><br><div style='margin-left: 3em;'>Read more about ProteinPaint <a href='https://genomepaint.stjude.cloud/#data-release' target='_blank' >data releases</a>.</div>",
-            "searchbar": "gene",
-            "availableGenomes": ["hg19", "hg38"],
-            "dsURLparam": "dataset=Pediatric",
-            "runargs": {
-                "nobox": true,
-                "parselurl": true,
-                "noheader": true, 
-                "dataset": "Pediatric"
-            }
-        },
-        {
-            "name": "Pediatric2 GenomePaint",
-            "id": 1001,
-            "intro": "The Pediatric2 dataset expanded the original Pediatric dataset with non-coding variants and expression data in GenomePaint. The additional data includes Genome for Kids <a href='https://pubmed.ncbi.nlm.nih.gov/34301788/' target='blank'>(PMID: 34301788)</a>, Shanghai Children's Medical Center relapsed ALL cohort <a href='https://pubmed.ncbi.nlm.nih.gov/32632335/' target='_blank'>(PMID: 32632335)</a>, St Jude's Clinical cancer genomic profiling by three-platform sequencing study<a href='https://pubmed.ncbi.nlm.nih.gov/30262806/' target='_blank'> (PMID: 30262806)</a>, and St Jude's Pan-neuroblastoma analysis data study<a href='https://pubmed.ncbi.nlm.nih.gov/33056981/' target='_blank'> (PMID: 33056981)</a>.<br><br><div style='margin-left: 3em;'>Read more about ProteinPaint <a href='https://genomepaint.stjude.cloud/#data-release' target='PP data release' >data releases</a>.</div>",
-            "searchbar": "all",
-            "availableGenomes": ["hg19", "hg38"],
-            "dsURLparam": "block=1&mds=Pediatric2,svcnv",
-            "runargs": {
-                "nobox": true,
-                "parselurl": true,
-                "noheader": true,
-                "block": true,
-                "datasetqueries":[ {"dataset": "Pediatric2", "querykey": "svcnv"} ]
-            }
-        },
-        {
-            "name": "NCI GDC",
-            "id": 1002,
-            "intro": "The NCI's Genomic Data Commmons <a href='https://gdc.cancer.gov/about-gdc' target='GDC homepage'>(GDC)</a> coagulates data from NCI-supported programs, such as TCGA and TARGET.<br><br><div style='margin-left: 3em;'>Read more about <a href='https://gdc.cancer.gov/about-data/data-sources' target='GDC data sources'>GDC data sources</a>.</div>",
-            "searchbar": "gene",
-            "availableGenomes": ["hg38"],
-            "dsURLparam": "mds3=GDC",
-            "runargs": {
-                "nobox": true,
-                "parselurl": true,
-                "noheader": true,
-                "genome": "hg38",
-                "tracks": [
-                    {
-                        "type": "mds3",
-                        "dslabel": "GDC"
-                    }
-                ]
-            }
-        },
-        {
-            "name": "CIViC",
-            "id": 1003,
-            "intro": "The <a href='https://civicdb.org' target='_blank'>Clinical Interpretation of Variants in Cancer</a> is \"an open-source platform for crowdsourced and expert-moderated cancer variant curation.\" Supported by the NIH, NHGRI, and NCI, CIViC is a richly curated oncology dataset <a href='https://pubmed.ncbi.nlm.nih.gov/28138153/' target='_blank'>(PMID: 28138153)</a>.", 
-            "searchbar": "gene",
-            "availableGenomes": ["hg19"],
-            "dsURLparam": "dataset=CIViC",
-            "runargs": {
-                "nobox": true,
-                "parselurl": true,
-                "noheader": true,
-                "dataset": "CIViC"
-            }
-        },
-        {
-            "name": "Survivorship Study",
-            "id": 1004,
-            "intro": "The survivorship dataset contains clinical, genomic, and patient-reported data from the <a href='https://sjlife.stjude.org/' target='sjlife'>St. Jude Life study</a> (SJLife) and <a href='https://ccss.stjude.org/' target='CCSS'> Childhood Cancer Survivor Study</a> (CCSS). The interface offers data analysis tools like regression analysis (linear, logistic, and Cox) and interactive statistical plots.<br><br>To change to the CCSS data or see combined data from both studies, click on the <span style='display: inline-block; opacity: 0.65;font-size:16px;'>COHORT</span> tab at the top, and select the desired dataset(s).",
-            "searchbar": "none",
-            "availableGenomes": ["hg38"],
-            "runargs": {
-                "nobox":true,
-                "noheader": true,
-                "mass": {
-                    "state": {
-                        "dslabel": "SJLife",
-                        "genome": "hg38"
-                    }
-                }
-            }
-        }
-    ]
-}

package/cards/fusioneditor.json

@@ -1,34 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true,
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "fusioneditor": { "uionly": true }
-            }
-        },
-        {
-            "message": "Click on the rating grades rows (i.e. HQ, LQ, etc.) to display the fusion events. Hover over the fusion event to display a richly annotated graphic. Please refer to the Graphical display of fusion gene and structural variation <a href='https://docs.google.com/document/d/1LgcMk_p1qyPgFPQChy4sLlU9GDL6oahffP7jJfD8ZwE/edit' target='_blank'>documentation</a> for more information. ",
-            "runargs": {
-                "noheader": 1,
-                "genome": "hg19",
-                "fusioneditor": { 
-                    "input": "sample\tgeneA\tchrA\tposA\tortA\tfeatureA\tgeneB\tchrB\tposB\tortB\tfeatureB\tsv_ort\treadsA\treadsB\tmatchA\tmatchB\trepeatA\trepeatB\tcoverageA\tcoverageB\tratioA\tratioB\tqposA\tqposB\tcontig\ttype\tscore\trating\tmedal\tfunctional effect\tframe\tsv_refseqA\tsv_refseqA_codon\tsv_refseqA_exon\tsv_refseqA_anchor_type\tsv_refseqA_coding_base_number\tsv_refseqA_last_coding_base_number\tsv_refseqA_AA_index\tsv_refseqA_contig_index\tsv_refseqB\tsv_refseqB_codon\tsv_refseqB_exon\tsv_refseqB_anchor_type\tsv_refseqB_coding_base_number\tsv_refseqB_last_coding_base_number\tsv_refseqB_AA_index\tsv_refseqB_contig_index\tsv_AA\tsv_desc\tsv_processing_exception\tsv_general_info\tsv_interstitial_AA\tsv_frame_index\nStJude_Sample\tCD74\tchr5\t149786753\t-\tcoding\tCD74\tchr5\t149792317\t-\tcoding\t>\t37\t614\t69\t81\t0.566\t0.000\t1337\t23908\t0.001\t0.517\t158\t220\tTGCTCATTGTTGGAGATAAGGTCGCGCTGGTCATCCATGACTGGCTTCTGATCTTCCCGACAGCTCCTGCTTCTCCTCCTGTGCATCTGGCCACCACCGCCTACTTCCTGTACCAGCAGCAGGGCCGGCTGGACAAACTGACAGTCACCTCCCAGAAGCTTCATGCGCAGGTTCTCCAGCTGCAGGTTCTGGGAGGTGACTGTCAGTTTGTCCAGCCGGCCCAGATGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGCCAGTCATGGATGACCAGCGCGACCTTATCTCCA\tInternal_dup\t20750.34\tHQ\t2\tITD\t1,1,1,1,1,1,1,1,1\tNM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355\t87,87,87,87,87,87,87,87,87\t2,2,2,2,2,2,2,2,2\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t260,260,260,260,260,260,260,260,260\t\t50,50,50,50,50,50,50,50,50\t154,154,154,154,154,154,154,154,154\tNM_001025158,NM_001025158,NM_001025158,NM_001025159,NM_001025159,NM_001025159,NM_004355,NM_004355,NM_004355\t-1,-1,-1,-1,-1,-1,-1,-1,-1\t1,1,1,1,1,1,1,1,1\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,,\t483,483,483,891,891,891,699,699,699\t74,74,74,74,74,74,74,74,74\t224,224,224,224,224,224,224,224,224\tLIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS,LIVGDKVALVIHDWLLIFPTAPASPPVHLATTAYFLYQQQGRLDKLTVTSQKLHAQVLQLQVLGGDCQFVQPAQMHRRRSRSCREDQKPVMDDQRDLIS\tCD74:NM_001025158[1,2]-CD74:NM_001025158[1,6];CD74:NM_001025159[1,2]-CD74:NM_001025158[1,6];CD74:NM_004355[1,2]-CD74:NM_001025158[1,6];CD74:NM_001025158[1,2]-CD74:NM_001025159[1,9];CD74:NM_001025159[1,2]-CD74:NM_001025159[1,9];CD74:NM_004355[1,2]-CD74:NM_001025159[1,9];CD74:NM_001025158[1,2]-CD74:NM_004355[1,8];CD74:NM_001025159[1,2]-CD74:NM_004355[1,8];CD74:NM_004355[1,2]-CD74:NM_004355[1,8]\t\tgeneB_transcripts=NM_001025158,NM_001025159,NM_004355;geneb_utr_codons=2\tKLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ,KLHAQVLQLQVLGGDCQFVQPAQ\t2,2,2,2,2,2,2,2,2\nStJude_Sample\tCD74\tchr5\t149786783\t-\tcoding\tCD74\tchr5\t149792317\t-\tcoding\t>\t8\t468\t83\t84\t0.024\t0.000\t334\t3003\t0.001\t0.517\t103\t104\tACACGACGCTCTTCCGATCTACACAGGCTTTTCCATCCTGGTGACTCTGCTCCTCGCTGGCCAGGCCACCACCGCCTACTTCCTGTACCAGCAGCAGGGCCGGCCCAGATGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGCCAGTCATGGATGACCAGCGCGACCTTATCTCCAACA\tInternal_dup\t5864.68\tHQ\t2\tITD\t0,0,0,0,0,0,0,0,0,2,2,2\tNM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355,,,\t,,,,,,,,,,,\t2,2,2,2,2,2,2,2,2,,,\t,,,,,,,,,,,\t230,230,230,230,230,230,230,230,230,,,\t\t,,,,,,,,,,,\t,,,,,,,,,,,\tNM_001025158,NM_001025158,NM_001025158,NM_001025159,NM_001025159,NM_001025159,NM_004355,NM_004355,NM_004355,NM_001025158,NM_001025159,NM_004355\t-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1\t1,1,1,1,1,1,1,1,1,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,,,,,\t483,483,483,891,891,891,699,699,699,483,891,699\t36,36,36,36,36,36,36,36,36,,,\t,,,,,,,,,,,\tTRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,TRRSSDLHRLFHPGDSAPRWPGHHRLLPVPAAGPAQMHRRRSRSCREDQKPVMDDQRDLISN,,,\tCD74:NM_001025158[1,2]-CD74:NM_001025158[1,6];CD74:NM_001025159[1,2]-CD74:NM_001025158[1,6];CD74:NM_004355[1,2]-CD74:NM_001025158[1,6];CD74:NM_001025158[1,2]-CD74:NM_001025159[1,9];CD74:NM_001025159[1,2]-CD74:NM_001025159[1,9];CD74:NM_004355[1,2]-CD74:NM_001025159[1,9];CD74:NM_001025158[1,2]-CD74:NM_004355[1,8];CD74:NM_001025159[1,2]-CD74:NM_004355[1,8];CD74:NM_004355[1,2]-CD74:NM_004355[1,8];;;\t\tgeneB_transcripts=NM_001025158,NM_001025159,NM_004355;geneb_utr_codons=2\t,,,,,,,,,,,\t0,0,0,0,0,0,0,0,0,,,\nStJude_Sample\tPAX5\tchr9\t37033986\t-\tcoding\tZCCHC7\tchr9\t37260450\t+\