##fileformat=VCFv4.1
##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/seq/dax/t2d_genes/v1/t2d_genes.padded.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=/seq/dax/t2d_genes/v1/t2d_genes.snps.unfiltered.vcf)] recal_file=(RodBinding name=recal_file source=/seq/dax/t2d_genes/v1/t2d_genes.snps.recal) tranches_file=/seq/dax/t2d_genes/v1/t2d_genes.snps.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=98.5 ignore_filter=null mode=SNP filter_mismatching_base_and_quals=false"
##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/seq/dax/t2d_genes/v1/t2d_genes.padded.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=/seq/dax/t2d_genes/v1/t2d_genes.snps.recalibrated.vcf), (RodBinding name=variant2 source=/seq/dax/t2d_genes/v1/t2d_genes.indels.filtered.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=true minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
##FILTER=<ID=Indel_FS,Description="FS>200.0">
##FILTER=<ID=Indel_InbreedingCoeff,Description="InbreedingCoeff<-0.8">
##FILTER=<ID=Indel_QD,Description="QD<2.0">
##FILTER=<ID=Indel_ReadPosRankSum,Description="ReadPosRankSum<-20.0">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP98.50to98.60,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -0.9687 <= x < -0.8298">
##FILTER=<ID=VQSRTrancheSNP98.60to98.80,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.2821 <= x < -0.9687">
##FILTER=<ID=VQSRTrancheSNP98.80to98.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.5011 <= x < -1.2821">
##FILTER=<ID=VQSRTrancheSNP98.90to99.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.7494 <= x < -1.5011">
##FILTER=<ID=VQSRTrancheSNP99.00to99.30,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -2.9782 <= x < -1.7494">
##FILTER=<ID=VQSRTrancheSNP99.30to99.50,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -4.7694 <= x < -2.9782">
##FILTER=<ID=VQSRTrancheSNP99.50to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -15.7985 <= x < -4.7694">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -4789.109">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -4789.109 <= x < -15.7985">
##FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele balance for each het genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DOS,Number=1,Type=Float,Description="Genotype Dosage">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=NALT,Number=1,Type=Integer,Description="Number of nonreference alleles for this individual">
##FORMAT=<ID=NALTT,Number=1,Type=Integer,Description="Number of nonreference alleles for this individual; thresholded">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HET_AB,Number=1,Type=Float,Description="Allele balance of heterozygotes, computed from HET_AD">
##INFO=<ID=HET_AD,Number=.,Type=Integer,Description="Sum, over heterozygotes, of allelic depths for the ref and alt alleles in the order listed">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SNPEFF_AMINO_ACID_CHANGE,Number=1,Type=String,Description="Old/New amino acid for the highest-impact effect resulting from the current variant (in HGVS style)">
##INFO=<ID=SNPEFF_CODON_CHANGE,Number=1,Type=String,Description="Old/New codon for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_EFFECT,Number=1,Type=String,Description="The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)">
##INFO=<ID=SNPEFF_EXON_ID,Number=1,Type=String,Description="Exon ID for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_FUNCTIONAL_CLASS,Number=1,Type=String,Description="Functional class of the highest-impact effect resulting from the current variant: [NONE, SILENT, MISSENSE, NONSENSE]">
##INFO=<ID=SNPEFF_GENE_BIOTYPE,Number=1,Type=String,Description="Gene biotype for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_GENE_NAME,Number=1,Type=String,Description="Gene name for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_IMPACT,Number=1,Type=String,Description="Impact of the highest-impact effect resulting from the current variant [MODIFIER, LOW, MODERATE, HIGH]">
##INFO=<ID=SNPEFF_TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID for the highest-impact effect resulting from the current variant">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##OriginalSnpEffCmd="SnpEff eff -v -onlyCoding true -c /seq/references/Homo_sapiens_assembly19/v1/snpEff/Homo_sapiens_assembly19.snpEff.config -i vcf -o vcf GRCh37.64 /seq/dax/t2d_genes/v1/t2d_genes.unannotated.vcf "
