-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.CPTAC.masked_somatic_mutation_hg38_gdc_current`
(
  project_short_name STRING OPTIONS(description="Project name abbreviation; the program name appended with a project name abbreviation; eg. TCGA-OV, etc."),
  case_barcode STRING OPTIONS(description="Original case barcode, eg TCGA-DX-A8BN"),
  primary_site STRING OPTIONS(description="Anatomical site of the cancer under investigation or review"),
  Hugo_Symbol STRING OPTIONS(description="HUGO symbol for the gene (HUGO symbols are always in all caps). Unknown is used for regions that do not correspond to a gene"),
  Entrez_Gene_Id INT64 OPTIONS(description="Entrez gene ID (an integer). 0 is used for regions that do not correspond to a gene region or Ensembl ID"),
  Center STRING OPTIONS(description="One or more genome sequencing center reporting the variant"),
  NCBI_Build STRING OPTIONS(description="The reference genome used for the alignment (GRCh38)"),
  Chromosome STRING OPTIONS(description="Chromosome, possible values: chr1-22, and chrX"),
  Start_Position INT64 OPTIONS(description="Lowest numeric position of the reported variant on the genomic reference sequence. Mutation start coordinate"),
  End_Position INT64 OPTIONS(description="Highest numeric genomic position of the reported variant on the genomic reference sequence. Mutation end coordinate"),
  Strand STRING OPTIONS(description="Either + or - to denote whether read mapped to the sense (+) or anti-sense (-) strand"),
  Variant_Classification STRING OPTIONS(description="Translational effect of variant allele"),
  Variant_Type STRING OPTIONS(description="Type of mutation. TNP (tri-nucleotide polymorphism) is analogous to DNP (di-nucleotide polymorphism) but for three consecutive nucleotides. ONP (oligo-nucleotide polymorphism) is analogous to TNP but for consecutive runs of four or more (SNP, DNP, TNP, ONP, INS, DEL, or Consolidated)"),
  Reference_Allele STRING OPTIONS(description="The plus strand reference allele at this position. Includes the deleted sequence for a deletion or - for an insertion"),
  Tumor_Seq_Allele1 STRING OPTIONS(description="Primary data genotype for tumor sequencing (discovery) allele 1. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases"),
  Tumor_Seq_Allele2 STRING OPTIONS(description="Primary data genotype for tumor sequencing (discovery) allele 2. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases"),
  dbSNP_RS STRING OPTIONS(description="The rs-IDs from the   dbSNP database, novel if not found in any database used, or null if there is no dbSNP record, but it is found in other databases"),
  dbSNP_Val_Status STRING OPTIONS(description="The dbSNP validation status is reported as a semicolon-separated list of statuses. The union of all rs-IDs is taken when there are multiple"),
  Tumor_Aliquot_Barcode STRING OPTIONS(description="Aliquot barcode for the tumor sample"),
  Matched_Norm_Aliquot_Barcode STRING OPTIONS(description="Aliquot barcode for the matched normal sample"),
  Match_Norm_Seq_Allele1 STRING OPTIONS(description="Primary data genotype. Matched normal sequencing allele 1. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases (cleared in somatic MAF)"),
  Match_Norm_Seq_Allele2 STRING OPTIONS(description="Matched normal sequencing allele 2"),
  Tumor_Validation_Allele1 STRING OPTIONS(description="Secondary data from orthogonal technology. Tumor genotyping (validation) for allele 1. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases"),
  Tumor_Validation_Allele2 STRING OPTIONS(description="Secondary data from orthogonal technology. Tumor genotyping (validation) for allele 2"),
  Match_Norm_Validation_Allele1 STRING OPTIONS(description="Secondary data from orthogonal technology. Matched normal genotyping (validation) for allele 1. A - symbol for a deletion represents a variant. A - symbol for an insertion represents wild-type allele. Novel inserted sequence for insertion does not include flanking reference bases (cleared in somatic MAF)"),
