# HG changeset patch
# User jjohnson
# Date 1529013099 14400
# Node ID 9f4ea174ce3d1ce2badbfbcf413ba3b4a9f1f91a

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty

diff -r 000000000000 -r 9f4ea174ce3d ensembl_variant_report.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ensembl_variant_report.py	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,253 @@
+#!/usr/bin/env python
+"""
+Report variants to Ensembl Transcripts
+
+FrameShift report line
+# Gene	Variant Position	Reference	Variation	Prevalence	Sequencing Depth	Transcript	AA Position	AA change	AA Length	Stop Codon	Stop Region	AA Variation
+TIGD6	chr5:149374879	AAG	AG	1.00	13	ENSG00000164296|ENST00000296736	345	Q344	522	A-TGA-T	KRWTSSRPST*
+
+MissSense report line
+# Gene	Variant Position	Reference	Variation	Prevalence	Sequencing Depth	Transcript	AA Position	AA change	AA Length	Stop Codon	Stop Region	AA Variation
+FN1	chr2:216235089	G	A	1.00	7394	ENSG00000115414|ENST00000354785	2261	V2261I	2478	G-TAA	TGLTRGATYN_I_IVEALKDQQR
+"""
+import sys
+import os.path
+import re
+import time
+import optparse
+from ensemblref import EnsemblRef
+from Bio.Seq import reverse_complement, translate
+
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    #I/O
+    parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' )
+    parser.add_option( '-s', '--format', dest='format', default='tabular', choices=['tabular','snpeff'], help='Tabular file with peptide_sequence column' )
+    #Columns for tabular input
+    parser.add_option( '-C', '--chrom_column', type='int', dest='chrom_column', default=1, help='column ordinal with Ensembl transctip ID' )
+    parser.add_option( '-P', '--pos_column', type='int', dest='pos_column', default=2, help='column ordinal with Ensembl transctip ID' )
+    parser.add_option( '-R', '--ref_column', type='int', dest='ref_column', default=3, help='column ordinal with Ensembl transctip ID' )
+    parser.add_option( '-A', '--alt_column', type='int', dest='alt_column', default=4, help='column ordinal with Ensembl transctip ID' )
+    parser.add_option( '-T', '--transcript_column', type='int', dest='transcript_column', default=1, help='column ordinal with Ensembl transctip ID' )
+    parser.add_option( '-F', '--dpr_column', type='int', dest='dpr_column', default=1, help='column with VCF: DPR or AD' )
+    parser.add_option( '-D', '--dp_column', type='int', dest='dp_column', default=1, help='column with VCF: DP' )
+    parser.add_option( '-g', '--gene_model', dest='gene_model', default=None, help='GTF gene model file. Used to annotate NSJ peptide entries.')
+    parser.add_option( '-2', '--twobit', dest='twobit', default=None, help='Reference genome in UCSC twobit format')
+    #Output file
+    parser.add_option( '-o', '--output', dest='output', default=None, help='The output report (else write to stdout)' )
+    #filters
+    parser.add_option( '-d', '--min_depth', type='int', dest='min_depth', default=None, help='Minimum read depth to report' )
+    parser.add_option( '-f', '--min_freq', type='float', dest='min_freq', default=None, help='Minimum variant frequency to report' )
+    #peptide options
+    parser.add_option( '-l', '--leading_aa', type='int', dest='leading_aa', default=10, help='Number AAs before missense variant' )
+    parser.add_option( '-t', '--trailing_aa', type='int', dest='trailing_aa', default=10, help='Number AAs after missense variant' )
+    parser.add_option( '-r', '--readthrough', type='int', dest='readthrough', default=0, help='' )
+    # 
+    parser.add_option('--debug', dest='debug', action='store_true', default=False, help='Print debugging messages')
+    (options, args) = parser.parse_args()
+    
+    ##INPUTS##
+    if options.input != None:
+        try:
+            inputPath = os.path.abspath(options.input)
+            inputFile = open(inputPath, 'r')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(2)
+    else:
+        inputFile = sys.stdin
+
+    if options.output != None:
+        try:
+            outputPath = os.path.abspath(options.output)
+            outputFile = open(outputPath, 'w')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(3)
+    else:
+        outputFile = sys.stdout
+
+    def parse_tabular():
+        ci = options.chrom_column - 1
+        pi = options.pos_column - 1
+        ri = options.ref_column - 1
+        ai = options.alt_column - 1
+        ti = options.transcript_column - 1
+        di = options.dp_column - 1
+        fi = options.dpr_column - 1
+        for linenum,line in enumerate(inputFile):
+            if options.debug:
+                print >> sys.stderr, "%d: %s\n" % (linenum,line)
+            if line.startswith('#'):
+                continue
+            if line.strip() == '':
+                continue
+            fields = line.rstrip('\r\n').split('\t')
+            transcript = fields[ti]
+            if not transcript:
+                print >> sys.stderr, "%d: %s\n" % (linenum,line)
+                continue
+            chrom = fields[ci]
+            pos = int(fields[pi])
+            ref = fields[ri]
+            alts = fields[ai]
+            dp = int(fields[di])
+            dpr = [int(x) for x in fields[fi].split(',')]
+            for i,alt in enumerate(alts.split(',')):