tintron\t>\t33\t8\t83\t175\t0.024\t0.000\t4247\t251\t0.127\t0.066\t83\t83\tCTTTTCCCTGTCCATTCCATCAAGTCCTGAAAAATCAAAATGGATTTAGAGAAAAATTATCCGACTCCTCGGACCAGCAGGACAGTACAAGTTCAAAGTCATTAACAAGTTCAAGATGGCGACAAAGGACCGTTCAACTAAATAGAGGCCCCTTTTGAGAGCAAGCCCATGTGTGACTGCACAAGTTACATACCTGGAGAAGATGGTATAAACTGGTCCATCAGTGACAAAGACATTGAGGCCCAGATAGCTAATAAC\tITX\t4361.34\tHQ\t4\tCLoss\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,3,3,3\tNM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,,,,\t16,16,16,16,,16,16,16,16,,16,16,16,16,16,,16,16,16,16,,16,16,16,16,16,,16,16,16,16,,16,16,16,16,16,,16,16,16,16,,16,,,,\t1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,,,,\ttuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,,,,\t43,43,43,43,,43,43,43,43,,43,43,43,43,43,,43,43,43,43,,43,43,43,43,43,,43,43,43,43,,43,43,43,43,43,,43,43,43,43,,43,,,,\t\t27,27,27,27,,27,27,27,27,,27,27,27,27,27,,27,27,27,27,,27,27,27,27,27,,27,27,27,27,,27,27,27,27,27,,27,27,27,27,,27,,,,\t83,83,83,83,,83,83,83,83,,83,83,83,83,83,,83,83,83,83,,83,83,83,83,83,,83,83,83,83,,83,83,83,83,83,,83,83,83,83,,83,,,,\tNM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226\t204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204\t3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611,611\t1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632\t65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,65,,,,\t195,195,195,195,,195,195,195,195,,195,195,195,195,195,,195,195,195,195,,195,195,195,195,195,,195,195,195,195,,195,195,195,195,195,,195,195,195,195,,195,,,,\tLFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,LFPVHSIKS*KIKMDLEKNYPTPRTSRTVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIPGEDGINWSISDKDIEAQIANN,,,,\tPAX5:NM_001280547[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280547[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280547[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280547[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_032226[3,9];;;;\t\tgeneB_transcripts=NM_001289119,NM_001289120,NM_001289121,NM_032226;not_inframe_due_to_intermediate_stop_codon\tVQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,VQVQSH*QVQDGDKGPFN*IEAPFESKPMCDCTSYIP,,,,\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,,,\nStJude_Sample\tPAX5\tchr9\t37033982\t-\tcoding\tZCCHC7\tchr9\t37302188\t+\tcoding\t>\t31\t63\t129\t293\t0.000\t0.017\t1041\t1903\t0.127\t0.051\t129\t131\tAAAAAAAAAAAAAAAAAAAAAAAAAGGCACAAAAAAGTGGAAACTTTTCCCTGTCCATTCCATCAAGTCCTGAAAAATCAAAATGGATTTAGAGAAAAATTATCCGACTCCTCGGACCAGCAGGACAGGAGAAGATGGTATAAACTGGTCCATCAGTGACAAAGACATTGAGGCCCAGATAGCTAATAACCGAACACCTGGAAGATGGACCCAGCGGTACTATTCAGCCAACAAAAACATTATCTGTAGAAATTGTGACAAACGTGGTCATTTATCAAAAAACTGCCCCTTACCACGAAAAGTTCGTCGCTGCTTCCTGTGCTCCAGGAGAGGACATCTCCTGTATTCCTGTCCAGCCCCCCTTTGCGAATACTGTCCTGTGCCTAAGATGTTGGACCACTCATGTCTTTTCAGACATTCCTGG\tITX\t3486.65\tHQ\t4\tFusion\t1,1,1,1,0,1,1,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1\tNM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734,NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734\t17,17,17,17,,17,17,17,17,,17,17,17,17,17,,17,17,17,17,,17,17,17,17,17,,17,17,17,17,,17,17,17,17,17,,17,17,17,17,,17\t1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\ttuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,tuple,,tuple,tuple,tuple,tuple,,tuple\t46,46,46,46,,46,46,46,46,,46,46,46,46,46,,46,46,46,46,,46,46,46,46,46,,46,46,46,46,,46,46,46,46,46,,46,46,46,46,,46\t\t42,42,42,42,,42,42,42,42,,42,42,42,42,42,,42,42,42,42,,42,42,42,42,42,,42,42,42,42,,42,42,42,42,42,,42,42,42,42,,42\t129,129,129,129,,129,129,129,129,,129,129,129,129,129,,129,129,129,129,,129,129,129,129,129,,129,129,129,129,,129,129,129,129,129,,129,129,129,129,,129\tNM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289119,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289120,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_001289121,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226,NM_032226\t205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205,205\t3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614,614\t1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632,1632\t43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43,43\t130,130,130,130,,130,130,130,130,,130,130,130,130,130,,130,130,130,130,,130,130,130,130,130,,130,130,130,130,,130,130,130,130,130,,130,130,130,130,,130\tKKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW,KKKKKKKKGTKKWKLFPVHSIKS*KIKMDLEKNYPTPRTSRTGEDGINWSISDKDIEAQIANNRTPGRWTQRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW\tPAX5:NM_001280547[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_001289119[3,9];PAX5:NM_001280547[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_001289120[3,9];PAX5:NM_001280547[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_001289121[3,9];PAX5:NM_001280547[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280548[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280549[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280550[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280551[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280552[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280553[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280554[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280555[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_001280556[1,1]-ZCCHC7:NM_032226[3,9];PAX5:NM_016734[1,1]-ZCCHC7:NM_032226[3,9]\t\tgeneB_transcripts=NM_001289119,NM_001289120,NM_001289121,NM_032226\t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\nStJude_Sample\tATF7IP\tchr12\t14634119\t+\tcoding\tJAK2\tchr9\t5080229\t+\tcoding\t>\t30\t49\t286\t210\t0.000\t0.000\t1184\t1475\t0.176\t0.025\t287\t287\tGTGTCACGACCATTGCAACCCATACAACCAGCACCGCCTCTTCAACCATCTGGGGTGCCAACAAGTGGACCATCTCAGACCACCATACACTTACTACCTACAGCTCCAACTACCGTGAATGTAACACATCGTCCAGTAACTCAGGTGACCACAAGACTCCCTGTACCAAGAGCTCCTGCAAACCACCAGGTGGTTTATACAACTCTTCCTGCACCACCAGCTCAGGCTCCCTTGCGAGGAACTGTTATGCAGGCTCCTGCTGTTCGGCAGGTCAATCCCCAAAATATTCTTCAGGAGAGAATACCATGGGTACCACCTGAATGCATTGAAAATCCTAAAAATTTAAATTTGGCAACAGACAAATGGAGTTTTGGTACCACTTTGTGGGAAATCTGCAGTGGAGGAGATAAACCTCTAAGTGCTCTGGATTCTCAAAGAAAGCTACAATTTTATGAAGATAGGCATCAGCTTCCTGCACCAAATTTGTTTACTCCAGAA\tCTX\t2767.24\tHQ\t4\tFusion\t1,1,1,1\tNM_001286514,NM_001286515,NM_018179,NM_181352\t1093,1093,1094,1102\t13,13,13,13\tperfect,perfect,perfect,perfect\t3277,3277,3280,3304\t\t94,94,94,94\t284,284,284,284\tNM_004972,NM_004972,NM_004972,NM_004972\t711,711,711,711\t17,17,17,17\ttuple,tuple,tuple,tuple\t2132,2132,2132,2132\t3399,3399,3399,3399\t95,95,95,95\t285,285,285,285\tVSRPLQPIQPAPPLQPSGVPTSGPSQTTIHLLPTAPTTVNVTHRPVTQVTTRLPVPRAPANHQVVYTTLPAPPAQAPLRGTVMQAPAVRQVNPQNILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPNLFTPE,VSRPLQPIQPAPPLQPSGVPTSGPSQTTIHLLPTAPTTVNVTHRPVTQVTTRLPVPRAPANHQVVYTTLPAPPAQAPLRGTVMQAPAVRQVNPQNILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPNLFTPE,VSRPLQPIQPAPPLQPSGVPTSGPSQTTIHLLPTAPTTVNVTHRPVTQVTTRLPVPRAPANHQVVYTTLPAPPAQAPLRGTVMQAPAVRQVNPQNILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPNLFTPE,VSRPLQPIQPAPPLQPSGVPTSGPSQTTIHLLPTAPTTVNVTHRPVTQVTTRLPVPRAPANHQVVYTTLPAPPAQAPLRGTVMQAPAVRQVNPQNILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPNLFTPE\tATF7IP:NM_001286514[1,13]-JAK2:NM_004972[17,25];ATF7IP:NM_001286515[1,13]-JAK2:NM_004972[17,25];ATF7IP:NM_018179[1,13]-JAK2:NM_004972[17,25];ATF7IP:NM_181352[1,13]-JAK2:NM_004972[17,25]\t\tgeneB_transcripts=NM_004972\t,,,\t0,0,0,0\nStJude_Sample\tJAK2\tchr9\t5077580\t+\tcoding\tATF7IP\tchr12\t14644992\t+\tintron\t>\t9\t8\t128\t199\t0.000\t0.000\t1295\t191\t0.099\t0.055\t160\t161\tAAATTATGGAGTATGTGTCTGTGGAGACGAGAATATTCTGGTTCAGGAGTTTGTAAAATTTGGATCACTAGATACATATCTGAAAAAGAATAAAAATTGTATAAATATATTATGGAAACTTGAAGTTGCTAAACAGTTGGCATGGGCCATGCATTTTCTATAGCCCTCACCTTACCAGTCAAGGAGCCAATGTGGTGGTTCTGCCAGCTGCTAAGTATGTCGATGCCAATTATGCATTTTGGCACTGCGGAAATGACCACAGGATGAATCCAGGAATCCACTGGATCCACTGTGTTACAGTTCGAGTGCCTCAAACAACCACATATGTTGTAAACAATGGACTAACCCTGGGATCAACAGTGGCACA\tCTX\t857.91\tHQ\t4\tCLoss\t0,0,0,3,3,3\tNM_004972,NM_004972,NM_004972,,,\t,,,,,\t15,15,15,,,\t,,,,,\t1992,1992,1992,,,\t\t,,,,,\t,,,,,\tNM_001286514,NM_018179,NM_181352,NM_001286514,NM_018179,NM_181352\t1093,1094,1102,1093,1094,1102\t14,14,14,,,\tblat,blat,blat,blat,blat,blat\t3278,3281,3305,3278,3281,3305\t3810,3813,3837,3810,3813,3837\t97,97,97,,,\t,,,,,\tIMEYVSVETRIFWFRSL*NLDH*IHI*KRIKIV*IYYGNLKLLNSWHGPCIFYSPHLTSQGANVVVLPAAKYVDANYAFWHCGNDHRMNPGIHWIHCVTVRVPQTTTYVVNNGLTLGSTVA,IMEYVSVETRIFWFRSL*NLDH*IHI*KRIKIV*IYYGNLKLLNSWHGPCIFYSPHLTSQGANVVVLPAAKYVDANYAFWHCGNDHRMNPGIHWIHCVTVRVPQTTTYVVNNGLTLGSTVA,IMEYVSVETRIFWFRSL*NLDH*IHI*KRIKIV*IYYGNLKLLNSWHGPCIFYSPHLTSQGANVVVLPAAKYVDANYAFWHCGNDHRMNPGIHWIHCVTVRVPQTTTYVVNNGLTLGSTVA,,,\tJAK2:NM_004972[1,15]-ATF7IP:NM_001286514[14,15];JAK2:NM_004972[1,15]-ATF7IP:NM_018179[14,15];JAK2:NM_004972[1,15]-ATF7IP:NM_181352[14,15];;;\t\tgeneB_transcripts=NM_001286514,NM_018179,NM_181352\t,,,,,\t2,2,2,,,\nStJude_Sample\tJAK2\tchr9\t5078418\t+\tcoding\tATF7IP\tchr12\t14644072\t+\tintron\t>\t21\t14\t233\t176\t0.000\t0.000\t750\t466\t0.274\t0.000\t234\t250\tGTTTCAGGAGTTTGTAAAATTTGGATCACTAGATACATATCTGAAAAAGAATAAAAATTGTATAAATATATTATGGAAACTTGAAGTTGCTAAACAGTTGGCATGGGCCATGCATTTTCTAGAAGAAAACACCCTTATTCATGGGAATGTATGTGCCAAAAATATTCTGCTTATCAGAGAAGAAGACAGGAAGACAGGAAATCCTCCTTTCATCAAACTTAGTGATCCTGGCATAGAAATTAGAACGGGGCCAAGTGGCAGAACAGCTTGCCCAGTAGCACGGACCTGCTGCAGAGCCTTCTCCTGTTCTGGACCACACTCAAAACTGGCAGCCTTTCAGGTCACTTGATAAATGGGCTGGAGTAACACACCCACATGAGGAATGTGTTGCCTCCAACATCCAAATAGGTCCACTAGACGTTGTGC\tCTX\t750.00\tHQ\t4\tCLoss\t,,\tNM_004972,NM_004972,NM_004972\t,,\t,,\t,,\t2105,2105,2105\t\t,,\t,,\tNM_001286514,NM_018179,NM_181352\t,,\t,,\t,,\t3278,3281,3305\t3810,3813,3837\t,,\t,,\t,,\t;;\tgeneB_no_inframe_contig_found