  Match_Norm_Validation_Allele2 STRING OPTIONS(description="Secondary data from orthogonal technology. Matched normal genotyping (validation) for allele 2 (cleared in somatic MAF)"),
  Verification_Status STRING OPTIONS(description="Second pass results from independent attempt using same methods as primary data source. Generally reserved for 3730 Sanger Sequencing"),
  Validation_Status STRING OPTIONS(description="Second pass results from orthogonal technology"),
  Mutation_Status STRING OPTIONS(description="An assessment of the mutation as somatic, germline, LOH, post transcriptional modification, unknown, or none. The values allowed in this field are constrained by the value in the Validation_Status field"),
  Sequencing_Phase STRING OPTIONS(description="TCGA sequencing phase (if applicable). Phase should change under any circumstance that the targets under consideration change"),
  Sequence_Source STRING OPTIONS(description="Molecular assay type used to produce the analytes used for sequencing. Allowed values are a subset of the SRA 1.5 library_strategy field values. This subset matches those used at CGHub"),
  Validation_Method STRING OPTIONS(description="The assay platforms used for the validation call"),
  Score STRING OPTIONS(description="Not in use"),
  BAM_File STRING OPTIONS(description="Not in use"),
  Sequencer STRING OPTIONS(description="Instrument used to produce primary sequence data"),
  Tumor_Aliquot_UUID STRING OPTIONS(description="Unique GDC identifier for tumor aliquot (10189 unique)"),
  Matched_Norm_Aliquot_UUID STRING OPTIONS(description="Unique GDC identifier for normal aliquot (10189 unique)"),
  HGVSc STRING OPTIONS(description="The coding sequence of the variant in HGVS recommended format"),
  HGVSp STRING OPTIONS(description="The protein sequence of the variant in HGVS recommended format. p.= signifies no change in the protein"),
  HGVSp_Short STRING OPTIONS(description="Same as the HGVSp column, but using 1-letter amino-acid codes"),
  Transcript_ID STRING OPTIONS(description="Ensembl ID of the transcript affected by the variant"),
  Exon_Number STRING OPTIONS(description="The exon number (out of total number)"),
  t_depth INT64 OPTIONS(description="Read depth across this locus in tumor BAM"),
  t_ref_count INT64 OPTIONS(description="Read depth supporting the reference allele in tumor BAM"),
  t_alt_count INT64 OPTIONS(description="Read depth supporting the variant allele in tumor BAM"),
  n_depth INT64 OPTIONS(description="Read depth across this locus in normal BAM"),
  n_ref_count STRING OPTIONS(description="Read depth supporting the reference allele in normal BAM (cleared in somatic MAF)"),
  n_alt_count STRING OPTIONS(description="Read depth supporting the variant allele in normal BAM (cleared in somatic MAF)"),
  all_effects STRING OPTIONS(description="A semicolon delimited list of all possible variant effects, sorted by priority ([Symbol,Consequence,HGVSp_Short,Transcript_ID,RefSeq,HGVSc,Impact,Canonical,Sift,PolyPhen,Strand])"),
  Allele STRING OPTIONS(description="The variant allele used to calculate the consequence"),
  Gene STRING OPTIONS(description="The gene symbol. In this table, gene symbol is gene name e.g. ACADVL"),
  Feature STRING OPTIONS(description="Stable Ensembl ID of feature (transcript, regulatory, motif)"),
  Feature_type STRING OPTIONS(description="Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature (or blank)"),
  One_Consequence STRING OPTIONS(description="The single consequence of the canonical transcript in  sequence ontology terms, eg missense_variant"),
  Consequence STRING OPTIONS(description="Consequence type of this variant; sequence ontology terms"),
  cDNA_position STRING OPTIONS(description="Relative position of base pair in the cDNA sequence as a fraction. A - symbol is displayed as the numerator if the variant does not appear in cDNA"),