+                freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None
+                yield (transcript,pos,ref,alt,dp,freq)
+
+    def parse_snpeff_vcf():
+        for linenum,line in enumerate(inputFile):
+            if line.startswith('##'): 
+                if line.find('SnpEffVersion=') > 0:
+                    SnpEffVersion = re.search('SnpEffVersion="?(\d+\.\d+)',line).groups()[0]
+            elif line.startswith('#CHROM'): 
+                pass
+            else:
+                fields = line.strip('\r\n').split('\t')
+                if options.debug: print >> sys.stderr, "\n%s" % (fields)
+                (chrom, pos, id, ref, alts, qual, filter, info) = fields[0:8]
+                alt_list = alts.split(',')
+                pos = int(pos)
+                qual = float(qual)
+                dp = None
+                dpr = None
+                for info_item in info.split(';'):
+                    if info_item.find('=') < 0: continue
+                    (key, val) = info_item.split('=', 1)
+                    if key == 'DP':
+                        dp = int(val)
+                    if key == 'DPR':
+                        dpr = [int(x) for x in val.split(',')]
+                    if key in ['EFF','ANN']:
+                        for effect in val.split(','):
+                            if options.debug: print >> sys.stderr, "\n%s" % (effect.split('|'))
+                            if key == 'ANN':
+                                (alt,eff,impact,gene_name,gene_id,feature_type,transcript,biotype,exon,c_hgvs,p_hgvs,cdna,cds,aa,distance,info) = effect.split('|')
+                            elif key == 'EFF':
+                                (eff, effs) = effect.rstrip(')').split('(')
+                                (impact, functional_class, codon_change, aa_change, aa_len, gene_name, biotype, coding, transcript, exon, alt) = effs.split('|')[0:11]
+                            i = alt_list.index(alt) if alt in alt_list else 0
+                            freq = float(dpr[i+1])/float(sum(dpr)) if dpr else None
+                            yield (transcript,pos,ref,alt,dp,freq)
+
+
+    #Process gene model
+    ens_ref = None
+    if options.gene_model != None:
+        try:
+            geneModelFile = os.path.abspath(options.gene_model)
+            twoBitFile = os.path.abspath(options.twobit)
+            print >> sys.stderr, "Parsing ensembl ref: %s %s" % (options.gene_model,options.twobit)
+            time1 = time.time()
+            ens_ref = EnsemblRef(geneModelFile,twoBitFile)
+            time2 = time.time()
+            print >> sys.stderr, "Parsing ensembl ref: %d seconds" % (int(time2-time1))
+        except Exception, e:
+            print >> sys.stderr, "Parsing gene model failed: %s" % e
+            exit(2)
+    try:
+        parse_input = parse_tabular if options.format == 'tabular' else parse_snpeff_vcf
+        for tid,pos1,ref,alt,dp,freq in parse_input():
+            if not tid:
+                continue
+            if options.min_depth and dp is not None and dp < options.min_depth:
+                continue
+            if options.min_freq and freq is not None and freq < options.min_freq:
+                continue
+            ## transcript_id, pos, ref, alt, dp, dpr
+            tx = ens_ref.get_gtf_transcript(tid)
+            if not tx:
+                continue
+            coding = ens_ref.transcript_is_coding(tid)
+            if not coding:
+                continue
+            frame_shift = len(ref) != len(alt)
+            cds = ens_ref.get_cds(tid)
+            pos0 = pos1 - 1 # zero based position
+            spos = pos0 if tx.gene.strand else pos0 + len(ref) - 1
+            alt_seq = alt if tx.gene.strand else reverse_complement(alt)
+            ref_seq = ref if tx.gene.strand else reverse_complement(ref)
+            cds_pos = ens_ref.genome_to_cds_pos(tid, spos)
+            alt_cds = cds[:cds_pos] + alt_seq + cds[cds_pos+len(ref):] if cds_pos+len(ref) < len(cds) else '' 
+            offset = 0
+            if tx.gene.strand:
+                for i in range(min(len(ref),len(alt))):
+                    if ref[i] == alt[i]:
+                        offset = i
+                    else:
+                        break
+            else:
+                for i in range(-1,-min(len(ref),len(alt)) -1,-1):
+                    if ref[i] == alt[i]:
+                        offset = i
+                    else:
+                        break
+            refpep = translate(cds[:len(cds)/3*3])
+            pep = translate(alt_cds[:len(alt_cds)/3*3])
+            peplen = len(pep)
+            aa_pos = (cds_pos + offset) / 3
+            if aa_pos >= len(pep):
+                print >> sys.stderr, "aa_pos %d >= peptide length %d : %s %d %s %s\n" % (aa_pos,len(pep),tid,pos1,ref,alt)
+                continue
+            if frame_shift:
+                #find stop_codons
+                nstops = 0
+                stop_codons = []
+                for i in range(aa_pos,peplen):
+                    if refpep[i] != pep[i]:
+                        aa_pos = i
+                        break
+                for i in range(aa_pos,peplen):
+                    if pep[i] == '*':
+                        nstops += 1