\tgeneB_transcripts=NM_001286514,NM_018179,NM_181352\t,,\t,,\nStJude_Sample\tPAX5\tchr9\t37033982\t-\tcoding\tNA\tchr14\t57508194\t+\tintergenic\t>\t31\t0\t129\t64\t0.000\t0.529\t876\t1\t0.127\t0.000\t130\t127\tAAAAAAAAAAAAAAAAAAAAAAAAAGGCACAAAAAAGTGGAAACTTTTCCCTGTCCATTCCATCAAGTCCTGAAAAATCAAAATGGATTTAGAGAAAAATTATCCGACTCCTCGGACCAGCAGGACAGGAGAAGATGGTATAAACTGGTCCATCAGTGACAAAGACATTGAGGCCCAGATAGCTAATAACCGAACACC\tCTX\t412.24\tHQ\t1\tCLoss\t,,,,,,,,,,\tNM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t46,46,46,46,,46,46,46,46,,46\t\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t,,,,,,,,,,\t;;;;;;;;;;\tgeneB_no_transcripts\t\t,,,,,,,,,,\t,,,,,,,,,,\nStJude_Sample\tERICH1-AS1\tchr8\t687825\t+\t5utr\tERICH1\tchr8\t624049\t-\tcoding\t>\t7\t1\t208\t184\t0.000\t0.000\t348\t22\t0.159\t0.034\t209\t207\tCCGGCCGTGAAGACCGACCGTGCGCCGGGCTCGAGCGCGGTCTGAGCGCGCGGCGCCTGCGGCGGCGAACGGACGGACGGACCGCGGACGGACGTACTGACCCCAACCCGCGAGCCCCGGGAGCCGTCGGTCTGAGGAGGGGCCGCTTCGCCATGTCGCCCCGCACCTGCTGAGCCCGGAGCGTCCGAGGATGTCCGCGCTGAGGAAGATCAGGATCCTCATGACCAGCCAAAGAGAAGAAGAATTAGGAAGCATAAATCAAAGAAAAAATTTAAAAATCCCAATAATGTTCTTATAGAACAAGCAGAATTAGAGAAACAGCAGAGTCTGTTACAGGAGAAATCTCAGCGACAGCACACAGATGGCACCACAATAAGCAAAAATAAAAAA\tITX\t353.16\tHQ\t0\tNLoss\t0\t\t\t\t\t\t\t\t\tNM_207332\t102\t\ttuple\t305\t1332\t\t\t\t\tgeneA_no_transcript_IDs_found\tgeneB_transcripts=NM_207332\t\t\nStJude_Sample\tJAK2\tchr9\t5077582\t+\tcoding\tATF7IP\tchr12\t14649165\t+\tcoding\t>\t7\t2\t78\t149\t0.000\t0.000\t321\t20\t0.099\t0.025\t79\t77\tAAAGAATAAAAATTGTATAAATATATTATGGAAACTTGAAGTTGCTAAACAGTTGGCATGGGCCATGCATTTTCTAGTGTTACAGTTCGAGTGCCTCAAACAACCACATATGTTGTAAACAATGGACTAACCCTGGGATCAACAGGACCTCAGCTCACAGTGCATCACCGACCACCACAAGTGCATACTGAGCCCCCACGCCCCGTGCACCCAGCACCCTTACCA\tCTX\t196.40\tHQ\t4\tFusion\t0,0,0,3,3,3\tNM_004972,NM_004972,NM_004972,,,\t,,,,,\t15,15,15,,,\t,,,,,\t1992,1992,1992,,,\t\t,,,,,\t,,,,,\tNM_001286514,NM_018179,NM_181352,NM_001286514,NM_018179,NM_181352\t1093,1094,1102,1093,1094,1102\t14,14,14,,,\ttuple,tuple,tuple,tuple,tuple,tuple\t3278,3281,3305,3278,3281,3305\t3810,3813,3837,3810,3813,3837\t25,25,25,,,\t,,,,,\tKE*KLYKYIMET*SC*TVGMGHAFSSVTVRVPQTTTYVVNNGLTLGSTGPQLTVHHRPPQVHTEPPRPVHPAPLP,KE*KLYKYIMET*SC*TVGMGHAFSSVTVRVPQTTTYVVNNGLTLGSTGPQLTVHHRPPQVHTEPPRPVHPAPLP,KE*KLYKYIMET*SC*TVGMGHAFSSVTVRVPQTTTYVVNNGLTLGSTGPQLTVHHRPPQVHTEPPRPVHPAPLP,,,\tJAK2:NM_004972[1,15]-ATF7IP:NM_001286514[14,15];JAK2:NM_004972[1,15]-ATF7IP:NM_018179[14,15];JAK2:NM_004972[1,15]-ATF7IP:NM_181352[14,15];;;\t\tgeneB_transcripts=NM_001286514,NM_018179,NM_181352\t,,,,,\t0,0,0,,,\nStJude_Sample\tCD74\tchr5\t149785840\t-\tcoding\tCD74\tchr5\t149792314\t-\tcoding\t>\t352\t206\t45\t62\t0.151\t0.000\t404\t1316\t0.000\t0.173\t60\t60\tGCCCTGCCCCAGGGGCCCATGCAGAATGCCACCAAGTATGGCAACATGACAGAGGACCAGAGATGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGCCAGTCATGGATGACCAG\tInternal_dup\t183.44\tHQ\t2\tITD\t0,0,0,0,0,0,0,0,0,2,2,2\tNM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355,,,\t,,,,,,,,,,,\t4,4,4,4,4,4,4,4,4,,,\t,,,,,,,,,,,\t423,423,423,423,423,423,423,423,423,,,\t\t,,,,,,,,,,,\t,,,,,,,,,,,\tNM_001025158,NM_001025158,NM_001025158,NM_001025159,NM_001025159,NM_001025159,NM_004355,NM_004355,NM_004355,NM_001025158,NM_001025159,NM_004355\t0,0,0,0,0,0,0,0,0,0,0,0\t1,1,1,1,1,1,1,1,1,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,,,,,\t483,483,483,891,891,891,699,699,699,483,891,699\t20,20,20,20,20,20,20,20,20,,,\t,,,,,,,,,,,\tPAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,PAPGAHAECHQVWQHDRGPEMHRRRSRSCREDQKPVMDDQ,,,\tCD74:NM_001025158[1,4]-CD74:NM_001025158[1,6];CD74:NM_001025159[1,4]-CD74:NM_001025158[1,6];CD74:NM_004355[1,4]-CD74:NM_001025158[1,6];CD74:NM_001025158[1,4]-CD74:NM_001025159[1,9];CD74:NM_001025159[1,4]-CD74:NM_001025159[1,9];CD74:NM_004355[1,4]-CD74:NM_001025159[1,9];CD74:NM_001025158[1,4]-CD74:NM_004355[1,8];CD74:NM_001025159[1,4]-CD74:NM_004355[1,8];CD74:NM_004355[1,4]-CD74:NM_004355[1,8];;;\t\tgeneB_transcripts=NM_001025158,NM_001025159,NM_004355;geneb_utr_codons=1\t,,,,,,,,,,,\t2,2,2,2,2,2,2,2,2,,,\nStJude_Sample\tATF7IP\tchr12\t14634119\t+\tcoding\tJAK2\tchr9\t5081725\t+\tcoding\t>\t1\t2\t67\t80\t0.000\t0.000\t81\t126\t0.176\t0.010\t67\t68\tGCTCAGGCTCCCTTGCGAGGAACTGTTATGCAGGCTCCTGCTGTTCGGCAGGTCAATCCCCAAAATAATTATGAACTATTAACAGAAAATGACATGTTACCAAATATGAGGATAGGTGCCCTGGGGTTTTCTGGTGCATTTGAAGACC\tCTX\t163.88\tHQ\t4\tFusion\t1,1,1,1\tNM_001286514,NM_001286515,NM_018179,NM_181352\t1093,1093,1094,1102\t13,13,13,13\ttuple,tuple,tuple,tuple\t3277,3277,3280,3304\t\t21,21,21,21\t65,65,65,65\tNM_004972,NM_004972,NM_004972,NM_004972\t812,812,812,812\t19,19,19,19\tblat,blat,blat,blat\t2435,2435,2435,2435\t3399,3399,3399,3399\t23,23,23,23\t69,69,69,69\tAQAPLRGTVMQAPAVRQVNPQNNYELLTENDMLPNMRIGALGFSGAFED,AQAPLRGTVMQAPAVRQVNPQNNYELLTENDMLPNMRIGALGFSGAFED,AQAPLRGTVMQAPAVRQVNPQNNYELLTENDMLPNMRIGALGFSGAFED,AQAPLRGTVMQAPAVRQVNPQNNYELLTENDMLPNMRIGALGFSGAFED\tATF7IP:NM_001286514[1,13]-JAK2:NM_004972[19,25];ATF7IP:NM_001286515[1,13]-JAK2:NM_004972[19,25];ATF7IP:NM_018179[1,13]-JAK2:NM_004972[19,25];ATF7IP:NM_181352[1,13]-JAK2:NM_004972[19,25]\t\tgeneB_transcripts=NM_004972\tN,N,N,N\t0,0,0,0\nStJude_Sample\tFBXL13\tchr7\t102608469\t-\tcoding\tHLA-DPB1\tchr6\t33043815\t+\tcoding\t>\t2\t4\t88\t51\t0.000\t0.000\t62\t74\t1.000\t0.000\t89\t89\tCTACCTCAGTTTAAAAGATGTGATAATATGTGGTCAAGTTAATCATGCCTGGATGTTGATGACACAACTAAACTCACTGTGGAATGCTCTCCATGATGGTTCTGCAGGTTTCTGCGGCCCCCCGGACAGTGGCTCTGAC\tCTX\t124.00\tHQ\t0\tupTSS\t0,0,0,2\tNM_001111038,NM_001287150,NM_145032,\t,,,\t7,7,7,\t,,,\t591,591,591,\t\t,,,\t,,,\tNM_002121,NM_002121,NM_002121,NM_002121\t-1,-1,-1,-1\t1,1,1,\ttuple,tuple,tuple,tuple\t,,,\t777,777,777,777\t30,30,30,\t,,,\tTSV*KM**YVVKLIMPGC**HN*THCGMLSMMVLQVSAAPRTVAL,TSV*KM**YVVKLIMPGC**HN*THCGMLSMMVLQVSAAPRTVAL,TSV*KM**YVVKLIMPGC**HN*THCGMLSMMVLQVSAAPRTVAL,\tFBXL13:NM_001111038[1,7]-HLA-DPB1:NM_002121[1,6];FBXL13:NM_001287150[1,7]-HLA-DPB1:NM_002121[1,6];FBXL13:NM_145032[1,7]-HLA-DPB1:NM_002121[1,6];\tgeneB_breakpoint_not_mapped_to_CDS=NM_001242524;geneB_breakpoint_not_mapped_to_CDS=NM_001242525\tgeneB_transcripts=NM_001242524,NM_001242525,NM_002121;geneB_transcript_strand_disagree=NM_001242524;geneB_intronic=NM_001242524;geneB_transcript_strand_disagree=NM_001242525;geneB_intronic=NM_001242525;geneb_utr_codons=2\t,,,\t2,2,2,\nStJude_Sample\tNDUFB2\tchr7\t140404764\t+\t3utr\tKRIT1\tchr7\t91864921\t-\tcoding\t>\t16\t2\t30\t75\t0.000\t0.000\t109\t63\t0.214\t0.028\t30\t38\tAGGTGTAGACTCAGCCTCACTCTGTACAAGAGCCAGGAAGCTTTATTCCGACCTTCTCCTCTTGAGCGGATAAAAACTAATGTCATAAATCCTGCATATGCTACTGAATCAGGA\tITX\t109.00\tHQ\t0\tNLoss\t0,0,0,0,0,0,0,0,0,0\tNM_004546,NM_004546,NM_004546,NM_004546,NM_004546,,,,,\t,,,,,,,,,\t3,3,3,3,3,,,,,\t,,,,,,,,,\t,,,,,,,,,\t\t,,,,,,,,,\t,,,,,,,,,\tNM_001013406,NM_004912,NM_194454,NM_194455,NM_194456,NM_001013406,NM_004912,NM_194454,NM_194455,NM_194456\t175,175,175,175,175,175,175,175,175,175\t7,8,8,8,9,,,,,\tblat,blat,blat,blat,blat,blat,blat,blat,blat,blat\t525,525,525,525,525,525,525,525,525,525\t2067,2211,2211,2211,2211,2067,2211,2211,2211,2211\t13,13,13,13,13,,,,,\t,,,,,,,,,\tRCRLSLTLYKSQEALFRPSPLERIKTNVINPAYATESG,RCRLSLTLYKSQEALFRPSPLERIKTNVINPAYATESG,RCRLSLTLYKSQEALFRPSPLERIKTNVINPAYATESG,RCRLSLTLYKSQEALFRPSPLERIKTNVINPAYATESG,RCRLSLTLYKSQEALFRPSPLERIKTNVINPAYATESG,,,,,\tNDUFB2:NM_004546[1,3]-KRIT1:NM_001013406[7,17];NDUFB2:NM_004546[1,3]-KRIT1:NM_004912[8,19];NDUFB2:NM_004546[1,3]-KRIT1:NM_194454[8,19];NDUFB2:NM_004546[1,3]-KRIT1:NM_194455[8,19];NDUFB2:NM_004546[1,3]-KRIT1:NM_194456[9,20];;;;;\t\tgeneB_transcripts=NM_001013406,NM_004912,NM_194454,NM_194455,NM_194456\t,,,,,,,,,\t0,0,0,0,0,,,,,\nStJude_Sample\tZCCHC7\tchr9\t37126940\t+\tcoding\tPAX5\tchr9\t37020808\t-\tintron\t>\t5\t2\t155\t71\t0.492\t0.101\t156\t48\t0.051\t0.000\t156\t142\tATGATTATAGAGGTCAGTTCAAGTGAAGAGGAAGAGAGCACCATTTCAGAAGGTGATAATGTGGAAAGCTGGATGCTACTGGGATGTGAAGTAGATGATAAAGATGATGATATCCTTCTCAACCTTGTGGGATGTGAAAACTCTGTTACTGAAGGACATGGAGGAGTGAATCAGCTTGGGGGGGTTTTTGTGAATGGACGGCCACTCCCGGATGTAGTCCGCCA\tITX\t105.39\tHQ\t4\tFusion\t1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\tNM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226,NM_001289119,NM_001289120,NM_001289121,NM_032226\t204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204,204\t2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2\tperfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect\t610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610,610\t\t50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50,50\t152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152,152\tNM_001280547,NM_001280547,NM_001280547,NM_001280547,NM_001280548,NM_001280548,NM_001280548,NM_001280548,NM_001280549,NM_001280549,NM_001280549,NM_001280549,NM_001280550,NM_001280550,NM_001280550,NM_001280550,NM_001280552,NM_001280552,NM_001280552,NM_001280552,NM_001280553,NM_001280553,NM_001280553,NM_001280553,NM_001280554,NM_001280554,NM_001280554,NM_001280554,NM_001280555,NM_001280555,NM_001280555,NM_001280555,NM_016734,NM_016734,NM_016734,NM_016734\t16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16,16\t2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47,47\t1074,1074,1074,1074,1089,1089,1089,1089,975,975,975,975,888,888,888,888,987,987,987,987,960,960,960,960,1047,1047,1047,1047,876,876,876,876,1176,1176,1176,1176\t51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51,51\t153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153,153\tMIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR,MIIEVSSSEEEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGHGGVNQLGGVFVNGRPLPDVVR\tZCCHC7:NM_001289119[1,2]-PAX5:NM_001280547[2,9];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280547[2,9];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280547[2,9];