  CDS_position STRING OPTIONS(description="Relative position of base pair in coding sequence. A - symbol is displayed as the numerator if the variant does not appear in coding sequence"),
  Protein_position STRING OPTIONS(description="Relative position of affected amino acid in protein. A - symbol is displayed as the numerator if the variant does not appear in coding sequence"),
  Amino_acids STRING OPTIONS(description="Amino acid substitution caused by the mutation. Only given if the variation affects the protein-coding sequence"),
  Codons STRING OPTIONS(description="The alternative codons with the variant base in upper case"),
  Existing_variation STRING OPTIONS(description="Known identifier of existing variation"),
  DISTANCE STRING OPTIONS(description="Shortest distance from the variant to transcript"),
  TRANSCRIPT_STRAND STRING OPTIONS(description="The DNA strand (1 or -1) on which the transcript/feature lies"),
  SYMBOL STRING OPTIONS(description="Eg TP53, LRP1B, etc (same as Hugo_Symbol field except blank instead of Unknown"),
  SYMBOL_SOURCE STRING OPTIONS(description="The source of the gene symbol, usually HGNC, rarely blank, other sources include Uniprot_gn, EntrezGene, etc"),
  HGNC_ID STRING OPTIONS(description="Gene identifier from the HUGO Gene Nomenclature Committee if applicable"),
  BIOTYPE STRING OPTIONS(description="Biotype of transcript"),
  CANONICAL STRING OPTIONS(description="A flag (YES) indicating that the VEP-based canonical transcript, the longest translation, was used for this gene. If not, the value is null"),
  CCDS STRING OPTIONS(description="The  CCDS identifier for this transcript, where applicable"),
  ENSP STRING OPTIONS(description="The Ensembl protein identifier of the affected transcript"),
  SWISSPROT STRING OPTIONS(description="UniProtKB/Swiss-Prot accession"),
  TREMBL STRING OPTIONS(description="UniProtKB/TrEMBL identifier of protein product"),
  UNIPARC STRING OPTIONS(description="UniParc identifier of protein product"),
  UNIPROT_ISOFORM STRING OPTIONS(description="Direct mappings to UniProtKB isoforms"),
  RefSeq STRING OPTIONS(description="RefSeq identifier for this transcript"),
  MANE STRING OPTIONS(description="MANE (Matched Annotation by NCBI and EMBL-EBI) Transcript"),
  APPRIS STRING OPTIONS(description="Annotates alternatively spliced transcripts as primary or alternate based on a range of computational methods"),
  FLAGS STRING OPTIONS(description="Transcript quality flags"),
  SIFT STRING OPTIONS(description="The SIFT prediction and/or score, with both given as prediction (score)"),
  PolyPhen STRING OPTIONS(description="The PolyPhen prediction and/or score"),
  EXON STRING OPTIONS(description="The exon number (out of total number)"),
  INTRON STRING OPTIONS(description="The intron number (out of total number)"),
  DOMAINS STRING OPTIONS(description="The source and identifier of any overlapping protein domains"),
  ThousG_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in 1000 Genomes"),
  ThousG_AFR_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in 1000 Genomes combined African population"),
  ThousG_AMR_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in 1000 Genomes combined American population"),
  ThousG_EAS_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in 1000 Genomes combined East Asian population"),
  ThousG_EUR_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in 1000 Genomes combined European population"),
  ThousG_SAS_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in 1000 Genomes combined South Asian population"),
  ESP_AA_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in NHLBI-ESP African American population"),
  ESP_EA_AF FLOAT64 OPTIONS(description="Non-reference allele and frequency of existing variant in NHLBI-ESP European American population"),
  gnomAD_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes combined population"),
  gnomAD_AFR_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes African/American population"),
  gnomAD_AMR_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes American population"),