##OriginalSnpEffVersion="2.0.5 (build 2011-12-24), by Pablo Cingolani"
##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/seq/dax/t2d_genes/v1/t2d_genes.padded.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/seq/dax/t2d_genes/v1/t2d_genes.unfiltered.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false regenotype=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[INDEL] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_mismatching_base_and_quals=false"
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/seq/dax/t2d_genes/v1/t2d_genes.bam.list] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/seq/dax/t2d_genes/v1/scatter/temp_0001_of_2500/scattered.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=75 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_INDEPENDENT contamination_fraction_to_filter=0.0 contamination_percentage_per_sample_file=/seq/dax/t2d_genes/v1/t2d_genes.v1.contamination_levels.txt logRemovedReadsFromContaminationFiltering=null exactcallslog=null dbsnp=(RodBinding name=dbsnp source=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dbsnp.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=50 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/seq/dax/t2d_genes/v1/t2d_genes.unannotated.vcf) snpEffFile=(RodBinding name=snpEffFile source=/seq/dax/t2d_genes/v1/t2d_genes.snpeff.vcf) dbsnp=(RodBinding name= source=UNBOUND) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub annotation=[SnpEff] excludeAnnotation=[] group=[] expression=[] useAllAnnotations=false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 requireStrictAlleleMatch=false filter_mismatching_base_and_quals=false"
##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/seq/dax/t2d_genes/v1/t2d_genes.padded.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/seq/dax/t2d_genes/v1/t2d_genes.indels.unfiltered.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[FS>200.0, QD<2.0, ReadPosRankSum<-20.0, InbreedingCoeff<-0.8] filterName=[Indel_FS, Indel_QD, Indel_ReadPosRankSum, Indel_InbreedingCoeff] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false"
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##contig=<ID=GL000232.1,length=40652,assembly=b37>
##contig=<ID=GL000206.1,length=41001,assembly=b37>
##contig=<ID=GL000240.1,length=41933,assembly=b37>
##contig=<ID=GL000236.1,length=41934,assembly=b37>
##contig=<ID=GL000241.1,length=42152,assembly=b37>
##contig=<ID=GL000243.1,length=43341,assembly=b37>
##contig=<ID=GL000242.1,length=43523,assembly=b37>
##contig=<ID=GL000230.1,length=43691,assembly=b37>
##contig=<ID=GL000237.1,length=45867,assembly=b37>
##contig=<ID=GL000233.1,length=45941,assembly=b37>
##contig=<ID=GL000204.1,length=81310,assembly=b37>
##contig=<ID=GL000198.1,length=90085,assembly=b37>
##contig=<ID=GL000208.1,length=92689,assembly=b37>
##contig=<ID=GL000191.1,length=106433,assembly=b37>
##contig=<ID=GL000227.1,length=128374,assembly=b37>
##contig=<ID=GL000228.1,length=129120,assembly=b37>
##contig=<ID=GL000214.1,length=137718,assembly=b37>
##contig=<ID=GL000221.1,length=155397,assembly=b37>
##contig=<ID=GL000209.1,length=159169,assembly=b37>
##contig=<ID=GL000218.1,length=161147,assembly=b37>
##contig=<ID=GL000220.1,length=161802,assembly=b37>
##contig=<ID=GL000213.1,length=164239,assembly=b37>
##contig=<ID=GL000211.1,length=166566,assembly=b37>
##contig=<ID=GL000199.1,length=169874,assembly=b37>
##contig=<ID=GL000217.1,length=172149,assembly=b37>
##contig=<ID=GL000216.1,length=172294,assembly=b37>
##contig=<ID=GL000215.1,length=172545,assembly=b37>
##contig=<ID=GL000205.1,length=174588,assembly=b37>
##contig=<ID=GL000219.1,length=179198,assembly=b37>
##contig=<ID=GL000224.1,length=179693,assembly=b37>
##contig=<ID=GL000223.1,length=180455,assembly=b37>
##contig=<ID=GL000195.1,length=182896,assembly=b37>
##contig=<ID=GL000212.1,length=186858,assembly=b37>
##contig=<ID=GL000222.1,length=186861,assembly=b37>
##contig=<ID=GL000200.1,length=187035,assembly=b37>