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280547[2,9];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280548[2,9];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280548[2,9];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280548[2,9];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280548[2,9];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280549[2,8];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280549[2,8];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280549[2,8];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280549[2,8];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280550[2,7];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280550[2,7];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280550[2,7];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280550[2,7];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280552[2,8];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280552[2,8];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280552[2,8];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280552[2,8];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280553[2,8];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280553[2,8];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280553[2,8];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280553[2,8];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280554[2,9];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280554[2,9];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280554[2,9];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280554[2,9];ZCCHC7:NM_001289119[1,2]-PAX5:NM_001280555[2,8];ZCCHC7:NM_001289120[1,2]-PAX5:NM_001280555[2,8];ZCCHC7:NM_001289121[1,2]-PAX5:NM_001280555[2,8];ZCCHC7:NM_032226[1,2]-PAX5:NM_001280555[2,8];ZCCHC7:NM_001289119[1,2]-PAX5:NM_016734[2,10];ZCCHC7:NM_001289120[1,2]-PAX5:NM_016734[2,10];ZCCHC7:NM_001289121[1,2]-PAX5:NM_016734[2,10];ZCCHC7:NM_032226[1,2]-PAX5:NM_016734[2,10]\tgeneB_no_inframe_contig_found\tgeneB_transcripts=NM_001280547,NM_001280548,NM_001280549,NM_001280550,NM_001280551,NM_001280552,NM_001280553,NM_001280554,NM_001280555,NM_001280556,NM_016734;geneb_utr_codons=13\t,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\nStJude_Sample\tAKAP13\tchr15\t85924029\t+\t5utr\tB2M\tchr15\t45007620\t+\tcoding\t>\t2\t7\t190\t85\t0.016\t0.000\t95\t26\t0.158\t0.005\t191\t191\tCAGGGCCAGCGCGGAGCCCGAGCAGCCGCGGTGAAGCGCCTGTGCTCTGCCGAGACTGCCGTGCCCATTGCTCGCCTCGGTCGCCGCCGCTTTAGCCGCCTCCGGGGGAGCGGCCGCCTATTGTCTTTCTCCGCGGCGAAGGTGAAGAGTTGTCCCAGCTCGGCCCGCGGGGGAGCCCCGGGAGCCGCACGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTC\tINS\t95.00\tHQ\t1\tNLoss\t0,0,0\tNM_006738,NM_007200,\t,,\t1,1,\t,,\t,,\t\t,,\t,,\tNM_004048,NM_004048,NM_004048\t23,23,23\t2,2,\tblat,blat,blat\t68,68,68\t360,360,360\t64,64,\t,,\tRASAEPEQPR*SACALPRLPCPLLASVAAALAASGGAAAYCLSPRRR*RVVPARPAGEPREPHGTPKIQVYSRHPAENGKSNFLNCYVSGF,RASAEPEQPR*SACALPRLPCPLLASVAAALAASGGAAAYCLSPRRR*RVVPARPAGEPREPHGTPKIQVYSRHPAENGKSNFLNCYVSGF,\tAKAP13:NM_006738[1,1]-B2M:NM_004048[2,4];AKAP13:NM_007200[1,1]-B2M:NM_004048[2,4];\t\tgeneB_transcripts=NM_004048\t,,\t1,1,\nStJude_Sample\tPAX5\tchr9\t37035717\t-\tintergenic\tZCCHC7\tchr9\t37302188\t+\tcoding\t>\t0\t4\t65\t60\t0.000\t0.528\t1\t208\t0.000\t0.051\t65\t67\tCTGGGGCTGGGCTGCGGAGGGAAAGAGTCGAGCACTCGGAGATGGCCAAAAATCAAATCTCGGGGAGAAGATGGTATAAACTGGTCCATCAGTGACAAAGACATTGAGGCCCAGATAGCTAATAACC\tITX\t78.67\tHQ\t4\tNLoss\t0,0,0,0\t,,,\t,,,\t,,,\t,,,\t,,,\t\t,,,\t,,,\tNM_001289119,NM_001289120,NM_001289121,NM_032226\t205,205,205,205\t,,,\ttuple,tuple,tuple,tuple\t614,614,614,614\t1632,1632,1632,1632\t,,,\t,,,\t,,,\t;;;\tgeneA_no_transcript_IDs_found\tgeneB_transcripts=NM_001289119,NM_001289120,NM_001289121,NM_032226\t,,,\t,,,\nStJude_Sample\tSTK24\tchr13\t99171500\t-\tcoding\tMIR17HG,MIR17,MIR18A,MIR19A,MIR20A,MIR19B1,MIR92A1\tchr13\t92001950\t+\t5utr\t>\t3\t2\t167\t86\t0.012\t0.000\t18\t66\t0.007\t0.250\t167\t167\tTGGAGAGGTGTTCAAAGGCATTGACAATCGGACTCAGAAAGTGGTTGCCATAAAGATCATTGATCTGGAAGAAGCTGAAGATGAGATAGAGGACATTCAACAAGAAATCACAGTGCTGAGTCAGTGTGACAGTCCATATGTAACCAAATATTATGGATCCTATCTGAAGTCATACACGTGGACCTAACTGCACCAGTAGCTTTTCTGAGAATACTTGCTGAAAAGGAAGTTTTCTGGAATGGGTAAGTGTATT\tITX\t65.23\tHQ\t0\tCLoss\t,,\tNM_001032296,NM_001286649,NM_003576\t,,\t,,\t,,\t270,270,306\t\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t;;\tgeneB_no_transcripts\t\t,,\t,,\nStJude_Sample\tJAK2\tchr9\t5077581\t+\tcoding\tATF7IP\tchr12\t14644504\t+\tintron\t>\t3\t4\t75\t138\t0.000\t0.738\t224\t102\t0.099\t0.026\t75\t74\tAGAATAAAAATTGTATAAATATATTATGGAAACTTGAAGTTGCTAAACAGTTGGCATGGGCCATGCATTTTCTAGAGCAAAAAGTGATCAAGGTCTCTCTGAATAAGATTATGACACAAAGCTGGAGAGTTGATACACCCCTGAGTAGCCCTCACCTTACCAGTCAAGGAGCCAATGTGGTGGTTCTGCCAGCTGCTAAGTATGTCGATGCC\tCTX\t50.85\tHQ\t4\tCLoss\t,,\tNM_004972,NM_004972,NM_004972\t,,\t,,\t,,\t1992,1992,1992\t\t,,\t,,\tNM_001286514,NM_018179,NM_181352\t,,\t,,\t,,\t3278,3281,3305\t3810,3813,3837\t,,\t,,\t,,\t;;\tgeneB_no_inframe_contig_found\tgeneB_transcripts=NM_001286514,NM_018179,NM_181352\t,,\t,,\nStJude_Sample\tCD74\tchr5\t149786809\t-\tcoding\tCD74\tchr5\t149792317\t-\tcoding\t>\t6\t440\t42\t48\t0.000\t0.000\t134\t1360\t0.001\t0.517\t43\t68\tATCCTGGTGACTCTGCTCCTCGCTGGCCAGGCCACCACCGCCACATACCGGGGCCCCAGGGCGCCGGCCCAGATGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGC\tInternal_dup\t49.82\tHQ\t2\tITD\t1,1,1,1,1,1,1,1,1\tNM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355,NM_001025158,NM_001025159,NM_004355\t69,69,69,69,69,69,69,69,69\t2,2,2,2,2,2,2,2,2\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t204,204,204,204,204,204,204,204,204\t\t13,13,13,13,13,13,13,13,13\t41,41,41,41,41,41,41,41,41\tNM_001025158,NM_001025158,NM_001025158,NM_001025159,NM_001025159,NM_001025159,NM_004355,NM_004355,NM_004355\t-1,-1,-1,-1,-1,-1,-1,-1,-1\t1,1,1,1,1,1,1,1,1\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,,\t483,483,483,891,891,891,699,699,699\t24,24,24,24,24,24,24,24,24\t72,72,72,72,72,72,72,72,72\tILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK,ILVTLLLAGQATTATYRGPRAPAQMHRRRSRSCREDQK\tCD74:NM_001025158[1,2]-CD74:NM_001025158[1,6];CD74:NM_001025159[1,2]-CD74:NM_001025158[1,6];CD74:NM_004355[1,2]-CD74:NM_001025158[1,6];CD74:NM_001025158[1,2]-CD74:NM_001025159[1,9];CD74:NM_001025159[1,2]-CD74:NM_001025159[1,9];CD74:NM_004355[1,2]-CD74:NM_001025159[1,9];CD74:NM_001025158[1,2]-CD74:NM_004355[1,8];CD74:NM_001025159[1,2]-CD74:NM_004355[1,8];CD74:NM_004355[1,2]-CD74:NM_004355[1,8]\t\tgeneB_transcripts=NM_001025158,NM_001025159,NM_004355;geneb_utr_codons=2\tTYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ,TYRGPRAPAQ\t0,0,0,0,0,0,0,0,0\nStJude_Sample\tSLC35E1\tchr19\t16683619\t+\tintergenic\tBRD4\tchr19\t15383946\t-\t5utr\t>\t1\t3\t49\t174\t0.000\t0.000\t7\t91\t0.150\t0.041\t49\t47\tGCTAACTAGATTCCTGATTCCTGATGGCTGGCGGCGGCTGACACCAAAGAGTGCCTGGTGAAGAATGTGATGGGATCACTAGCATGTCTGCGGAGAGCGGCCCTGGGACGAGATTGAGAAATCTGCCAGTAATGGGGGATGGACTAGAAACTTCCCAAATGTCTACAACACAGGCCCAGGCCCAACCCCAGCCAGCCAACGCAGCCAGCACCAACCCCCCG\tITX\t46.43\tHQ\t2\tupTSS\t2,2\t,\t,\t,\t,\t,\t\t,\t,\tNM_014299,NM_058243\t-11,-11\t,\ttuple,tuple\t,\t2169,4089\t,\t,\t,\t;\tgeneA_no_transcript_IDs_found\tgeneB_transcripts=NM_014299,NM_058243;geneb_utr_codons=12\t,\t,\nStJude_Sample\tCD74\tchr5\t149786833\t+\tcoding\tCD74\tchr5\t149792314\t-\tcoding\t?\t2\t800\t77\t90\t0.000\t0.072\t172\t8110\t0.000\t0.173\t122\t127\tTTCTGATCTTCCCGACAGCTCCTGCTTCTCCTCCCGTGCAGCTCGGGGAGGTGACTGTCAGTTTGTCCAGCCGGCCCTGCTGCTGGTACAGGAAGTAGGCGGTGGTGGCCTGGCCAGCGAGGTCCCAGATGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGCCAGTCATGGATGACCAGCGCGACCTTATCTCCAACAATGAGCAACT\tInternal_inv\t40.55\tHQ\t3\tFusion\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tunhandled orientation ?\t\t\t\nStJude_Sample\tCD74\tchr5\t149786859\t+\tcoding\tCD74\tchr5\t149792314\t-\tcoding\t?\t2\t499\t69\t85\t0.000\t0.034\t159\t6042\t0.000\t0.173\t103\t104\tCTGGCTTCTGATCTTCCCGACAGCTCCTGCTTCTCTGCTGGTACAGGAAGTAGGCGGTGGTGGCCTGGCCAGCGAGGAGCAGAGTCACCAGGATGGAAAAGCCAGATGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGCCAGTCATGGATGACCAGCGCGACCTTATCTCCAACAATGAG\tInternal_inv\t30.21\tHQ\t3\tFusion\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tunhandled orientation ?\t\t\t\nStJude_Sample\tCCND3\tchr6\t42016238\t-\t5utr\tIGH\tchr14\t106322323\t-\t5utr\t>\t1\t6\t189\t68\t0.000\t0.029\t29\t170\t0.011\t0.028\t189\t188\tAAACACTTCGCCACTGCAGGGGTGGAGACTGGCTCTGTTCGGATGCCGGCCGGGGGGGAGAGGTGCAATCCTCTCCTCGCGGCTGGTGGTTGCGACCACCCCCACTCCCCAAAGGCAGGCTCCGGAGGCGGCGGGACAGAGCGCCTGCGACCCCAGTCGGTGCTCCGGGGAGGTCACCTGACGAGGAGGGAGTGCATCCGCCCCAACCCTTTTCCCCCTCGTCTCCTGTGAGAATTCCCCGTCGGATACGAGCAGC\tCTX\t28.33\tHQ\t4\tother\t,,\tNM_001136017,NM_001136126,NM_001287434\t,,\t,,\t,,\t,,\t\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t,,\t;;\tgeneB_no_transcripts\t\t,,\t,,\nStJude_Sample\tCD74\tchr5\t149786797\t+\tcoding\tCD74\tchr5\t149792310\t-\tcoding\t?\t10\t389\t62\t98\t0.127\t0.000\t348\t4175\t0.000\t0.173\t118\t118\tCCATGACTGGCTTCTGATCTTCCCGACAGCTCCTGCTTCTCCTCCTGTGCATCTGCAGGTTCTCCAGCTGCAGGTTCTGGGAGGTGACTGTCAGTTTGTCCAGCCGGCCCTGCTGCTGGCACAGGAGGAGAAGCAGGAGCTGTCGGGAAGATCAGAAGCCAGTCATGGATGACCAGCGCGACCTTATCTCCAACAATGAGCAACTGCCCATGCTGG\tInternal_inv\t18.23\tHQ\t3\tFusion\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tunhandled orientation ?