  gnomAD_ASJ_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes Ashkenazi Jewish population"),
  gnomAD_EAS_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes East Asian population"),
  gnomAD_FIN_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes Finnish population"),
  gnomAD_NFE_AF FLOAT64 OPTIONS(description="tFrequency of existing variant in gnomAD exomes Non-Finnish European population"),
  gnomAD_OTH_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes other combined population"),
  gnomAD_SAS_AF FLOAT64 OPTIONS(description="Frequency of existing variant in gnomAD exomes South Asian population"),
  MAX_AF FLOAT64 OPTIONS(description="Maximum observed allele frequency in 1000 Genomes, ESP and ExAC/gnomAD"),
  MAX_AF_POPS STRING OPTIONS(description="Populations in which maximum allele frequency was observed"),
  gnomAD_non_cancer_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes combined non-cancer population"),
  gnomAD_non_cancer_AFR_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer African/American population"),
  gnomAD_non_cancer_AMI_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Amish population"),
  gnomAD_non_cancer_AMR_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Latino population"),
  gnomAD_non_cancer_ASJ_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Ashkenazi Jewish population"),
  gnomAD_non_cancer_EAS_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer East Asian population"),
  gnomAD_non_cancer_FIN_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Finnish population"),
  gnomAD_non_cancer_MID_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Middle Eastern population"),
  gnomAD_non_cancer_NFE_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Non-Finnish European population"),
  gnomAD_non_cancer_OTH_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer Other population"),
  gnomAD_non_cancer_SAS_AF FLOAT64 OPTIONS(description="Frequency of exisiting variant in gnomAD genomes non-cancer South Asian population"),
  gnomAD_non_cancer_MAX_AF_adj FLOAT64 OPTIONS(description="Maximum observed allele frequency in non-cancer gnomAD genomes populations after removing subpopulations with less than 2 allele counts"),
  gnomAD_non_cancer_MAX_AF_POPS_adj STRING OPTIONS(description="Non-cancer gnomAD genomes populations in which the maximum allele frequency was observed after removing those with less than 2 allele counts"),
  CLIN_SIG STRING OPTIONS(description="Clinical significance of variant from dbSNP"),
  SOMATIC STRING OPTIONS(description="Somatic status of each ID reported under Existing_variation (0, 1, or null)"),
  PUBMED STRING OPTIONS(description="Pubmed ID(s) of publications that cite existing variant"),
  TRANSCRIPTION_FACTORS STRING OPTIONS(description="List of transcription factors which bind to the transcription factor binding profile"),
  MOTIF_NAME STRING OPTIONS(description="The source and identifier of a transcription factor binding profile aligned at this position"),
  MOTIF_POS STRING OPTIONS(description="The relative position of the variation in the aligned TFBP"),
  HIGH_INF_POS STRING OPTIONS(description="A flag indicating if the variant falls in a high information position of a transcription factor binding profile (TFBP) (Y, N, or null)"),
  MOTIF_SCORE_CHANGE STRING OPTIONS(description="The difference in motif score of the reference and variant sequences for the TFBP"),
  miRNA STRING OPTIONS(description="SO terms of overlapped miRNA secondary structure feature(s)"),
  IMPACT STRING OPTIONS(description="The impact modifier for the consequence type"),
  PICK STRING OPTIONS(description="Indicates if this block of consequence data was picked by VEP's   pick feature (1 or null)"),
  VARIANT_CLASS STRING OPTIONS(description="Sequence Ontology variant class"),
  TSL STRING OPTIONS(description="Transcript support level, which is based on independent RNA analyses"),