##contig=<ID=GL000193.1,length=189789,assembly=b37>
##contig=<ID=GL000194.1,length=191469,assembly=b37>
##contig=<ID=GL000225.1,length=211173,assembly=b37>
##contig=<ID=GL000192.1,length=547496,assembly=b37>
##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta
##source=SelectVariants
##SnpEffVersion="SnpEff 3.3 (build 2013-04-15), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -lof -nextProt GRCh37.70 "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon  | GenotypeNum [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=Private,Number=1,Type=String,Description="If the variant is private (i.e. belongs only to one group or family) the group name is shown. Groups from file = '/lb/project/diabetes_analysis/t2d1/pheno.cohort_id.tfam'">
##SnpSiftVersion="1.9c (build 2013-04-11), by Pablo Cingolani"
##SnpSiftCmd="SnpSift gwasCat /home/pcingola/snpEff/db/gwasCatalog/gwascatalog.txt - "
##INFO=<ID=GWASCAT,Number=.,Type=String,Description="Trait related to this chromosomal position, according to GWAS catalog">
##SnpSiftCmd="SnpSift casecontrol -tfam /lb/project/diabetes_analysis/t2d1/pheno.cohort_id.tfam - "
##INFO=<ID=Cases,Number=3,Type=Integer,Description="Number of variants in cases: Hom, Het, Count">
##INFO=<ID=Controls,Number=3,Type=Integer,Description="Number of variants in controls: Hom, Het, Count">
##INFO=<ID=CC_DOM,Number=1,Type=Float,Description="p-value using dominant model (Fisher exact)">
##INFO=<ID=CC_REC,Number=1,Type=Float,Description="p-value using recessive model (Fisher exact)">
##INFO=<ID=CC_ALL,Number=1,Type=Float,Description="p-value using allele count model (Fisher exact)">
##INFO=<ID=CC_GENO,Number=1,Type=Float,Description="p-value using genotype / codominant model (CochranArmitage)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	17577975	var_22_17577975	T	C	1011.18	PASS	AC=1;AF=3.888e-05;AN=25718;BaseQRankSum=8.748;DP=1359761;Dels=0.00;FS=3.759;HET_AB=0.528;HET_AD=38,34;HaplotypeScore=0.0288;InbreedingCoeff=-0.0000;MQ=59.11;MQ0=0;MQRankSum=5.158;QD=14.04;ReadPosRankSum=-2.706;VQSLOD=6.11;culprit=InbreedingCoeff;set=snps;EFF=EXON(MODIFIER|||||IL17RA|retained_intron|CODING|ENST00000459971|2|1),INTRON(MODIFIER|||||IL17RA|processed_transcript|CODING|ENST00000477874|1|1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|10|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|11|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|1|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|3|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|5|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|6|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|9|1),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N54|866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),UPSTREAM(MODIFIER|||||AC006946.12|processed_pseudogene|NON_CODING|ENST00000429106||1);Private=HS;Cases=0,1,1;Controls=0,0,0;CC_GENO=1.604e-01;CC_ALL=5.037e-01;CC_DOM=5.037e-01;CC_REC=1.000e+00
22	17583047	var_22_17583047	A	G	1054.18	PASS	AC=1;AF=3.888e-05;AN=25718;BaseQRankSum=0.913;DP=1311188;Dels=0.00;FS=0.598;HET_AB=0.514;HET_AD=38,36;HaplotypeScore=0.0681;InbreedingCoeff=-0.0000;MQ=59.53;MQ0=0;MQRankSum=3.057;QD=14.25;ReadPosRankSum=-4.130;VQSLOD=6.74;culprit=InbreedingCoeff;set=snps;EFF=DOWNSTREAM(MODIFIER|||||IL17RA|processed_transcript|CODING|ENST00000477874||1),DOWNSTREAM(MODIFIER|||||IL17RA|retained_intron|CODING|ENST00000459971||1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|10|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|11|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|1|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|3|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|5|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|6|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|9|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N206S|866|IL17RA|protein_coding|CODING|ENST00000319363|7|1);Private=AW;Cases=0,0,0;Controls=0,1,1;CC_GENO=1.569e-01;CC_ALL=4.963e-01;CC_DOM=4.963e-01;CC_REC=1.000e+00