\t\t\t\nStJude_Sample\tGLTSCR2\tchr19\t48249040\t+\tcoding\tDHX34\tchr19\t47885236\t+\tcoding\t>\t36\t3\t48\t94\t0.534\t0.000\t28\t67\t0.003\t0.105\t49\t49\tGAGGTTGACCAGTTCCTGGAAGACGTGCGGCTACAGGAGCGCACGAGCGGGGGCTGAGGAAGCTGCCCTCGAAACCCTCCAGAAGACATCTGTCCTGCAGAGGCCCTACCACTGCGAGGCCTGCGGGAAGGACTTCCTCTTTA\tINS\t11.49\tHQ\t0\tFusion\t0,0\tNM_015710,\t,\t1,\t,\t224,\t\t,\t,\tNM_014681,NM_014681\t1100,1100\t17,\ttuple,tuple\t3299,3299\t3432,3432\t16,\t,\tRLTSSWKTCGYRSARAGAEEAALETLQKTSVLQRPYHCEACGKDFLF,\tGLTSCR2:NM_015710[1,1]-DHX34:NM_014681[17,17];\t\tgeneB_transcripts=NM_014681\t,\t1,\nStJude_Sample\tATF7IP\tchr12\t14634119\t+\tcoding\tJAK2\tchr9\t5080301\t+\tcoding\t>\t0\t3\t66\t80\t0.000\t0.000\t0\t131\t0.176\t0.011\t66\t66\tCTCAGGCTCCCTTGCGAGGAACTGTTATGCAGGCTCCTGCTGTTCGGCAGGTCAATCCCCAAAATAACAAATGGAGTTTTGGTACCACTTTGTGGGAAATCTGCAGTGGAGGAGATAAACCTCTAAGTGCTCTGGATTCTCAAAGAA\tCTX\t2.98\tHQ\t4\tFusion\t1,1,1,1\tNM_001286514,NM_001286515,NM_018179,NM_181352\t1093,1093,1094,1102\t13,13,13,13\ttuple,tuple,tuple,tuple\t3277,3277,3280,3304\t\t20,20,20,20\t64,64,64,64\tNM_004972,NM_004972,NM_004972,NM_004972\t735,735,735,735\t17,17,17,17\tblat,blat,blat,blat\t2204,2204,2204,2204\t3399,3399,3399,3399\t22,22,22,22\t68,68,68,68\tQAPLRGTVMQAPAVRQVNPQNNKWSFGTTLWEICSGGDKPLSALDSQR,QAPLRGTVMQAPAVRQVNPQNNKWSFGTTLWEICSGGDKPLSALDSQR,QAPLRGTVMQAPAVRQVNPQNNKWSFGTTLWEICSGGDKPLSALDSQR,QAPLRGTVMQAPAVRQVNPQNNKWSFGTTLWEICSGGDKPLSALDSQR\tATF7IP:NM_001286514[1,13]-JAK2:NM_004972[17,25];ATF7IP:NM_001286515[1,13]-JAK2:NM_004972[17,25];ATF7IP:NM_018179[1,13]-JAK2:NM_004972[17,25];ATF7IP:NM_181352[1,13]-JAK2:NM_004972[17,25]\t\tgeneB_transcripts=NM_004972\tN,N,N,N\t2,2,2,2\nStJude_Sample\tMNT\tchr17\t2303934\t-\tcoding\tSEPT9\tchr17\t75478225\t+\tcoding\t>\t1\t2\t138\t58\t0.000\t0.000\t47\t52\t0.077\t0.033\t139\t139\tCTGACCTGTGCCCGGCTCGCGGGCCGCCGCCTCGGCCCCGGCGCGCCCCCGGCAGCTCTCGGCGCGATGAGCATAGAGACGCTACTGGAGGCGGCCCGCTTCCTGGAATGGCAAGCGCAGCAACAACAGAGAGCACGTGCCACTGAGGCGGCTCCCAGCTGCGTTGGCGACATGGCCGACACCCCCAGAGATGCCG\tITX\t72.03\tLQ\t2\tFusion\t1,1,1,1,1,1,1,1,1,1,1\tNM_020310,NM_020310,NM_020310,NM_020310,NM_020310,NM_020310,NM_020310,NM_020310,NM_020310,NM_020310,NM_020310\t25,25,25,25,25,25,25,25,25,25,25\t1,1,1,1,1,1,1,1,1,1,1\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t73,73,73,73,73,73,73,73,73,73,73\t\t45,45,45,45,45,45,45,45,45,45,45\t137,137,137,137,137,137,137,137,137,137,137\tNM_001113491,NM_001113492,NM_001113493,NM_001113494,NM_001113495,NM_001113496,NM_001293695,NM_001293696,NM_001293697,NM_001293698,NM_006640\t241,77,234,77,129,-10,222,17,-10,-10,223\t4,4,3,3,2,2,3,2,2,2,3\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t722,230,701,230,386,,665,50,,,668\t1761,1269,1740,1269,1425,1008,1704,1089,1008,1008,1707\t46,46,46,46,46,49,46,46,49,49,46\t138,138,138,138,138,147,138,138,147,147,138\tLTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA,LTCARLAGRRLGPGAPPAALGAMSIETLLEAARFLEWQAQQQQRARATEAAPSCVGDMADTPRDA\tMNT:NM_020310[1,1]-SEPT9:NM_001113491[4,12];MNT:NM_020310[1,1]-SEPT9:NM_001113492[4,12];MNT:NM_020310[1,1]-SEPT9:NM_001113493[3,11];MNT:NM_020310[1,1]-SEPT9:NM_001113494[3,11];MNT:NM_020310[1,1]-SEPT9:NM_001113495[2,10];MNT:NM_020310[1,1]-SEPT9:NM_001113496[2,10];MNT:NM_020310[1,1]-SEPT9:NM_001293695[3,11];MNT:NM_020310[1,1]-SEPT9:NM_001293696[2,10];MNT:NM_020310[1,1]-SEPT9:NM_001293697[2,10];MNT:NM_020310[1,1]-SEPT9:NM_001293698[2,10];MNT:NM_020310[1,1]-SEPT9:NM_006640[3,11]\t\tgeneB_transcripts=NM_001113491,NM_001113492,NM_001113493,NM_001113494,NM_001113495,NM_001113496,NM_001293695,NM_001293696,NM_001293697,NM_001293698,NM_006640;geneb_utr_codons=11\t,,,,,ATE,,,ATE,ATE,\t0,0,0,0,0,0,0,0,0,0,0\nStJude_Sample\tHIPK2\tchr7\t139415730\t-\tcoding\tTCF12\tchr15\t57212088\t+\t5utr\t>\t2\t0\t138\t136\t0.000\t0.000\t55\t0\t0.080\t0.019\t139\t137\tCGCTGACCTCAAACCAGAAAACATCATGCTGGTGGATCCATCTAGACAACCATACAGAGTCAAGGTCATCGACTTTGGTTCAGCCAGCCACGTGTCCAAGGCTGTGTGCTCCACCTACTTGCAGTCCAGATATTACAGGACCTGCTAGAAGTGGCCGAAGATGAATCCCCAGCAACAACGCATGGCCGCTATAGGGACCGACAAGGAGCTGAGCGACCTACTGGACTTCAGTGCGATGTTTTCCCCACCTGTTAATAGTGGGAAAACTAGAC\tCTX\t58.67\tLQ\t2\tupTSS\t0,0,0,0,0,0,0,0,2,2,2,2\tNM_001113239,NM_022740,NM_001113239,NM_022740,NM_001113239,NM_022740,NM_001113239,NM_022740,,,,\t369,369,369,369,369,369,369,369,,,,\t2,2,2,2,2,2,2,2,,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,,,,\t1103,1103,1103,1103,1103,1103,1103,1103,,,,\t\t45,45,45,45,45,45,45,45,,,,\t138,138,138,138,138,138,138,138,,,,\tNM_003205,NM_003205,NM_207036,NM_207036,NM_207037,NM_207037,NM_207038,NM_207038,NM_003205,NM_207036,NM_207037,NM_207038\t-7,-7,-3,-3,-7,-7,-3,-3,-7,-3,-7,-3\t2,2,2,2,2,2,2,2,,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,,,,,\t2049,2049,2121,2121,2121,2121,2049,2049,2049,2121,2121,2049\t48,48,52,52,48,48,52,52,,,,\t145,145,157,157,145,145,157,157,,,,\tADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,ADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,,,,\tHIPK2:NM_001113239[1,2]-TCF12:NM_003205[2,20];HIPK2:NM_022740[1,2]-TCF12:NM_003205[2,20];HIPK2:NM_001113239[1,2]-TCF12:NM_207036[2,21];HIPK2:NM_022740[1,2]-TCF12:NM_207036[2,21];HIPK2:NM_001113239[1,2]-TCF12:NM_207037[2,21];HIPK2:NM_022740[1,2]-TCF12:NM_207037[2,21];HIPK2:NM_001113239[1,2]-TCF12:NM_207038[2,20];HIPK2:NM_022740[1,2]-TCF12:NM_207038[2,20];;;;\t\tgeneB_transcripts=NM_003205,NM_207036,NM_207037,NM_207038;geneb_utr_codons=8;not_inframe_due_to_intermediate_stop_codon;geneb_utr_codons=4\tTC,TC,TC*KWP,TC*KWP,TC,TC,TC*KWP,TC*KWP,,,,\t1,1,1,1,1,1,1,1,,,,\nStJude_Sample\tGUSBP4\tchr6\t58285306\t-\t3utr\tHLA-DPB1\tchr6\t33043816\t+\tcoding\t>\t1\t5\t85\t48\t0.656\t0.020\t48\t176\t0.111\t0.026\t97\t97\tGTTCGGGGTTCGGTAAAAAAGCTCACACATTTGACTTGGAAGCAATGTTTGAACAAACTCAAAGAACAGCTGTGGAAAGAAGTCACAAAACACTGGCTCCATGATGGTTCTGCAGGTTTCTGCGGCCCCCCGGACAGTGGCTCT\tITX\t52.26\tLQ\t0\tupTSS\t2\t\t\t\t\t\t\t\t\tNM_002121\t0\t\ttuple\t\t777\t\t\t\t\tgeneB_breakpoint_not_mapped_to_CDS=NM_001242524;geneB_breakpoint_not_mapped_to_CDS=NM_001242525;geneA_no_transcript_IDs_found\tgeneB_transcripts=NM_001242524,NM_001242525,NM_002121;geneB_transcript_strand_disagree=NM_001242524;geneB_intronic=NM_001242524;geneB_transcript_strand_disagree=NM_001242525;geneB_intronic=NM_001242525;geneb_utr_codons=1\t\t\nStJude_Sample\tTRAK2\tchr2\t202260037\t-\tcoding\tRFPL1S\tchr22\t29819177\t-\tintergenic\t>\t1\t3\t130\t53\t0.000\t0.500\t53\t50\t0.008\t0.224\t142\t143\tTAAAGAACTTCGTGAAACAAATGCTCAGATGTCCAGAATGACTGAAGAATTGTCAGGGAAGAGTGATGAGCTGATTCGATACCAAGAAGAGCTTTCCTCTCTTTTGTCACAGATTGTAGACCTTCAGCATAAACTTAAAGAAAAGCCTGGCTACAGATAAGGGACCAAAATGACTGACTCAAAATATTTCACCAC\tCTX\t50.05\tLQ\t0\tCLoss\t\tNM_015049\t\t\t\t900\t\t\t\t\t\t\t\t\t\t\t\t\t\tgeneB_no_transcripts\t\t\t\nStJude_Sample\tLOC440311\tchr15\t95398934\t+\t5utr\tDHX34\tchr19\t47885236\t+\tcoding\t>\t0\t3\t52\t94\t0.495\t0.000\t1\t67\t0.000\t0.105\t55\t49\tGAGGTTGACCAGTTCCTGGAAGACGTGCGGCTACAGGAGCGCACGAGCGGGGGCTGAGGAAGCTGCCCTCGAAACCCTCCAGAAGACATCTGTCCTGCAGAGGCCCTACCACTGCGAGGCCTGCGGGAAGGACTTCCTCTTTA\tCTX\t33.83\tLQ\t0\tNLoss\t0\t\t\t\t\t\t\t\t\tNM_014681\t1100\t\ttuple\t3299\t3432\t\t\t\t\tgeneA_no_transcript_IDs_found\tgeneB_transcripts=NM_014681\t\t\nStJude_Sample\tGPSM1\tchr9\t139235450\t+\tcoding\tSEPT9\tchr17\t75478221\t+\tcoding\t>\t1\t0\t190\t55\t0.000\t0.000\t49\t0\t0.040\t0.000\t191\t185\tGTGTCCATGGGGCGCCCAGCGCAGGCCCTGACCTTCGCCAAGAAGCACCTGCAGATCTCCCAGGAGATCGGGGACCGCCATGGGGAGCTCACGGCCCGCATGAACGTGGCGCAGCTGCAGCTGGTGCTCGGCCGCCTGACCAGCCCGGCAGCCTCAGAGAAGCCTGACCTGGCCGGCTATGAGGCCCAGGCCACTGAGGCGGCTCCCAGCTGCGTTGGCGACATGGCCGACACCCCCAGA\tCTX\t28.36\tLQ\t2\tFusion\t1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\tNM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597,NM_001145638,NM_015597\t403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403,403\t9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9\tperfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,perfect,tuple,tuple,perfect,perfect,perfect,perfect,tuple,tuple,tuple,tuple,perfect,perfect\t,,,,,,,,,,,,,,,,,,,,,\t\t62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62,62\t188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188,188\tNM_001113491,NM_001113491,NM_001113492,NM_001113492,NM_001113493,NM_001113493,NM_001113494,NM_001113494,NM_001113495,NM_001113495,NM_001113496,NM_001113496,NM_001293695,NM_001293695,NM_001293696,NM_001293696,NM_001293697,NM_001293697,NM_001293698,NM_001293698,NM_006640,NM_006640\t241,241,77,77,234,234,77,77,129,129,-10,-10,222,222,17,17,-10,-10,-10,-10,223,223\t4,4,4,4,3,3,3,3,2,2,2,2,3,3,2,2,2,2,2,2,3,3\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t722,722,230,230,701,701,230,230,386,386,,,665,665,50,50,,,,,668,668\t1761,1761,1269,1269,1740,1740,1269,1269,1425,1425,1008,1008,1704,1704,1089,1089,1008,1008,1008,1008,1707,1707\t63,63,63,63,63,63,63,63,63,63,66,66,63,63,63,63,66,66,66,66,63,63\t189,189,189,189,189,189,189,189,189,189,198,198,189,189,189,189,198,198,198,198,189,189\tVSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR,VSMGRPAQALTFAKKHLQISQEIGDRHGELTARMNVAQLQLVLGRLTSPAASEKPDLAGYEAQATEAAPSCVGDMADTPR\tGPSM1:NM_001145638[1,9]-SEPT9:NM_001113491[4,12];GPSM1:NM_015597[1,9]-SEPT9:NM_001113491[4,12];GPSM1:NM_001145638[1,9]-SEPT9:NM_001113492[4,12];GPSM1:NM_015597[1,9]-SEPT9:NM_001113492[4,12];GPSM1:NM_001145638[1,9]-SEPT9:NM_001113493[3,11];GPSM1:NM_015597[1,9]-SEPT9:NM_001113493[3,11];GPSM1:NM_001145638[1,9]-SEPT9:NM_001113494[3,11];GPSM1:NM_015597[1,9]-SEPT9:NM_001113494[3,11];GPSM1:NM_001145638[1,9]-SEPT9:NM_001113495[2,10];GPSM1:NM_015597[1,9]-SEPT9:NM_001113495[2,10];GPSM1:NM_001145638[1,9]-SEPT9:NM_001113496[2,10];GPSM1:NM_015597[1,9]-SEPT9:NM_001113496[2,10];GPSM1:NM_001145638[1,9]-SEPT9:NM_001293695[3,11];GPSM1:NM_015597[1,9]-SEPT9:NM_001293695[3,11];GPSM1:NM_001145638[1,9]-SEPT9:NM_001293696[2,10];GPSM1:NM_015597[1,9]-SEPT9:NM_001293696[2,10];GPSM1:NM_001145638[1,9]-SEPT9:NM_001293697[2,10];GPSM1:NM_015597[1,9]-SEPT9:NM_001293697[2,10];GPSM1:NM_001145638[1,9]-SEPT9:NM_001293698[2,10];GPSM1:NM_015597[1,9]-SEPT9:NM_001293698[2,10];GPSM1:NM_001145638[1,9]-SEPT9:NM_006640[3,11];GPSM1:NM_015597[1,9]-SEPT9:NM_006640[3,11]\t\tgeneB_transcripts=NM_001113491,NM_001113492,NM_001113493,NM_001113494,NM_001113495,NM_001113496,NM_001293695,NM_001293696,NM_001293697,NM_