+                        stop_codons.append("%s-%s%s" % (alt_cds[i*3-1],alt_cds[i*3:i*3+3],"-%s" % alt_cds[i*3+4] if len(alt_cds) > i*3 else ''))
+                        if nstops > options.readthrough:
+                            reported_peptide = pep[aa_pos:i+1]
+                            reported_stop_codon = ','.join(stop_codons)
+                            break
+            else:
+                reported_stop_codon = "%s-%s" % (alt_cds[peplen*3-4],alt_cds[peplen*3-3:peplen*3])
+                reported_peptide = "%s_%s_%s" % (pep[max(aa_pos-options.leading_aa,0):aa_pos],
+                                                 pep[aa_pos],
+                                                 pep[aa_pos+1:min(aa_pos+1+options.trailing_aa,len(pep))])
+            cs_pos = aa_pos * 3
+            aa_pos = (cds_pos + offset) / 3
+            ref_codon = cds[cs_pos:cs_pos+3]
+            ref_aa = translate(ref_codon)
+            alt_codon = alt_cds[cs_pos:cs_pos+3]
+            alt_aa = translate(alt_codon)
+            gene = tx.gene.names[0]
+            report_fields = [tx.gene.names[0],
+             '%s:%d %s' % (tx.gene.contig,pos1,'+' if tx.gene.strand else '-'),
+             ref_seq,
+             alt_seq,
+             "%1.2f" % freq if freq is not None else '',
+             str(dp),
+             "%s|%s" % (tx.gene.gene_id,tx.cdna_id),
+             "%d" % (aa_pos + 1),
+             "%s%d%s" % (ref_aa,aa_pos + 1,alt_aa),
+             "%d" % len(pep),
+             reported_stop_codon,
+             reported_peptide
+             ]
+            if options.debug:
+                report_fields.append("%d %d %d %d  %s  %s" % (cds_pos, offset, cs_pos,aa_pos,ref_codon,alt_codon))
+            outputFile.write('\t'.join(report_fields))
+            if options.debug:
+                print >> sys.stderr, "%s %s\n%s\n%s\n%s %s" % (
+                         cds[cs_pos-6:cs_pos], cds[cs_pos:cs_pos+15],
+                         translate(cds[cs_pos-6:cs_pos+15]),
+                         translate(alt_cds[cs_pos-6:cs_pos+15]),
+                         alt_cds[cs_pos-6:cs_pos], alt_cds[cs_pos:cs_pos+15])
+            outputFile.write('\n')
+    except Exception, e:
+        print >> sys.stderr, "failed: %s" % e
+        exit(1)
+
+
+if __name__ == "__main__" : __main__()
+
diff -r 000000000000 -r 9f4ea174ce3d ensembl_variant_report.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ensembl_variant_report.xml	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,193 @@
+<tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.40">gtf_to_genes</requirement>
+        <requirement type="package" version="3.1.4">twobitreader</requirement>
+        <requirement type="package" version="1.62">biopython</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+         python '$__tool_directory__/ensembl_variant_report.py'
+         #if $ref.ref_source == 'cached':
+             --twobit="$ref.ref_loc.fields.path"
+         #else
+             --twobit="$ref.ref_file"
+         #end if
+         --gene_model="$gtf_file"
+         #if $variant.fmt == 'vcf':
+             --input="$variant.input_vcf"
+             --format=snpeff
+         #else
+             --input="$variant.input_tsv"
+            --pos_column=$variant.pos_column
+            --ref_column=$variant.ref_column
+            --alt_column=$variant.alt_column
+            --transcript_column=$variant.transcript_column
+            --dp_column=$variant.dp_column
+            --dpr_column=$variant.dpr_column
+         #end if
+         #if str($filter.min_depth) != '':
+             --min_depth=$filter.min_depth
+         #end if
+         #if str($filter.min_freq) != '':
+             --min_freq=$filter.min_freq
+         #end if
+         #if str($report.readthrough) != '':
+             --readthrough=$report.readthrough
+         #end if
+         #if str($report.leading_aa) != '':
+             --leading_aa=$report.leading_aa
+         #end if
+         #if str($report.trailing_aa) != '':
+             --trailing_aa=$report.trailing_aa
+         #end if
+         --output="$output"
+    ]]></command>
+    <inputs>
+        <conditional name="variant">
+            <param name="fmt" type="select" label="Input format for variants">
+                <option value="vcf">snpEff vcf</option>
+                <option value="tsv">tabular from snpsift extract</option>
+            </param>
+            <when value="vcf">
+                <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/>
+            </when>
+            <when value="tsv">
+                <param name="input_tsv" type="data" format="tabular" label="tabular file"/>
+                <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/>
+                <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/>
+                <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/>
+                <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/>
+                <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/>
+                <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/>
+            </when>
+        </conditional>
+        <conditional name="ref">