22	17583105	var_22_17583105	C	T	1049.18	PASS	AC=1;AF=3.888e-05;AN=25718;BaseQRankSum=-2.752;DP=1572738;Dels=0.00;FS=5.605;HET_AB=0.507;HET_AD=38,37;HaplotypeScore=0.0234;InbreedingCoeff=-0.0000;MQ=59.67;MQ0=0;MQRankSum=6.916;QD=13.99;ReadPosRankSum=-6.988;VQSLOD=7.82;culprit=FS;set=snps;EFF=DOWNSTREAM(MODIFIER|||||IL17RA|processed_transcript|CODING|ENST00000477874||1),DOWNSTREAM(MODIFIER|||||IL17RA|retained_intron|CODING|ENST00000459971||1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|10|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|11|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|1|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|3|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|5|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|6|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|9|1),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N225|866|IL17RA|protein_coding|CODING|ENST00000319363|7|1);Private=SS;Cases=0,1,1;Controls=0,0,0;CC_GENO=1.604e-01;CC_ALL=5.037e-01;CC_DOM=5.037e-01;CC_REC=1.000e+00
22	17584415	var_22_17584415	A	G	1231.6	PASS	AC=3;AF=1.166e-04;AN=25718;BaseQRankSum=5.581;DP=511516;Dels=0.00;FS=2.851;HET_AB=0.545;HET_AD=54,45;HaplotypeScore=0.1967;InbreedingCoeff=-0.0001;MQ=59.17;MQ0=2;MQRankSum=3.603;QD=12.44;ReadPosRankSum=0.280;VQSLOD=6.21;culprit=MQRankSum;set=snps;EFF=DOWNSTREAM(MODIFIER|||||IL17RA|processed_transcript|CODING|ENST00000477874||1),NEXT_PROT[beta_strand](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[disulfide_bond](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[disulfide_bond](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|10|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|11|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|1|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|3|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|5|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|6|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|9|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N265S|866|IL17RA|protein_coding|CODING|ENST00000319363|8|1);Private=EK;Cases=0,2,2;Controls=0,0,0;CC_GENO=8.015e-02;CC_ALL=2.537e-01;CC_DOM=2.536e-01;CC_REC=1.000e+00
22	17584416	var_22_17584416	C	T	500.18	PASS	AC=2;AF=7.777e-05;AN=25718;BaseQRankSum=-7.341;DP=509848;Dels=0.00;FS=2.628;HET_AB=0.627;HET_AD=42,25;HaplotypeScore=0.2143;InbreedingCoeff=-0.0001;MQ=59.17;MQ0=2;MQRankSum=5.608;QD=7.47;ReadPosRankSum=-2.143;VQSLOD=4.79;culprit=QD;set=snps;EFF=DOWNSTREAM(MODIFIER|||||IL17RA|processed_transcript|CODING|ENST00000477874||1),NEXT_PROT[beta_strand](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[disulfide_bond](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[disulfide_bond](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|10|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|11|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|1|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|3|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|5|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|6|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|8|1),NEXT_PROT[topological_domain:Extracellular](LOW||||866|IL17RA|protein_coding|CODING|ENST00000319363|9|1),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N265|866|IL17RA|protein_coding|CODING|ENST00000319363|8|1);Private=HS;Cases=0,1,1;Controls=0,0,0;CC_GENO=1.604e-01;CC_ALL=5.037e-01;CC_DOM=5.037e-01;CC_REC=1.000e+00
22	17688123	var_22_17688123	T	C	886.18	PASS	AC=1;AF=3.888e-05;AN=25718;BaseQRankSum=-3.371;DP=1366085;Dels=0.00;FS=1.091;HET_AB=0.560;HET_AD=42,33;HaplotypeScore=0.9143;InbreedingCoeff=-0.0000;MQ=59.43;MQ0=8;MQRankSum=5.189;QD=11.82;ReadPosRankSum=-0.459;VQSLOD=0.766;culprit=InbreedingCoeff;set=snps;EFF=NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||511|CECR1|protein_coding|CODING|ENST00000399837|3|1),NEXT_PROT[region_of_interest:PRB_domain](LOW||||511|CECR1|protein_coding|CODING|ENST00000399837|3|1),NEXT_PROT[region_of_interest:PRB_domain](LOW||||511|CECR1|protein_coding|CODING|ENST00000399837|4|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N127S|134|CECR1|protein_coding|CODING|ENST00000441548|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N127S|151|CECR1|protein_coding|CODING|ENST00000543038|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N127S|511|CECR1|protein_coding|CODING|ENST00000262607|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N127S|511|CECR1|protein_coding|CODING|ENST00000399837|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N127S|511|CECR1|protein_coding|CODING|ENST00000399839|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N85S|469|CECR1|protein_coding|CODING|ENST00000449907|3|1),UPSTREAM(MODIFIER|||||AC005399.1|pseudogene|NON_CODING|ENST00000600045||1);Private=ES;Cases=0,1,1;Controls=0,0,0;CC_GENO=1.604e-01;CC_ALL=5.037e-01;CC_DOM=5.037e-01;CC_REC=1.000e+00