001293698,NM_006640;geneb_utr_codons=11\t,,,,,,,,,,ATE,ATE,,,,,ATE,ATE,ATE,ATE,,\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\nStJude_Sample\tBMP2K\tchr4\t79800045\t+\tcoding\tBMPR1B\tchr4\t96025559\t+\tcoding\t>\t0\t1\t54\t160\t0.000\t0.000\t1\t53\t0.000\t0.036\t54\t54\tCTAAGTTAACAGAAGAGGAACTATTGGACAGAGAATTTGACCTTCTAAGATCAACAAACTTCCTTGATAACATGCTTTTGCGAAGTGCAGGAAAATTAAATGTGGGCACCAAGAAAGAGGATGGTGAGAGTACAGCCCCCACCCCCCGTCCAAAGGTCTTGCGTTGTAAATGCCACCACCATTGTCCAGAAGACTCAGTCAACAATATTTGCAGC\tDEL\t26.80\tLQ\t2\tFusion\t1,1,1,1,1,1,1,1\tNM_017593,NM_198892,NM_017593,NM_198892,NM_017593,NM_198892,NM_017593,NM_198892\t651,651,651,651,651,651,651,651\t14,14,14,14,14,14,14,14\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t1951,1951,1951,1951,1951,1951,1951,1951\t\t16,16,16,16,16,16,16,16\t52,52,52,52,52,52,52,52\tNM_001203,NM_001203,NM_001256792,NM_001256792,NM_001256793,NM_001256793,NM_001256794,NM_001256794\t-5,-5,-5,-5,25,25,-5,-5\t4,4,2,2,2,2,2,2\ttuple,tuple,tuple,tuple,blat,blat,tuple,tuple\t,,,,74,74,,\t1509,1509,1509,1509,1599,1599,1509,1509\t20,20,20,20,18,18,20,20\t62,62,62,62,56,56,62,62\tKLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS,KLTEEELLDREFDLLRSTNFLDNMLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICS\tBMP2K:NM_017593[1,14]-BMPR1B:NM_001203[4,13];BMP2K:NM_198892[1,14]-BMPR1B:NM_001203[4,13];BMP2K:NM_017593[1,14]-BMPR1B:NM_001256792[2,11];BMP2K:NM_198892[1,14]-BMPR1B:NM_001256792[2,11];BMP2K:NM_017593[1,14]-BMPR1B:NM_001256793[2,11];BMP2K:NM_198892[1,14]-BMPR1B:NM_001256793[2,11];BMP2K:NM_017593[1,14]-BMPR1B:NM_001256794[2,11];BMP2K:NM_198892[1,14]-BMPR1B:NM_001256794[2,11]\t\tgeneB_transcripts=NM_001203,NM_001256792,NM_001256793,NM_001256794;geneb_utr_codons=6\tTNF,TNF,TNF,TNF,T,T,TNF,TNF\t2,2,2,2,2,2,2,2\nStJude_Sample\tFUS\tchr16\t31191548\t+\tcoding\tCXCR4\tchr2\t136873483\t-\tcoding\t>\t4\t4\t57\t60\t0.000\t0.000\t28\t153\t0.004\t0.025\t57\t56\tGTTGGAACTTCGTTGCTTGCTTGCCTGTGCGCGCGTGCGCGGACATGGCCTCAAACGATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAA\tCTX\t21.52\tLQ\t3\tFusion\t0,0,0,0,0,0,0,0\tNM_001170634,NM_001170937,NM_004960,NM_001170634,NM_001170937,NM_004960,,\t,,,,,,,\t1,1,1,1,1,1,,\t,,,,,,,\t13,13,13,13,13,13,,\t\t,,,,,,,\t,,,,,,,\tNM_001008540,NM_001008540,NM_001008540,NM_003467,NM_003467,NM_003467,NM_001008540,NM_003467\t9,9,9,6,6,6,9,6\t1,1,1,2,2,2,,\tblat,blat,blat,tuple,tuple,tuple,blat,tuple\t27,27,27,16,16,16,27,16\t1071,1071,1071,1059,1059,1059,1071,1059\t19,19,19,19,19,19,,\t,,,,,,,\tVGTSLLACLCARARTWPQTIYTSDNYTEEMGSGDYDSM,VGTSLLACLCARARTWPQTIYTSDNYTEEMGSGDYDSM,VGTSLLACLCARARTWPQTIYTSDNYTEEMGSGDYDSM,VGTSLLACLCARARTWPQTIYTSDNYTEEMGSGDYDSM,VGTSLLACLCARARTWPQTIYTSDNYTEEMGSGDYDSM,VGTSLLACLCARARTWPQTIYTSDNYTEEMGSGDYDSM,,\tFUS:NM_001170634[1,1]-CXCR4:NM_001008540[1,1];FUS:NM_001170937[1,1]-CXCR4:NM_001008540[1,1];FUS:NM_004960[1,1]-CXCR4:NM_001008540[1,1];FUS:NM_001170634[1,1]-CXCR4:NM_003467[2,2];FUS:NM_001170937[1,1]-CXCR4:NM_003467[2,2];FUS:NM_004960[1,1]-CXCR4:NM_003467[2,2];;\t\tgeneB_transcripts=NM_001008540,NM_003467\t,,,,,,,\t0,0,0,0,0,0,,\nStJude_Sample\tTTYH3\tchr7\t2671914\t+\tcoding\tSKI\tchr1\t2234413\t+\tcoding\t>\t4\t0\t81\t47\t0.000\t0.000\t74\t0\t0.077\t0.000\t82\t77\tTGCACCGGCTGCCCCACTTCGACCTGAGCTGGGAGGCCCCTAGCAGCCAGTTCCGGCCCGAGGACACCGACTACCAGCAGGTCTCCTCTGAGCCTCCGGCCTCCATAAGACCCAAAACAGATG\tCTX\t17.19\tLQ\t2\tFusion\t1\tNM_025250\t42\t1\ttuple\t123\t\t25\t79\tNM_003036\t324\t2\ttuple\t970\t2187\t26\t80\tHRLPHFDLSWEAPSSQFRPEDTDYQQVSSEPPASIRPKTD\tTTYH3:NM_025250[1,1]-SKI:NM_003036[2,7]\t\tgeneB_transcripts=NM_003036\t\t2\nStJude_Sample\tFNBP1\tchr9\t132805231\t-\tcoding\tCXCR4\tchr2\t136873483\t-\tcoding\t>\t0\t7\t54\t82\t0.000\t0.000\t0\t120\t0.030\t0.025\t54\t54\tCGCGGAGCGCCCCTTCGCGTCCCCTGCACCATGAGCTGGGGCACCGAGCTCTGGATATACACTTAAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAA\tCTX\t16.88\tLQ\t3\tFusion\t0,0,3,3\tNM_015033,NM_015033,,\t,,,\t1,1,,\t,,,\t24,24,,\t\t,,,\t,,,\tNM_001008540,NM_003467,NM_001008540,NM_003467\t9,6,9,6\t1,2,,\tblat,blat,blat,blat\t27,16,27,16\t1071,1059,1071,1059\t21,21,,\t,,,\tRGAPLRVPCTMSWGTELWIYT*DNYTEEMGSGDYDSMKEPCFREE,RGAPLRVPCTMSWGTELWIYT*DNYTEEMGSGDYDSMKEPCFREE,,\tFNBP1:NM_015033[1,1]-CXCR4:NM_001008540[1,1];FNBP1:NM_015033[1,1]-CXCR4:NM_003467[2,2];;\t\tgeneB_transcripts=NM_001008540,NM_003467\t,,,\t0,0,,\nStJude_Sample\tTFEB\tchr6\t41703086\t-\t5utr\tCCND3\tchr6\t41908322\t-\tcoding\t>\t2\t3\t95\t61\t0.000\t0.076\t91\t40\t0.027\t0.012\t96\t96\tGCGGGCACAGCTTGCGGGCCAGGCACCCGAACTTGCGACAAGTTGCCGGAGCCGCGGGGCGCGGGCGGCGGACAGATTGACCTTCAGAGCGAGGTATGTGAGGAGCAGCGCTGTGAGGAGGAAGTCTTCCCCCTGGCCATGAACTACCTGGATCGATA\tINS\t13.72\tLQ\t3\tNLoss\t0,0,0,0,0,0,0,0,0,0,0,0\tNM_001167827,NM_001271943,NM_001271944,NM_001167827,NM_001271943,NM_001271944,NM_001167827,NM_001271943,NM_001271944,,,\t,,,,,,,,,,,\t1,1,1,1,1,1,1,1,1,,,\t,,,,,,,,,,,\t20,,,20,,,20,,,,,\t\t,,,,,,,,,,,\t,,,,,,,,,,,\tNM_001136017,NM_001136017,NM_001136017,NM_001287427,NM_001287427,NM_001287427,NM_001760,NM_001760,NM_001760,NM_001136017,NM_001287427,NM_001760\t-14,-14,-14,17,17,17,67,67,67,-14,17,67\t2,2,2,2,2,2,2,2,2,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,50,50,50,200,200,200,,50,200\t636,636,636,729,729,729,879,879,879,636,729,879\t34,34,34,31,31,31,31,31,31,,,\t,,,,,,,,,,,\tAGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,AGTACGPGTRTCDKLPEPRGAGGGQIDLQSEVCEEQRCEEEVFPLAMNYLDR,,,\tTFEB:NM_001167827[1,1]-CCND3:NM_001136017[2,5];TFEB:NM_001271943[1,1]-CCND3:NM_001136017[2,5];TFEB:NM_001271944[1,1]-CCND3:NM_001136017[2,5];TFEB:NM_001167827[1,1]-CCND3:NM_001287427[2,5];TFEB:NM_001271943[1,1]-CCND3:NM_001287427[2,5];TFEB:NM_001271944[1,1]-CCND3:NM_001287427[2,5];TFEB:NM_001167827[1,1]-CCND3:NM_001760[2,5];TFEB:NM_001271943[1,1]-CCND3:NM_001760[2,5];TFEB:NM_001271944[1,1]-CCND3:NM_001760[2,5];;;\tgeneB_breakpoint_not_mapped_to_CDS=NM_001136125;geneB_breakpoint_not_mapped_to_CDS=NM_001136126;geneB_breakpoint_not_mapped_to_CDS=NM_001287434\tgeneB_transcripts=NM_001136017,NM_001136125,NM_001136126,NM_001287427,NM_001287434,NM_001760;geneb_utr_codons=13;geneB_intronic=NM_001136125;geneB_intronic=NM_001136126;geneB_intronic=NM_001287434\t,,,,,,,,,,,\t0,0,0,0,0,0,0,0,0,,,\nStJude_Sample\tCUX1\tchr7\t101882864\t+\tcoding\tGOLGA4\tchr3\t37396590\t+\tcoding\t>\t0\t2\t52\t94\t0.480\t0.000\t1\t66\t0.000\t0.045\t52\t50\tCCCAGCTCAACCTGAAAACCAGCACCGTCATCAACTGGTTCCACAACTACAGACCATGGCAAAAGTTATAACCACCGTACTGAAGTTCCCTGATGATCAGACTCAGAAAATTTTGGAAAGAGAAGATGCTCGGCTGATGTTTAC\tCTX\t11.42\tLQ\t3\tFusion\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,3\tNM_001202543,NM_001202544,NM_001202545,NM_001202546,NM_001913,NM_181500,NM_181552,NM_001202543,NM_001202544,NM_001202545,NM_001202546,NM_001913,NM_181500,NM_181552,,\t,,,,,,,,,,,,,,,\t23,13,13,13,14,14,23,23,13,13,13,14,14,23,,\t,,,,,,,,,,,,,,,\t3920,,,,,,3887,3920,,,,,,3887,,\t\t,,,,,,,,,,,,,,,\t,,,,,,,,,,,,,,,\tNM_001172713,NM_001172713,NM_001172713,NM_001172713,NM_001172713,NM_001172713,NM_001172713,NM_002078,NM_002078,NM_002078,NM_002078,NM_002078,NM_002078,NM_002078,NM_001172713,NM_002078\t2208,2208,2208,2208,2208,2208,2208,2193,2193,2193,2193,2193,2193,2193,2208,2193\t22,22,22,22,22,22,22,22,22,22,22,22,22,22,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t6622,6622,6622,6622,6622,6622,6622,6577,6577,6577,6577,6577,6577,6577,6622,6577\t6732,6732,6732,6732,6732,6732,6732,6693,6693,6693,6693,6693,6693,6693,6732,6693\t17,17,17,17,17,17,17,17,17,17,17,17,17,17,,\t,,,,,,,,,,,,,,,\tPAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,PAQPENQHRHQLVPQLQTMAKVITTVLKFPDDQTQKILEREDARLMF,,\tCUX1:NM_001202543[1,23]-GOLGA4:NM_001172713[22,23];CUX1:NM_001202544[1,13]-GOLGA4:NM_001172713[22,23];CUX1:NM_001202545[1,13]-GOLGA4:NM_001172713[22,23];CUX1:NM_001202546[1,13]-GOLGA4:NM_001172713[22,23];CUX1:NM_001913[1,14]-GOLGA4:NM_001172713[22,23];CUX1:NM_181500[1,14]-GOLGA4:NM_001172713[22,23];CUX1:NM_181552[1,23]-GOLGA4:NM_001172713[22,23];CUX1:NM_001202543[1,23]-GOLGA4:NM_002078[22,24];CUX1:NM_001202544[1,13]-GOLGA4:NM_002078[22,24];CUX1:NM_001202545[1,13]-GOLGA4:NM_002078[22,24];CUX1:NM_001202546[1,13]-GOLGA4:NM_002078[22,24];CUX1:NM_001913[1,14]-GOLGA4:NM_002078[22,24];CUX1:NM_181500[1,14]-GOLGA4:NM_002078[22,24];CUX1:NM_181552[1,23]-GOLGA4:NM_002078[22,24];;\t\tgeneB_transcripts=NM_001172713,NM_002078\t,,,,,,,,,,,,,,,\t1,1,1,1,1,1,1,1,1,1,1,1,1,1,,\nStJude_Sample\tERICH1-AS1\tchr8\t687825\t+\t5utr\tHMGB1\tchr13\t31037833\t-\t5utr\t>\t3\t1\t77\t61\t0.000\t0.947\t91\t7\t0.159\t0.023\t78\t76\tCTGAGGAGGGGCCGCTTCGCCATGTCGCCCCGCACCTGCTGAGCCCGGAGCGTCCGAGGATGTCCGCGCTGAGGAAGAAAAATAACTAAACATGGGCAAAGGAGATCCTAAGAAGCCGAGAGGCAAAATGTCATCA\tCTX\t11.20\tLQ\t0\tupTSS\t2\t\t\t\t\t\t\t\t\tNM_002128\t-4\t\ttuple\t\t648\t\t\t\t\tgeneA_no_transcript_IDs_found\tgeneB_transcripts=NM_002128;geneb_utr_codons=5\t\t\nStJude_Sample\tAKAP8\tchr19\t15490523\t-\tcoding\tTCF12\tchr15\t57212088\t+\t5utr\t>\t2\t0\t84\t136\t0.000\t0.000\t64\t0\t0.019\t0.019\t85\t82\tCGCTGAACGCATGCGTGCTGTGGTCGCCTAGTAAACGGGGCTGCTGGTGGGCCGCGTCGAAGACATGGACCAGGGCTACGGAGGACCTGCTAGAAGTGGCCGAAGATGAATCCCCAGCAACAACGCATGGCCGCTATAGGGACCGACAAGGAGCTGAGCGACCTACTGGACTTCAGTGCGATGTTTTCCCCACCTGTTAATAGTGGGAAAACTAGAC\tCTX\t9.04\tLQ\t2\tupTSS\t0,0,0,0,2,2,2,2\tNM_005858,NM_005858,NM_005858,NM_005858,,,,\t,,,,,,,\t1,1,1,1,,,,\t,,,,,,,\t19,19,19,19,,,,\t\t,,,,,,,\t,,,,,,,\tNM_003205,NM_207036,NM_207037,NM_207038,NM_003205,NM_207036,NM_207037,NM_207038\t-7,-3,-7,-3,-7,-3,-7,-3\t2,2,2,2,,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,\t2049,2121,2121,2049,2049,2121,2121,2049\t30,34,30,34,,,,\t,,,,,,,\tR*THACCGRLVNGAAGGPRRRHGPGLRRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,R*THACCGRLVNGAAGGPRRRHGPGLRRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,R*THACCGRLVNGAAGGPRRRHGPGLRRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