  HGVS_OFFSET STRING OPTIONS(description="Indicates by how many bases the HGVS notations for this variant have been shifted"),
  PHENO STRING OPTIONS(description="Indicates if existing variant is associated with a phenotype, disease or trait (0, 1, or null)"),
  GENE_PHENO STRING OPTIONS(description="Indicates if gene that the variant maps to is associated with a phenotype, disease or trait (0, 1, or null)"),
  CONTEXT STRING OPTIONS(description="The reference allele per VCF specs, and its five flanking base pairs"),
  tumor_submitter_uuid STRING OPTIONS(description="Unique GDC identifier for the tumor file submitter"),
  normal_submitter_uuid STRING OPTIONS(description="Unique GDC identifier for the normal file submitter"),
  case_id STRING OPTIONS(description="Unique GDC identifier for the underlying case"),
  GDC_FILTER STRING OPTIONS(description="GDC filters applied universally across all MAFs"),
  COSMIC STRING OPTIONS(description="Overlapping COSMIC variants"),
  hotspot BOOL OPTIONS(description="A flag indicating if the variant is a known hotspot (Y, N, or null)"),
  RNA_Support STRING OPTIONS(description="Indicates if the variant is found and alleles (Match), simply (Overlap), or is not supported (No) by tumor RNA-Seq. If it has not been checked against RNA-Seq data, the value will be 'Unknown'."),
  RNA_depth STRING OPTIONS(description="Read depth at this locus if the variant is supported by tumor RNA-seq data."),
  RNA_ref_count STRING OPTIONS(description="Read depth supporting the reference allele at this locus if the variant is supported by tumor RNA-seq data."),
  RNA_alt_count STRING OPTIONS(description="Read depth supporting the variant allele at this locus if the variant is supported by tumor RNA-seq data."),
  callers STRING OPTIONS(description="|-delimited list of mutation caller(s) that agreed on this particular call, always in alphabetical order: muse, mutect, somaticsniper, varscan"),
  file_gdc_id STRING OPTIONS(description="|-delimited list of unique GDC identifiers for underlying MAF file"),
  muse STRING OPTIONS(description="Muse caller identified the variant at this position"),
  mutect2 STRING OPTIONS(description="Mutect2 caller identified the variant at this position"),
  pindel STRING OPTIONS(description="pindel caller identified the variant at this position"),
  varscan2 STRING OPTIONS(description="Varscan2 caller identified the variant at this position"),
  sample_barcode_tumor STRING OPTIONS(description="TCGA sample barcode for the tumor, eg TCGA-12-1089-01A. One sample may have multiple sets of CN segmentations corresponding to multiple aliquots; use GROUP BY appropriately in queries"),
  sample_barcode_normal STRING OPTIONS(description="TCGA sample barcode for the normal control, eg TCGA-12-1089-01A. One sample may have multiple sets of CN segmentations corresponding to multiple aliquots; use GROUP BY appropriately in queries"),
  aliquot_barcode_tumor STRING OPTIONS(description="TCGA aliquot barcode for the tumor, eg TCGA-12-1089-01A-01D-0517-01"),
  aliquot_barcode_normal STRING OPTIONS(description="TCGA aliquot barcode for the normal control, eg TCGA-12-1089-01A-01D-0517-01]")
)
OPTIONS(
  friendly_name="CPTAC HG38 SOMATIC MUTATION",
  description="Data was extracted from r40 of the active GDC archive in JULY, 2024 for CPTAC somatic mutation data. More details:https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#400 Note: Some files may contain no mutation data after GDC filtering processes. They are not included in this table. Please reference the GDC documentation for more information on somatic mutation filtering processes: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/.",
  labels=[("access", "open"), ("program_0", "cptac2"), ("program_1", "cptac3"), ("data_type", "somatic_mutation"), ("reference_genome_0", "hg38"), ("source", "gdc"), ("category", "processed_-omics_data"), ("status", "current"), ("version", "r40")]
);