22	18613691	var_22_18613691	A	G	813.18	PASS	AC=1;AF=3.888e-05;AN=25718;BaseQRankSum=-2.418;DP=1053381;Dels=0.00;FS=1.283;HET_AB=0.520;HET_AD=39,36;HaplotypeScore=0.0457;InbreedingCoeff=-0.0000;MQ=59.39;MQ0=1;MQRankSum=7.076;QD=10.84;ReadPosRankSum=-4.010;VQSLOD=6.80;culprit=InbreedingCoeff;set=snps;EFF=NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||383|TUBA8|protein_coding|CODING|ENST00000316027|5|1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||449|TUBA8|protein_coding|CODING|ENST00000330423|5|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N314D|383|TUBA8|protein_coding|CODING|ENST00000316027|5|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N380D|449|TUBA8|protein_coding|CODING|ENST00000330423|5|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N404D|466|TUBA8|protein_coding|CODING|ENST00000416740|4|1),UTR_3_PRIME(MODIFIER|||||PEX26|nonsense_mediated_decay|CODING|ENST00000474897|6|1);Private=EK;Cases=0,1,1;Controls=0,0,0;CC_GENO=1.604e-01;CC_ALL=5.037e-01;CC_DOM=5.037e-01;CC_REC=1.000e+00
22	19052463	var_22_19052463	T	C	517.18	PASS	AC=1;AF=3.888e-05;AN=25718;BaseQRankSum=3.044;DP=816781;Dels=0.00;FS=2.622;HET_AB=0.528;HET_AD=19,17;HaplotypeScore=0.0566;InbreedingCoeff=-0.0000;MQ=59.58;MQ0=0;MQRankSum=3.882;QD=14.37;ReadPosRankSum=-3.378;VQSLOD=6.51;culprit=InbreedingCoeff;set=snps;EFF=EXON(MODIFIER|||||DGCR2|processed_transcript|CODING|ENST00000473832|2|1),NEXT_PROT[disulfide_bond](LOW||||509|DGCR2|protein_coding|CODING|ENST00000537045|3|1),NEXT_PROT[disulfide_bond](LOW||||509|DGCR2|protein_coding|CODING|ENST00000537045|4|1),NEXT_PROT[disulfide_bond](LOW||||509|DGCR2|protein_coding|CODING|ENST00000537045|5|1),NEXT_PROT[disulfide_bond](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|4|1),NEXT_PROT[disulfide_bond](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|5|1),NEXT_PROT[disulfide_bond](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|6|1),NEXT_PROT[domain:C-type_lectin](LOW||||509|DGCR2|protein_coding|CODING|ENST00000537045|3|1),NEXT_PROT[domain:C-type_lectin](LOW||||509|DGCR2|protein_coding|CODING|ENST00000537045|4|1),NEXT_PROT[domain:C-type_lectin](LOW||||509|DGCR2|protein_coding|CODING|ENST00000537045|5|1),NEXT_PROT[domain:C-type_lectin](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|4|1),NEXT_PROT[domain:C-type_lectin](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|5|1),NEXT_PROT[domain:C-type_lectin](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|6|1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||509|DGCR2|protein_coding|CODING|ENST00000537045|3|1),NEXT_PROT[glycosylation_site:N-linked_(GlcNAc...)](HIGH||||550|DGCR2|protein_coding|CODING|ENST00000263196|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|1|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|2|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|3|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|4|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|5|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|6|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|7|1),NEXT_PROT[topological_domain:Extracellular](LOW||||550|DGCR2|protein_coding|CODING|ENST00000263196|8|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N108S|509|DGCR2|protein_coding|CODING|ENST00000537045|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N146S|269|DGCR2|protein_coding|CODING|ENST00000545799|4|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N149S|550|DGCR2|protein_coding|CODING|ENST00000263196|4|1),UTR_5_PRIME(MODIFIER|||||DGCR2|nonsense_mediated_decay|CODING|ENST00000389262|4|1);Private=SS;Cases=0,0,0;Controls=0,1,1;CC_GENO=1.569e-01;CC_ALL=4.963e-01;CC_DOM=4.963e-01;CC_REC=1.000e+00