,R*THACCGRLVNGAAGGPRRRHGPGLRRTC*KWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTR,,,,\tAKAP8:NM_005858[1,1]-TCF12:NM_003205[2,20];AKAP8:NM_005858[1,1]-TCF12:NM_207036[2,21];AKAP8:NM_005858[1,1]-TCF12:NM_207037[2,21];AKAP8:NM_005858[1,1]-TCF12:NM_207038[2,20];;;;\t\tgeneB_transcripts=NM_003205,NM_207036,NM_207037,NM_207038;geneb_utr_codons=8;geneb_utr_codons=4\t,,,,,,,\t0,0,0,0,,,,\nStJude_Sample\tECHDC3\tchr10\t11797608\t+\tcoding\tARHGAP24\tchr4\t86491673\t+\t5utr\t>\t2\t3\t90\t46\t0.000\t0.000\t54\t70\t0.125\t0.000\t91\t88\tACAAGTCCTCTTTTGCCACTCCTGGGGTGAACGTCGGGCTCTTCTGTTCTACCCCTGGGGTTGCCTTGGCAAGAGCAGTGCCTAGAAAGGAAAGTCCATCAGCTTGATAATGGAGGAGAACAATGACTCCACG\tCTX\t7.31\tLQ\t0\tCLoss\t0,0\tNM_024693,\t,\t4,\t,\t,\t\t,\t,\tNM_001025616,NM_001025616\t-6,-6\t2,\ttuple,tuple\t,\t2247,2247\t32,\t,\tQVLFCHSWGERRALLFYPWGCLGKSSA*KGKSISLIMEENNDST,\tECHDC3:NM_024693[1,4]-ARHGAP24:NM_001025616[2,10];\t\tgeneB_transcripts=NM_001025616;geneb_utr_codons=7\t,\t1,\nStJude_Sample\tCASD1\tchr7\t94164835\t+\tcoding\tSND1\tchr7\t127731889\t+\tcoding\t>\t1\t0\t95\t49\t0.000\t0.000\t50\t1\t0.022\t0.000\t96\t96\tATGTTAAGATGTTCAGTGTTTCCAAATTAATTGCTCAAGAAACCATCATGGAATCTTTGGATGGCTTACATCTTCCTGAATCGAGCAGAGAAACTATCACAGAATACCTGAATACCCAAGAGTCAGCCAAGAGCGCCAGGCTGAA\tDEL\t6.39\tLQ\t2\tFusion\t1\tNM_022900\t282\t8\tperfect\t843\t\t30\t94\tNM_014390\t875\t23\tblat\t2623\t2733\t31\t95\tVKMFSVSKLIAQETIMESLDGLHLPESSRETITEYLNTQESAKSARL\tCASD1:NM_022900[1,8]-SND1:NM_014390[23,24]\t\tgeneB_transcripts=NM_014390\t\t2\nStJude_Sample\tNIN\tchr14\t51288594\t-\tcoding\tKLC1\tchr14\t104120900\t+\tcoding\t>\t0\t1\t171\t103\t0.006\t0.000\t0\t47\t0.015\t0.018\t171\t171\tGGAGCAGGACCAGCATGAGGCCCGACTCAAGGAGCTGTTTGACAGTTTTGACACGACGGGCACAGGGTCCCTGGGGCAGGAGGAACTCACCGACCTTTGCCACATGTTGAGCTTGGAGGAGGTGGCCCCAGTGCTGCAGCAGACATTACTTCAGGACAACCTCTTGGGCAGGAATGTATGACAACATGTCCACAATGGTGTACATAAAGGAAGACAAGTTGGAGAAGCTTACACAGGATGAAATTATTTCTAAGACAAAGCAAGTAATTCAGGG\tITX\t5.50\tLQ\t3\tupTSS\t0,0,0,0,0,0,0,0,0,0,0,0,2,2,2\tNM_016350,NM_020921,NM_182944,NM_182946,NM_016350,NM_020921,NM_182944,NM_182946,NM_016350,NM_020921,NM_182944,NM_182946,,,\t,,,,,,,,,,,,,,\t3,3,3,3,3,3,3,3,3,3,3,3,,,\t,,,,,,,,,,,,,,\t181,,,,181,,,,181,,,,,,\t\t,,,,,,,,,,,,,,\t,,,,,,,,,,,,,,\tNM_001130107,NM_001130107,NM_001130107,NM_001130107,NM_005552,NM_005552,NM_005552,NM_005552,NM_182923,NM_182923,NM_182923,NM_182923,NM_001130107,NM_005552,NM_182923\t0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\t2,2,2,2,2,2,2,2,2,2,2,2,,,\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,,,,,,,,,,,,,,\t1857,1857,1857,1857,1683,1683,1683,1683,1722,1722,1722,1722,1857,1683,1722\t57,57,57,57,57,57,57,57,57,57,57,57,,,\t,,,,,,,,,,,,,,\tSRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,SRTSMRPDSRSCLTVLTRRAQGPWGRRNSPTFATC*AWRRWPQCCSRHYFRTTSWAGMYDNMSTMVYIKEDKLEKLTQDEIISKTKQVIQ,,,\tNIN:NM_016350[1,3]-KLC1:NM_001130107[2,16];NIN:NM_020921[1,3]-KLC1:NM_001130107[2,16];NIN:NM_182944[1,3]-KLC1:NM_001130107[2,16];NIN:NM_182946[1,3]-KLC1:NM_001130107[2,16];NIN:NM_016350[1,3]-KLC1:NM_005552[2,15];NIN:NM_020921[1,3]-KLC1:NM_005552[2,15];NIN:NM_182944[1,3]-KLC1:NM_005552[2,15];NIN:NM_182946[1,3]-KLC1:NM_005552[2,15];NIN:NM_016350[1,3]-KLC1:NM_182923[2,15];NIN:NM_020921[1,3]-KLC1:NM_182923[2,15];NIN:NM_182944[1,3]-KLC1:NM_182923[2,15];NIN:NM_182946[1,3]-KLC1:NM_182923[2,15];;;\t\tgeneB_transcripts=NM_001130107,NM_005552,NM_182923;geneb_utr_codons=1\t,,,,,,,,,,,,,,\t2,2,2,2,2,2,2,2,2,2,2,2,,,\nStJude_Sample\tGNA12\tchr7\t2834562\t-\tcoding\tAFF3\tchr2\t100203737\t-\tcoding\t>\t1\t0\t217\t101\t0.005\t0.000\t50\t0\t0.017\t0.000\t254\t257\tGGACCGCGCGCCGCTCGCGGGCCAGCAGCGCGTCACGGGCTCAAGGGTTCTTGTTGATGCACGAGATAAGCTTGGCATTCCTTGGCAGTATTCTGAAAATGAGAAGCATGGGATGTTCCTGATGGCCTTCGAGAACAAGGCGGGGCTGCCTGTGGAGCCGGCCACCTTCCAGCTGTACGTCCCGGCCCTGAGCGCACTCTGGAGGGATTCTGGCATCAGGGAGGCTTTCAGCCGGAGAAGCGAGTTTCAGCTGGGGGACAACGAAGACGACTACAGGGAGATCAAGAAGTCCCAGGGAGAGAAAGACAGCTCTTCAAGACTGGCCACCTCCACCAGTAATACTTTGTCTGCAAACCA\tCTX\t5.37\tLQ\t2\tFusion\t1,1,1,1,1,1\tNM_001282441,NM_001293092,NM_007353,NM_001282441,NM_001293092,NM_007353\t118,176,177,118,176,177\t3,2,2,3,2,2\ttuple,tuple,tuple,tuple,tuple,tuple\t348,525,525,348,525,525\t\t84,83,84,84,83,84\t255,252,255,255,252,255\tNM_001025108,NM_001025108,NM_001025108,NM_002285,NM_002285,NM_002285\t849,849,849,824,824,824\t15,15,15,15,15,15\ttuple,tuple,tuple,tuple,tuple,tuple\t,,,,,\t,,,,,\t85,85,85,85,85,85\t256,256,256,256,256,256\tDRAPLAGQQRVTGSRVLVDARDKLGIPWQYSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGDNEDDYREIKKSQGEKDSSSRLATSTSNTLSAN,DRAPLAGQQRVTGSRVLVDARDKLGIPWQYSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGDNEDDYREIKKSQGEKDSSSRLATSTSNTLSAN,DRAPLAGQQRVTGSRVLVDARDKLGIPWQYSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGDNEDDYREIKKSQGEKDSSSRLATSTSNTLSAN,DRAPLAGQQRVTGSRVLVDARDKLGIPWQYSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGDNEDDYREIKKSQGEKDSSSRLATSTSNTLSAN,DRAPLAGQQRVTGSRVLVDARDKLGIPWQYSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGDNEDDYREIKKSQGEKDSSSRLATSTSNTLSAN,DRAPLAGQQRVTGSRVLVDARDKLGIPWQYSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGDNEDDYREIKKSQGEKDSSSRLATSTSNTLSAN\tGNA12:NM_001282441[1,3]-AFF3:NM_001025108[15,24];GNA12:NM_001293092[1,2]-AFF3:NM_001025108[15,24];GNA12:NM_007353[1,2]-AFF3:NM_001025108[15,24];GNA12:NM_001282441[1,3]-AFF3:NM_002285[15,24];GNA12:NM_001293092[1,2]-AFF3:NM_002285[15,24];GNA12:NM_007353[1,2]-AFF3:NM_002285[15,24]\tgeneB_CDS_mapping_exception=NM_001025108:-2;geneB_CDS_mapping_exception=NM_002285:-2\tgeneB_transcripts=NM_001025108,NM_002285\t,G,,,G,\t1,1,1,1,1,1\nStJude_Sample\tUSP10\tchr16\t84733718\t+\tcoding\tDYRK1A\tchr21\t38877584\t+\tcoding\t>\t0\t1\t104\t92\t0.665\t0.011\t0\t45\t0.010\t0.025\t137\t134\tCACACAGGCTGTGGATAAACTACCTGATGGGGTTGTGCGGGCGAGAAGATGGCGGCGGCGGGGGAAGCAGCGTGAGCAGCCGGAGGATCGCGGAGTCCCAATGAAACGGGCAGCCATGGCCCTCCACAGCCCGCAGGAGTACAAACCACCAGGAACCCGTAAACTTCATAACATTCTTGGAGTGGAAACAGGAGGACCTGGTGGGCGACGTGCTGGGGAGTCAGGTAGATCGGAAGAGCGTCGT\tCTX\t4.22\tLQ\t2\tFusion\t1,1,1,1,1,1,1,1\tNM_001272075,NM_005153,NM_001272075,NM_005153,NM_001272075,NM_005153,NM_001272075,NM_005153\t56,52,56,52,56,52,56,52\t1,1,1,1,1,1,1,1\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t,21,,21,,21,,21\t\t9,9,9,9,9,9,9,9\t30,30,30,30,30,30,30,30\tNM_001396,NM_001396,NM_101395,NM_101395,NM_130436,NM_130436,NM_130438,NM_130438\t414,414,414,414,405,405,414,414\t9,9,11,11,9,9,9,9\ttuple,tuple,tuple,tuple,tuple,tuple,tuple,tuple\t1240,1240,1240,1240,1213,1213,1240,1240\t2292,2292,1755,1755,2265,2265,1590,1590\t45,45,45,45,45,45,45,45\t136,136,136,136,136,136,136,136\tTQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR,TQAVDKLPDGVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQEYKPPGTRKLHNILGVETGGPGGRRAGESGRSEERR\tUSP10:NM_001272075[1,1]-DYRK1A:NM_001396[9,11];USP10:NM_005153[1,1]-DYRK1A:NM_001396[9,11];USP10:NM_001272075[1,1]-DYRK1A:NM_101395[11,13];USP10:NM_005153[1,1]-DYRK1A:NM_101395[11,13];USP10:NM_001272075[1,1]-DYRK1A:NM_130436[9,11];USP10:NM_005153[1,1]-DYRK1A:NM_130436[9,11];USP10:NM_001272075[1,1]-DYRK1A:NM_130438[9,10];USP10:NM_005153[1,1]-DYRK1A:NM_130438[9,10]\t\tgeneB_transcripts=NM_001396,NM_101395,NM_130436,NM_130438\tVVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ,VVRARRWRRRGKQREQPEDRGVPMKRAAMALHSPQ\t1,1,1,1,1,1,1,1\nStJude_Sample\tZFP41\tchr8\t144337292\t+\tintron\tCXCR4\tchr2\t136873486\t-\tcoding\t>\t1\t3\t131\t47\t0.000\t0.598\t43\t51\t0.154\t0.000\t143\t139\tGCCCAGCATTCAGGGCCAATAGGACGGATTCCCAGGTGTGGATTGACATCTCACCAAATGCCAGCCCCAGGTCATGCCCACAGAGACGCCTGCAGCAGCGCATGGCTGGCAGGACCACCTCAGCCTCTCTAGCAGCAGGCAGATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGG\tCTX\t3.85\tLQ\t2\tNLoss\t0,0,3,3\tNM_173832,NM_173832,,\t,,,\t2,2,,\t,,,\t,,,\t\t,,,\t,,,\tNM_001008540,NM_003467,NM_001008540,NM_003467\t8,6,8,6\t1,2,,\tblat,tuple,blat,tuple\t24,16,24,16\t1071,1059,1071,1059\t46,47,,\t,,,\tPSIQGQ*DGFPGVD*HLTKCQPQVMPTETPAAAHGWQDHLSLSSSRQIYTSDNYTEEMGSG,PSIQGQ*DGFPGVD*HLTKCQPQVMPTETPAAAHGWQDHLSLSSSRQIYTSDNYTEEMGSG,,\tZFP41:NM_173832[1,2]-CXCR4:NM_001008540[1,1];ZFP41:NM_173832[1,2]-CXCR4:NM_003467[2,2];;\t\tgeneB_transcripts=NM_001008540,NM_003467\t,,,\t1,1,,", 
-                    "dataname": "Cicero demo"
-                }
-            },
-            "testSpec": {
-                "timeout": 7000,
-                "expected": { "span": 2, "li": 1 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1DRVzE_WenG490eRYB7VGFOygtSqtF5L97rhK0HOUCNY/edit"
-        }
-    ],
-    "citation_id": 1003
-}

package/cards/gdcbam.json

@@ -1,23 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true,
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "parseurl": false,
-                "gdcbamslice": { "uionly": true }
-            },
-            "testSpec": {
-                "expected": {"image": 1 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Launch App from Link",
-            "link": "https://proteinpaint.stjude.org/?gdcbamslice=1"
-        }
-    ],
-    "citation_id": 1004
-}

package/cards/genefusion.json

@@ -1,57 +0,0 @@
-{
-    "ppcalls": [
-        {
-            "isUi": true, 
-            "runargs": {
-                "noheader": true,
-                "nobox": 1, 
-                "parseurl": false, 
-                "tkui": "genefusion"
-            }
-        },
-        {
-            "label": "Gene fusion",
-            "message": "<p>Call the gene fusion view by defining the following, separated by commas, in the <span style='font-family: courier; display: inline-block; color:gray;font-size:16px;'>text</span> key. <ol><li>N-term gene symbol</li><li>N-term gene isoform</li><li>N-term gene break-end position</li><li>C-term gene symbol</li><li>C-term gene isoform</li><li>C-term gene break-end position</li><li>(optional) interstitial sequence AA length</li></ol></p>",