+            <param name="ref_source" type="select" label="Source for Genomic Data">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_loc" type="select" label="Select reference 2bit file">
+                    <options from_data_table="twobit" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
+            </when>
+        </conditional>
+        <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/>
+        <section name="filter" expanded="false" title="Filter Options">
+            <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report" 
+                   help="If a value is entered, ignore variants with DP INFO field less than this value"/>
+            <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report"
+                   help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/>
+        </section>
+        <section name="report" expanded="false" title="Report Options">
+            <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/>
+            <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display"
+                   help="Ignored for frame shifts"/>
+            <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display"
+                   help="Ignored for frame shifts"/>
+        </section>
+        
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fmt" value="vcf"/>
+            <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
+            <param name="ref_source" value="history"/>
+            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
+            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="MGGQ_A_SASNSFSRLH" />
+                    <not_has_text text="*REDHAAGPEA" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="fmt" value="vcf"/>
+            <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
+            <param name="ref_source" value="history"/>
+            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
+            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="MGGQ_A_SASNSFSRLH" />
+                    <not_has_text text="*REDHAAGPEA" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="fmt" value="vcf"/>
+            <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
+            <param name="ref_source" value="history"/>
+            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
+            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
+            <param name="readthrough" value="1"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="MGGQ_A_SASNSFSRLH" />
+                    <has_text text="*REDHAAGPEA" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="fmt" value="vcf"/>
+            <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
+            <param name="ref_source" value="history"/>
+            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
+            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
+            <param name="min_depth" value="100"/>
+            <param name="min_freq" value=".80"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" />
+                    <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="fmt" value="tsv"/>
+            <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
+            <param name="ref_source" value="history"/>
+            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
+            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
+            <param name="pos_column" value="2"/>
+            <param name="ref_column" value="3"/>
+            <param name="alt_column" value="4"/>
+            <param name="transcript_column" value="7"/>
+            <param name="dp_column" value="8"/>
+            <param name="dpr_column" value="9"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="MGGQ_A_SASNSFSRLH" />
+                    <not_has_text text="*REDHAAGPEA" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants.
+Allows readthrough of stop codons, and reports the stop codons.  
+
+Input can be a snpEff vcf file using either ANN or EFF annotations.
+Alternatively, the input can be a tabular file that has columns:
+
+  - pos
+  - ref
+  - alt
+  - Ensembl Transcript ID
+  - Read Depth (DP)
+  - AlleleDepth (DPR)
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt385</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 9f4ea174ce3d ensemblref.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ensemblref.py	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,185 @@
+"""
+with gtf and twobit
+get_bed(transcript_id)  
+"""
+from gtf_to_genes import gene, gene_utilities
+from twobitreader import TwoBitFile
+from Bio.Seq import reverse_complement, translate
+import logging
+logger = logging.getLogger("test")
+
+class EnsemblRef(object):
+
+    def __init__(self,gtf_file,twobitfile,read_now=True):
+        self.gtf_file = gtf_file
+        self.twobitfile = twobitfile
+        self.twobit = TwoBitFile(self.twobitfile)
+        self.gene_dict = None
+        self.transcript_idx = None
+        self.name_idx = None
+        if read_now:
+            self.get_transcript_idx()
+        
+
+    def get_gene_dict(self):
+        if self.gene_dict is None:
+            gene_structures = gene.t_parse_gtf('test')
+            self.gene_dict = gene_structures.get_genes(self.gtf_file,logger=logger)