INSERT INTO `isb-cgc-bq.CPTAC.masked_somatic_mutation_hg38_gdc_current` (project_short_name, case_barcode, primary_site, Hugo_Symbol, Entrez_Gene_Id, Center, NCBI_Build, Chromosome, Start_Position, End_Position, Strand, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2, dbSNP_RS, dbSNP_Val_Status, Tumor_Aliquot_Barcode, Matched_Norm_Aliquot_Barcode, Match_Norm_Seq_Allele1, Match_Norm_Seq_Allele2, Tumor_Validation_Allele1, Tumor_Validation_Allele2, Match_Norm_Validation_Allele1, Match_Norm_Validation_Allele2, Verification_Status, Validation_Status, Mutation_Status, Sequencing_Phase, Sequence_Source, Validation_Method, Score, BAM_File, Sequencer, Tumor_Aliquot_UUID, Matched_Norm_Aliquot_UUID, HGVSc, HGVSp, HGVSp_Short, Transcript_ID, Exon_Number, t_depth, t_ref_count, t_alt_count, n_depth, n_ref_count, n_alt_count, all_effects, Allele, Gene, Feature, Feature_type, One_Consequence, Consequence, cDNA_position, CDS_position, Protein_position, Amino_acids, Codons, Existing_variation, DISTANCE, TRANSCRIPT_STRAND, SYMBOL, SYMBOL_SOURCE, HGNC_ID, BIOTYPE, CANONICAL, CCDS, ENSP, SWISSPROT, TREMBL, UNIPARC, UNIPROT_ISOFORM, RefSeq, MANE, APPRIS, FLAGS, SIFT, PolyPhen, EXON, INTRON, DOMAINS, ThousG_AF, ThousG_AFR_AF, ThousG_AMR_AF, ThousG_EAS_AF, ThousG_EUR_AF, ThousG_SAS_AF, ESP_AA_AF, ESP_EA_AF, gnomAD_AF, gnomAD_AFR_AF, gnomAD_AMR_AF, gnomAD_ASJ_AF, gnomAD_EAS_AF, gnomAD_FIN_AF, gnomAD_NFE_AF, gnomAD_OTH_AF, gnomAD_SAS_AF, MAX_AF, MAX_AF_POPS, gnomAD_non_cancer_AF, gnomAD_non_cancer_AFR_AF, gnomAD_non_cancer_AMI_AF, gnomAD_non_cancer_AMR_AF, gnomAD_non_cancer_ASJ_AF, gnomAD_non_cancer_EAS_AF, gnomAD_non_cancer_FIN_AF, gnomAD_non_cancer_MID_AF, gnomAD_non_cancer_NFE_AF, gnomAD_non_cancer_OTH_AF, gnomAD_non_cancer_SAS_AF, gnomAD_non_cancer_MAX_AF_adj, gnomAD_non_cancer_MAX_AF_POPS_adj, CLIN_SIG, SOMATIC, PUBMED, TRANSCRIPTION_FACTORS, MOTIF_NAME, MOTIF_POS, HIGH_INF_POS, MOTIF_SCORE_CHANGE, miRNA, IMPACT, PICK, VARIANT_CLASS, TSL, HGVS_OFFSET, PHENO, GENE_PHENO, CONTEXT, tumor_submitter_uuid, normal_submitter_uuid, case_id, GDC_FILTER, COSMIC, hotspot, RNA_Support, RNA_depth, RNA_ref_count, RNA_alt_count, callers, file_gdc_id, muse, mutect2, pindel, varscan2, sample_barcode_tumor, sample_barcode_normal, aliquot_barcode_tumor, aliquot_barcode_normal) VALUES ('CPTAC-3', 'C464694', 'Brain', 'ZIM3', 114026, 'BI', 'GRCh38', 'chr19', 57135869, 57135869, '+', 'Silent', 'SNP', 'G', 'G', 'A', 'rs758265716', NULL, '7316UP-1220', '7316UP-1220-1105273', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'Somatic', NULL, NULL, NULL, NULL, NULL, 'Illumina HiSeq X Ten', '737a37b7-31a5-4187-a4fa-5e7171bb6569', '79ab7960-710a-4fb4-b7fb-d8d374ac0273', 'c.468C>T', 'p.Gly156=', 'p.G156=', 'ENST00000269834', '5/5', 110, 79, 31, 209, NULL, NULL, 'ZIM3,synonymous_variant,p.G156=,ENST00000269834,NM_052882.1,c.468C>T,LOW,YES,,,-1;USP29,downstream_gene_variant,,ENST00000254181,NM_020903.2,,MODIFIER,YES,,,1;USP29,downstream_gene_variant,,ENST00000598197,,,MODIFIER,,,,1', 'A', 'ENSG00000141946', 'ENST00000269834', 'Transcript', 'synonymous_variant', 'synonymous_variant', '854/2627', '468/1419', '156/472', 'G', 'ggC/ggT', 'rs758265716', NULL, '-1', 'ZIM3', 'HGNC', 'HGNC:16366', 'protein_coding', 'YES', 'CCDS33125.1', 'ENSP00000269834', 'Q96PE6.160', NULL, 'UPI000013C3E0', NULL, 'NM_052882.1', 'NM_052882.1', 'P1', NULL, NULL, NULL, '5/5', NULL, 'Gene3D:3.30.160.60;PANTHER:PTHR24377;PANTHER:PTHR24377:SF30', nan, nan, nan, nan, nan, nan, nan, nan, 1.989e-05, 0.0, 5.785e-05, 9.921e-05, 0.0, 0.0, 1.758e-05, 0.0, 0.0, 9.921e-05, 'gnomAD_ASJ', 2.707130079215858e-05, 4.870209886576049e-05, 0.0, 0.0001329079968854785, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0001329079968854785, 'amr', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'LOW', '1', 'SNV', '1', NULL, NULL, NULL, 'TTATTGCCAAC', '0b11c59a-e8b5-40b6-a8b5-c2cf096326ea', '52bd0e81-8114-4931-94fb-768b6cf49174', 'df5cca46-9ea2-4105-b298-901a9329614f', NULL, NULL, False, 'Unknown', NULL, NULL, NULL, 'muse;mutect2;varscan2', '7b670b4c-a4f6-40a7-a573-b91a66b3d189', 'Yes', 'Yes', 'No', 'Yes', 'SM-JU334', '1105273', '7316UP-1220', '7316UP-1220-1105273'), ('CPTAC-3', 'C464694', 'Brain', 'LMO2', 4005, 'BI', 'GRCh38', 'chr11', 33869726, 33869726, '+', '5''UTR', 'SNP', 'G', 'G', 'A', 'rs1248384002', NULL, '7316UP-1220', '7316UP-1220-1105273', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'Somatic', NULL, NULL, NULL, NULL, NULL, 'Illumina HiSeq X Ten', '737a37b7-31a5-4187-a4fa-5e7171bb6569', '79ab7960-710a-4fb4-b7fb-d8d374ac0273', 'c.