-            "runargs": {
-                "noheader": true,
-                "nobox": 1, 
-                "parseurl": false, 
-                "genome": "hg19",
-                "genefusion": {
-                    "text": "PAX5,NM_016734,201,JAK2,NM_004972,812",
-		            "positionType": "codon"
-                }
-            },
-            "testSpec": {
-                "expected": {"rect": 2, "svg": 1 }
-            }
-        },
-        {
-            "label": "Protein view with gene fusion",
-            "runargs": {
-                "noheader": true,
-                "nobox": 1, 
-                "parseurl": false, 
-                "genome": "hg19",
-                "gene": "NM_016734",
-                "tracks":[{
-                    "type":"mds3",
-                    "name":"custom snvindel and fusion",
-                    "custom_variants":[
-                        {
-                            "chr":"chr9","pos":37015165,"mname":"P80R","class":"M","dt":1,"ref":"G","alt":"C"
-                        },
-                        {
-                            "gene1":"PAX5","chr1":"chr9","pos1":37002646, "strand1":"-",
-                            "gene2":"JAK2","chr2":"chr9","pos2":5081726, "strand2":"+","dt":2,"class":"Fuserna"
-                        }
-                    ]
-                }]
-            },
-            "testSpec": {
-                "expected": {"rect": 1, "svg": 1, "table": 1 }
-            }
-        }
-    ],
-    "ribbonMessage": "<p style='display: inline-block;'>Explore gene fusions! Use the new form on the <span style='color:#1575ad; font-weight:600;'>Add Your Data</span> tab to see the gene fusion view. Please see the <span style='color:#1575ad; font-weight:600;'>Examples</span> tab for an example and how to display custom data.</p>"
-}

package/cards/genomepaint.json

@@ -1,122 +0,0 @@
-{
-    "ppcalls":[
-        {
-            "label":"Launch a Custom Dataset",
-            "urlparam":"?genome=hg38&block=1&position=chr22:22569655-23013766&svcnvfpkmfile=TCGA_DLBC,svcnv,proteinpaint_demo/hg38/GP/TCGA_DLBC.CNV.gz,vcf,proteinpaint_demo/hg38/GP/TCGA_DLBC.vcf.gz,fpkm,proteinpaint_demo/hg38/GP/TCGA_DLBC.fpkm.gz",
-            "runargs":{
-                "parseurl": true,
-                "nobox": 1,
-                "noheader": 1,
-                "block": true,
-                "genome": "hg38",
-                "position": "chr22:22569655-23013766",
-                "nativetracks": "RefGene",
-                "tracks":[
-                    {
-                        "type": "mdssvcnv",
-                        "name": "TCGA_DLBC",
-                        "file": "proteinpaint_demo/hg38/GP/TCGA_DLBC.CNV.gz",
-                        "checkvcf": {
-                            "file": "proteinpaint_demo/hg38/GP/TCGA_DLBC.vcf.gz"
-                        },
-                        "checkexpressionrank": {
-                            "file": "proteinpaint_demo/hg38/GP/TCGA_DLBC.fpkm.gz"
-                        }
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "Custom Dataset Documentation",
-                    "link": "https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit#heading=h.2sz0rhdexazf"
-                }
-            ],
-            "testSpec": {
-                "expected": {"rect": 20 }
-            }
-        },
-        {
-            "label":"Launch an Official Dataset",
-            "message": "This is an example of how to launch one of the official datasets available in ProteinPaint.",
-            "urlparam": "?genome=hg19&block=1&mds=Pediatric2,svcnv",
-            "runargs": {
-                "parseurl": true,
-                "nobox": 1,
-                "noheader": 1,
-                "block": true,
-                "genome": "hg19",
-                "position": "chr8:128688997-128888997",
-                "datasetqueries": [
-                    {
-                        "dataset":"Pediatric2",
-                        "querykey": "svcnv"
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "Official Dataset Documentation",
-                    "link": "https://docs.google.com/document/d/1KNx4pVCKd4wgoHI4pjknBRTLrzYp6AL_D-j6MjcQSvQ/edit#heading=h.jibbdhrfuw7f"
-                }
-            ],
-            "testSpec": {
-                "expected": {"rect": 20 }
-            }
-        },
-        {
-            "label":"Customize with a Mds JSON",
-            "message": "<div>This example of a mdsjson demostrates how to separate samples into subgroups. The json file may available from the server and accessed via the <span style='font-family: courier; display: inline-block; color:gray;font-size:16px;'>mdsjsonfile</span> key or available from a URL and accessed via the <span style='font-family: courier; display: inline-block; color:gray; font-size:16px;'>mdsjsonurl</span> key.",
-            "urlparam": "?genome=hg38&block=1&position=chr22:22569655-23013766&mdsjson=proteinpaint_demo/hg38/GP/mdsjson/mdsjsondemo.json",
-            "jsonpath":"proteinpaint_demo/hg38/GP/mdsjson/mdsjsonDemo.json",
-            "runargs": {
-                "nobox": 1,
-                "noheader": 1,
-                "block": true,
-                "genome": "hg38",
-                "position": "chr22:22569655-23013766",
-                "nativetracks": "RefGene",
-                "tracks": [
-                    {
-                        "mdsjsonfile":"proteinpaint_demo/hg38/GP/mdsjson/mdsjsonDemo.json"
-                    }
-                ]
-            },
-            "buttons": [
-                {
-                    "name": "Mds JSON Documentation",
-                    "link": "https://docs.google.com/document/d/1_eUrRsR9D-6AD5buNe30tmGICU-B3w67nz-XjpjnDyI/edit#heading=h.pmuzrkapwipq"
-                }
-            ],
-            "testSpec": {
-                "expected": {"rect": 20 }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Launch GenomePaint",
-            "link": "https://genomepaint.stjude.cloud/"
-        },
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit?usp=sharing"
-        }
-    ],
-    "arrowButtons": [
-        {
-            "name": "Data Processing",
-            "message": "<p>Download the data and data processing scripts from the Download Data & Processing Pipeline link. Please use the Data Processing Docs for instructions</p>",
-            "links": [
-                {
-                    "name": "Download Data & Processing Pipeline",
-                    "download": "https://proteinpaint.stjude.org/ppdemo/hg38/GP/GDC.variation.datafile.processing.zip"
-                },
-                {
-                    "name": "Data Processing Docs",
-                    "link": "https://docs.google.com/document/d/1TC6pcAByqugzMWQ0C7mhHIHIkIxkqqDt1ATBBt_ehes/edit"
-                }
-            ]
-        }
-    ],
-    "citation_id": 1002
-}

package/cards/hic.json

@@ -1,79 +0,0 @@
-{
-    "ribbonMessage": "Versions 7, 8 and 9 Hi-C files are accepted.<br> See the new example for displaying a hic data across two chromosomes.",
-    "ppcalls": [
-        {
-            "label": "Hi-C",
-            "urlparam": "?block=1&genome=hg19&position=chr7:13749862-20841903&hictkfile=Test_HiC,MboI,proteinpaint_demo/hg19/hic/hic_demo.hic&&hictknorm=VC",
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": 1,
-                "noheader": 1,
-                "genome": "hg19",
-                "position": "chr7:13749862-20841903",
-                "nativetracks": "RefGene",
-                "tracks": [
-                    {
-                        "type": "hicstraw",
-                        "file": "proteinpaint_demo/hg19/hic/hic_demo.hic",
-                        "name": "Hi-C Demo",
-                        "percentile_max": 95,
-                        "mincutoff": 1,
-                        "pyramidup": 1,
-                        "enzyme": "MboI",
-                        "normalizationmethod": "VC"
-                    }
-                ]
-            },
-            "testSpec": {
-                "expected": {
-                    "image": 1
-                }
-            }
-        },
-        {
-            "label": "Two chromosome view",
-            "runargs": {
-                "parseurl": true,
-                "block": true,
-                "nobox": true,
-                "noheader": true,
-                "genome": "hg19",
-                "position": "chr8:128688997-128888997",
-                "nativetracks": "RefGene",
-                "width": 300,
-                "subpanels": [
-                    {
-                        "chr": "chr4",
-                        "start": 174408608,
-                        "stop": 175268609,
-                        "width": 600,
-                        "leftborder": "rgba(200,0,0,.1)"
-                    }
-                ],
-                "tracks": [
-                    {
-                        "type": "hicstraw",
-                        "file": "files/hg19/nbl-hic/hic_NB69.inter.hic",
-                        "name": "SJNBL046418_C1/NB69 Hi-C",
-                        "percentile_max": 95,
-                        "mincutoff": 1,
-                        "pyramidup": 1,
-                        "enzyme": "MboI"
-                    }
-                ]
-            },
-            "testSpec": {
-                "expected": {
-                    "image": 1
-                }
-            }
-        }
-    ],
-    "buttons": [
-        {
-            "name": "Documentation",
-            "link": "https://docs.google.com/document/d/1MQ0Z_AD5moDmaSx2tcn7DyVKGp49TS63pO0cceGL_Ns/edit"
-        }
-    ]
-}