+        return self.gene_dict
+
+
+    def get_transcript_idx(self):
+        if self.transcript_idx is None:
+            self.transcript_idx = gene_utilities.index_transcripts(self.get_gene_dict(),by_prot_id=False)
+        return self.transcript_idx
+
+
+    def get_name_idx(self):
+        if self.name_idx is None:
+            self.name_idx = dict()
+            for i,t in self.get_transcript_idx().items():
+                for name in t.gene.names:
+                   self.name_idx[name] = t.gene
+                for name in t.names:
+                   self.name_idx[name] = t
+                if t.prot_id:
+                   self.name_idx[t.prot_id] = t
+        return self.name_idx
+
+
+    def get_gtf_transcript(self,name):
+        idx = self.get_transcript_idx()
+        if name in idx:
+            return idx[name]
+        else:
+            nidx = self.get_name_idx()
+            if name in nidx:
+                return nidx[name]
+        return None
+
+
+    def transcript_is_coding(self,transcript_id):
+        tx = self.get_transcript_idx()[transcript_id]
+        return len(tx.start_codons) > 0
+
+
+    def get_transcript_start_codon(self,transcript_id):
+        tx = self.get_transcript_idx()[transcript_id]
+        return tx.start_codons[0] if len(tx.start_codons) > 0 else None
+
+
+    def get_bed_line(self,transcript_id,score=0,itemRgb='0,0,0',coding=False):
+        tx = self.get_transcript_idx()[transcript_id]
+        chrom = tx.gene.contig
+        chromStart = tx.coding_beg if coding else tx.beg 
+        chromEnd = tx.coding_end if coding else tx.end
+        name = transcript_id
+        strand = '+' if tx.gene.strand else '-'
+        thickStart = tx.coding_beg if tx.coding_beg else chromStart
+        thickEnd = tx.coding_end if tx.coding_end else chromEnd
+        exons = tx.get_coding_exons() if coding else tx.get_exons()
+        blockCount = len(exons)
+        if tx.gene.strand:
+            strand = '+'
+            blockSizes = [abs(e-s) for s,e in exons]
+            blockStarts = [s - chromStart for s,e in exons]
+        else:
+            strand = '-'
+            blockSizes = [abs(e-s) for s,e in reversed(exons)]
+            blockStarts = [s - chromStart for s,e in reversed(exons)]
+        blockSizes = ','.join([str(x) for x in blockSizes])
+        blockStarts = ','.join([str(x) for x in blockStarts])
+        return '%s\t%d\t%d\t%s\t%s\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts)
+
+
+    def transcripts_in_range(self,chrom,startpos,endpos,strand=None):
+        spos = min(startpos,endpos) if endpos else startpos
+        epos = max(startpos,endpos) if endpos else startpos
+        transcripts = []
+        for i,t in self.get_transcript_idx().items():
+            if t.gene.contig == chrom and t.beg <= epos and spos <= t.end:
+                if strand and t.gene.strand != strand:
+                    continue
+                transcripts.append(t)
+        return transcripts
+
+
+    def genes_in_range(self,chrom,startpos,endpos,strand=None,gene_types=None):
+        spos = min(startpos,endpos) if endpos else startpos
+        epos = max(startpos,endpos) if endpos else startpos
+        gene_dict = self.get_gene_dict()
+        gtypes = set(gene_types)  & set(gene_dict.keys()) if gene_types else set(gene_dict.keys())
+        genes = []
+        for gt in gtypes:
+            for gene in gene_dict[gt]:
+                if gene.contig == chrom and gene.beg <= epos and spos <= gene.end:
+                    if strand and gene.strand != strand:
+                        continue
+                    genes.append(gene)
+        return genes
+
+
+    def get_sequence(self,chrom,start,end):
+        if self.twobit:
+            if chrom in self.twobit:
+                return self.twobit[chrom][start:end]
+            contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom
+            if contig in self.twobit:
+                return self.twobit[contig][start:end]
+        return None
+
+
+    def sequence_sizes(self):
+       return self.twobit.sequence_sizes()
+
+
+    def get_transcript_seq(self,transcript_id,coding=False):
+        tx = self.get_transcript_idx()[transcript_id]
+        chrom = tx.gene.contig
+        exonbnds = tx.get_coding_exons() if coding else tx.get_exons()
+        if tx.gene.strand:
+            seqs = [self.get_sequence(chrom,s,e) for s,e in exonbnds]
+        else:
+            seqs = [reverse_complement(self.get_sequence(chrom,s,e)) for s,e in exonbnds]
+        return ''.join(seqs)
+
+
+    def get_cdna(self,transcript_id):
+        return self.get_transcript_seq(transcript_id,coding=False)
+
+
+    def get_cds(self,transcript_id):
+        return self.get_transcript_seq(transcript_id,coding=True)
+
+
+    def genome_to_transcript_pos(self,transcript_id,genome_pos,coding=False):
+        tx = self.get_transcript_idx()[transcript_id]
+        if not tx.beg <= genome_pos < tx.end:
+            return None
+        exonbnds = tx.get_coding_exons() if coding else tx.get_exons()
+        cdna_pos = 0
+        if tx.gene.strand:
+            for s,e in exonbnds:
+                if s <= genome_pos < e:
+                    cdna_pos += genome_pos - s
+                    break
+                else:
+                    cdna_pos += e - s
+        else:
+            for s,e in exonbnds:
+                if s <= genome_pos < e:
+                    cdna_pos += e - genome_pos - 1
+                    break
+                else:
+                    cdna_pos += e - s
+        return cdna_pos
+
+
+    def genome_to_cdna_pos(self,transcript_id,genome_pos):
+        return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=False)
+
+
+    def genome_to_cds_pos(self,transcript_id,genome_pos):
+        return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=True)
+
+
diff -r 000000000000 -r 9f4ea174ce3d test-data/GRCh38_X.2bit
Binary file test-data/GRCh38_X.2bit has changed
diff -r 000000000000 -r 9f4ea174ce3d test-data/GRCh38_X.83.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GRCh38_X.83.gtf	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,280 @@
+#!genome-build GRCh38.p5
+#!genome-version GRCh38
+#!genome-date 2013-12
+#!genome-build-accession NCBI:GCA_000001405.20
+#!genebuild-last-updated 2015-10
+X	havana	gene	253743	255091	.	+	.	gene_id "ENSG00000228572"; gene_version "7"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2";
+X	havana	transcript	253743	255091	.	+	.	gene_id "ENSG00000228572"; gene_version "7"; transcript_id "ENST00000431238"; transcript_version "7"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; transcript_name "LL0YNC03-29C1.1-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; havana_transcript "OTTHUMT00000107057"; havana_transcript_version "2"; tag "basic"; transcript_support_level "NA (assigned to previous version 6)";
+X	havana	exon	253743	253846	.	+	.	gene_id "ENSG00000228572"; gene_version "7"; transcript_id "ENST00000431238"; transcript_version "7"; exon_number "1"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; transcript_name "LL0YNC03-29C1.1-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; havana_transcript "OTTHUMT00000107057"; havana_transcript_version "2"; exon_id "ENSE00001702291"; exon_version "1"; tag "basic"; transcript_support_level "NA (assigned to previous version 6)";
+X	havana	exon	254937	255091	.	+	.	gene_id "ENSG00000228572"; gene_version "7"; transcript_id "ENST00000431238"; transcript_version "7"; exon_number "2"; gene_name "LL0YNC03-29C1.1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; havana_gene "OTTHUMG00000046372"; havana_gene_version "2"; transcript_name "LL0YNC03-29C1.1-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; havana_transcript "OTTHUMT00000107057"; havana_transcript_version "2"; exon_id "ENSE00001655436"; exon_version "1"; tag "basic"; transcript_support_level "NA (assigned to previous version 6)";
+X	ensembl_havana	gene	276322	303356	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5";
+X	havana	transcript	276322	303353	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	276322	276394	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00001489430"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	281482	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00001306908"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	290648	290776	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	290648	290776	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	291499	291654	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00002143117"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	291499	291654	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	293035	293218	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00002167778"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	293035	293218	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	299097	303353	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; exon_id "ENSE00001489377"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	299097	299332	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; protein_id "ENSP00000381976"; protein_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	stop_codon	299333	299335	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	276322	276394	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	281482	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	three_prime_utr	299336	303353	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000399012"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058878"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	transcript	276324	291537	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; transcript_support_level "4 (assigned to previous version 6)";
+X	havana	exon	276324	276394	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00001536003"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00003657744"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00003581159"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)";
+X	havana	exon	290648	290792	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00001939272"; exon_version "2"; transcript_support_level "4 (assigned to previous version 6)";
+X	havana	exon	291499	291537	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000484611"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-009"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000393211"; havana_transcript_version "1"; exon_id "ENSE00002190604"; exon_version "1"; transcript_support_level "4 (assigned to previous version 6)";