-340C>T', NULL, NULL, 'ENST00000395833', '1/3', 48, 44, 4, 138, NULL, NULL, 'LMO2,5_prime_UTR_variant,,ENST00000257818,NM_005574.4,c.-10C>T,MODIFIER,YES,,,-1;LMO2,5_prime_UTR_variant,,ENST00000395833,NM_001142315.2&NM_001142316.2,c.-340C>T,MODIFIER,,,,-1;LMO2,intron_variant,,ENST00000493667,,n.348+99C>T,MODIFIER,,,,-1;LMO2,non_coding_transcript_exon_variant,,ENST00000465614,,n.435C>T,MODIFIER,,,,-1;LMO2,upstream_gene_variant,,ENST00000411482,,,MODIFIER,,,,-1;LMO2,upstream_gene_variant,,ENST00000464025,,,MODIFIER,,,,-1', 'A', 'ENSG00000135363', 'ENST00000395833', 'Transcript', '5_prime_UTR_variant', '5_prime_UTR_variant', '91/1687', NULL, NULL, NULL, NULL, 'rs1248384002', NULL, '-1', 'LMO2', 'HGNC', 'HGNC:6642', 'protein_coding', NULL, 'CCDS44567.1', 'ENSP00000379175', 'P25791.191', NULL, 'UPI0000000F36', 'P25791-1', 'NM_001142315.2;NM_001142316.2', NULL, 'P1', NULL, NULL, NULL, '1/3', NULL, NULL, nan, nan, nan, nan, nan, nan, nan, nan, 5.613e-05, 0.0, 0.0001623, 0.0, 0.0, 0.0, 5.237e-05, 0.0, 7.124e-05, 0.0001623, 'gnomAD_AMR', nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'MODIFIER', NULL, 'SNV', '1', NULL, NULL, '1', 'GTCCCGCCGCC', '0b11c59a-e8b5-40b6-a8b5-c2cf096326ea', '52bd0e81-8114-4931-94fb-768b6cf49174', 'df5cca46-9ea2-4105-b298-901a9329614f', NULL, NULL, False, 'Unknown', NULL, NULL, NULL, 'muse;mutect2', '7b670b4c-a4f6-40a7-a573-b91a66b3d189', 'Yes', 'Yes', 'No', 'No', 'SM-JU334', '1105273', '7316UP-1220', '7316UP-1220-1105273'), ('CPTAC-3', 'C464694', 'Brain', 'AC098591.2', 0, 'BI', 'GRCh38', 'chr4', 40043480, 40043480, '+', 'RNA', 'SNP', 'G', 'G', 'A', 'rs761360875', NULL, '7316UP-1220', '7316UP-1220-1105273', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'Somatic', NULL, NULL, NULL, NULL, NULL, 'Illumina HiSeq X Ten', '737a37b7-31a5-4187-a4fa-5e7171bb6569', '79ab7960-710a-4fb4-b7fb-d8d374ac0273', 'n.1050C>T', NULL, NULL, 'ENST00000381811', '3/3', 271, 221, 48, 502, NULL, NULL, 'AC098591.2,non_coding_transcript_exon_variant,,ENST00000381811,,n.1050C>T,MODIFIER,YES,,,-1;AC098591.2,non_coding_transcript_exon_variant,,ENST00000507914,,n.656C>T,MODIFIER,,,,-1', 'A', 'ENSG00000205794', 'ENST00000381811', 'Transcript', 'non_coding_transcript_exon_variant', 'non_coding_transcript_exon_variant', '1050/1613', NULL, NULL, NULL, NULL, 'rs761360875', NULL, '-1', 'AC098591.2', 'Clone_based_ensembl_gene', NULL, 'processed_transcript', 'YES', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, '3/3', NULL, NULL, nan, nan, nan, nan, nan, nan, nan, nan, 4.662e-06, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 3.666e-05, 3.666e-05, 'gnomAD_SAS', nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'MODIFIER', '1', 'SNV', '2', NULL, NULL, NULL, 'GTGGCGTGCAG', '0b11c59a-e8b5-40b6-a8b5-c2cf096326ea', '52bd0e81-8114-4931-94fb-768b6cf49174', 'df5cca46-9ea2-4105-b298-901a9329614f', NULL, NULL, False, 'Unknown', NULL, NULL, NULL, 'muse;mutect2;varscan2', '7b670b4c-a4f6-40a7-a573-b91a66b3d189', 'Yes', 'Yes', 'No', 'Yes', 'SM-JU334', '1105273', '7316UP-1220', '7316UP-1220-1105273'), ('CPTAC-3', 'C464694', 'Brain', 'COL1A2', 1278, 'BI', 'GRCh38', 'chr7', 94427228, 94427228, '+', 'Missense_Mutation', 'SNP', 'G', 'G', 'A', 'rs530026906', NULL, '7316UP-1220', '7316UP-1220-1105273', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'Somatic', NULL, NULL, NULL, NULL, NULL, 'Illumina HiSeq X Ten', '737a37b7-31a5-4187-a4fa-5e7171bb6569', '79ab7960-710a-4fb4-b7fb-d8d374ac0273', 'c.3200G>A', 'p.Arg1067His', 'p.R1067H', 'ENST00000297268', '48/52', 669, 529, 138, 650, NULL, NULL, 'COL1A2,missense_variant,p.R1067H,ENST00000297268,NM_000089.4,c.3200G>A,MODERATE,YES,tolerated(0.56),benign(0.011),1;COL1A2,missense_variant,p.R1065H,ENST00000620463,,c.3194G>A,MODERATE,,tolerated(0.56),benign(0.006),1;COL1A2,non_coding_transcript_exon_variant,,ENST00000481570,,n.3650G>A,MODIFIER,,,,1;COL1A2,non_coding_transcript_exon_variant,,ENST00000492110,,n.320G>A,MODIFIER,,,,1;COL1A2,non_coding_transcript_exon_variant,,ENST00000488121,,n.116G>A,MODIFIER,,,,1;COL1A2,upstream_gene_variant,,ENST00000464916,,,MODIFIER,,,,1;COL1A2,downstream_gene_variant,,ENST00000469732,,,MODIFIER,,,,1;COL1A2,downstream_gene_variant,,ENST00000478215,,,MODIFIER,,,,1;COL1A2,downstream_gene_variant,,ENST00000497316,,,MODIFIER,,,,1', 'A', 'ENSG00000164692', 'ENST00000297268', 'Transcript', 'missense_variant', 'missense_variant', '3337/5072', '3200/4101', '1067/1366', 'R/H', 'cGc/cAc', 'rs530026906;COSV51955410', NULL, '1', 'COL1A2', 'HGNC', 'HGNC:2198', 'protein_coding', 'YES', 'CCDS34682.1', 'ENSP00000297268', 'P08123.227', 'A0A0S2Z3H5.25', 'UPI00003B0CFC', NULL, 'NM_000089.4', 'NM_000089.4', 'P1', NULL, 'tolerated(0.56)', 'benign(0.011)', '48/52', NULL, 'Pfam:PF01391;PANTHER:PTHR24023;PANTHER:PTHR24023:SF568', nan, nan, nan, nan, nan, nan, nan, nan, 0.0001117, 0.0, 2.895e-05, 0.0, 0.000872, 0.0, 8.83e-06, 0.0001632, 0.0002947, 0.000872, 'gnomAD_EAS', 2.7083000532002188e-05, 4.8716301535023376e-05, 0.0, 0.0, 0.0, 0.0004068349953740835, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0004068349953740835, 'eas', 'uncertain_significance', '0;1', NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'MODERATE', '1', 'SNV', '1', NULL, '1;1', '1', 'TGGTCGCACTG', '0b11c59a-e8b5-40b6-a8b5-c2cf096326ea', '52bd0e81-8114-4931-94fb-768b6cf49174', 'df5cca46-9ea2-4105-b298-901a9329614f', NULL, 'COSM5008000', False, 'Unknown', NULL, NULL, NULL, 'muse;mutect2;varscan2', '7b670b4c-a4f6-40a7-a573-b91a66b3d189', 'Yes', 'Yes', 'No', 'Yes', 'SM-JU334', '1105273', '7316UP-1220', '7316UP-1220-1105273'), ('CPTAC-3', 'C464694', 'Brain', 'DYNC2I1', 55112, 'BI', 'GRCh38', 'chr7', 158905146, 158905146, '+', 'Intron', 'SNP', 'T', 'T', 'C', 'rs934500344', NULL, '7316UP-1220', '7316UP-1220-1105273', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'Somatic', NULL, NULL, NULL, NULL, NULL, 'Illumina HiSeq X Ten', '737a37b7-31a5-4187-a4fa-5e7171bb6569', '79ab7960-710a-4fb4-b7fb-d8d374ac0273', 'c.1358-843T>C', NULL, NULL, 'ENST00000407559', NULL, 45, 39, 6, 60, NULL, NULL, 'DYNC2I1,intron_variant,,ENST00000407559,NM_001350914.1&NM_001350918.2&NM_001350917.2&NM_018051.5&NM_001350916.2&NM_001350915.2,c.1358-843T>C,MODIFIER,YES,,,1;DYNC2I1,non_coding_transcript_exon_variant,,ENST00000467220,,n.3019T>C,MODIFIER,,,,1;DYNC2I1,intron_variant,,ENST00000444851,,c.689-843T>C,MODIFIER,,,,1', 'C', 'ENSG00000126870', 'ENST00000407559', 'Transcript', 'intron_variant', 'intron_variant', NULL, NULL, NULL, NULL, NULL, 'rs934500344', NULL, '1', 'DYNC2I1', 'HGNC', 'HGNC:21862', 'protein_coding', 'YES', 'CCDS47757.1', 'ENSP00000384290', 'Q8WVS4.151', 'A0A140VK66.23', 'UPI000020E761', NULL, 'NM_001350914.1;NM_001350918.2;NM_001350917.2;NM_018051.5;NM_001350916.2;NM_001350915.2', 'NM_018051.5', 'P1', NULL, NULL, NULL, NULL, '10/24', NULL, nan, nan, nan, nan, nan, nan, nan, nan, 7.36e-05, 0.0001838, 0.0001195, 0.0, 0.0, 0.0, 5.135e-05, 0.0, 0.0001426, 0.0001838, 'gnomAD_AFR', 6.287900032475591e-05, 0.0, 0.0, 0.0001359799935016781, 0.0003065599885303527, 0.0, 0.0, 0.0, 7.899390038801357e-05, 0.0, 0.0002197800058638677, 0.0001359799935016781, 'amr', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 'MODIFIER', '1', 'SNV', '1', NULL, NULL, '1', 'TTTTTTTTTTT', '0b11c59a-e8b5-40b6-a8b5-c2cf096326ea', '52bd0e81-8114-4931-94fb-768b6cf49174', 'df5cca46-9ea2-4105-b298-901a9329614f', NULL, NULL, False, 'Unknown', NULL, NULL, NULL, 'muse;varscan2', '7b670b4c-a4f6-40a7-a573-b91a66b3d189', 'Yes', 'No', 'No', 'Yes', 'SM-JU334', '1105273', '7316UP-1220', '7316UP-1220-1105273');