+X	havana	transcript	276353	291629	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	276353	276394	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00002160563"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	290648	290776	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	CDS	290648	290776	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	291499	291629	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; exon_id "ENSE00001740378"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	CDS	291499	291629	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; protein_id "ENSP00000394848"; protein_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	five_prime_utr	276353	276394	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000430923"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-010"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000393212"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	transcript	281055	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	281055	281121	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00001750899"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	281482	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00001306908"; exon_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; protein_id "ENSP00000412018"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; protein_id "ENSP00000412018"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	281055	281121	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	281482	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000445062"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-005"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313973"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	ensembl_havana	transcript	281192	303356	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	281192	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00001489388"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	290648	290776	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	CDS	290648	290776	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	291499	291654	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00002143117"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	CDS	291499	291654	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	293035	293218	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00002167778"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	CDS	293035	293218	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	exon	299097	303356	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; exon_id "ENSE00001489383"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	CDS	299097	299332	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; protein_id "ENSP00000371073"; protein_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	stop_codon	299333	299335	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	five_prime_utr	281192	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	three_prime_utr	299336	303356	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381657"; transcript_version "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-002"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; havana_transcript "OTTHUMT00000058879"; havana_transcript_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	havana	transcript	281194	288787	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	281194	281256	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00001719251"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	281482	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00001306908"; exon_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; protein_id "ENSP00000400904"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	288733	288787	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; exon_id "ENSE00001763472"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	288733	288787	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; protein_id "ENSP00000400904"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	281194	281256	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	281482	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000429181"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-006"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313974"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	ensembl	transcript	281462	303353	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	281462	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002204149"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00003594438"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00003789340"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	290648	290776	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002162116"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	CDS	290648	290776	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	291499	291654	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002143117"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	CDS	291499	291654	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	293035	293218	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00002167778"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	CDS	293035	293218	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	299097	299465	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00001334714"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	CDS	299097	299332	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; protein_id "ENSP00000371079"; protein_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	stop_codon	299333	299335	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "7"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	exon	302837	303353	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; exon_number "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; exon_id "ENSE00001489403"; exon_version "3"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	five_prime_utr	281462	281684	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	three_prime_utr	299336	299465	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	ensembl	three_prime_utr	302837	303353	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000381663"; transcript_version "8"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14103"; tag "basic"; transcript_support_level "5 (assigned to previous version 7)";
+X	havana	transcript	283163	288829	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	283163	283201	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; exon_id "ENSE00002195046"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; protein_id "ENSP00000408558"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	288733	288829	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; exon_id "ENSE00002178523"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	288733	288829	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; protein_id "ENSP00000408558"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	283163	283201	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000443019"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-003"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058880"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	transcript	283465	291639	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	283465	283488	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00001626975"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	290648	290776	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00002162116"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	290648	290776	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	291499	291639	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; exon_id "ENSE00001603661"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	CDS	291499	291639	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; protein_id "ENSP00000399510"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	283465	283488	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000415337"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-007"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313975"; havana_transcript_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	transcript	283479	291629	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	283479	283520	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00001691645"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	284167	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00003594438"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	290648	290776	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00002162116"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	290648	290776	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "4"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	exon	291499	291629	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; exon_id "ENSE00001740378"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	CDS	291499	291629	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; exon_number "5"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; protein_id "ENSP00000405307"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	283479	283520	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	five_prime_utr	284167	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000447472"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-008"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000313976"; havana_transcript_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "4 (assigned to previous version 5)";
+X	havana	transcript	283734	290757	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	283734	284314	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; exon_id "ENSE00001621688"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	CDS	284188	284314	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; protein_id "ENSP00000414181"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	start_codon	284188	284190	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "1"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	288733	288869	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; exon_id "ENSE00003789340"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	CDS	288733	288869	.	+	2	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "2"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; protein_id "ENSP00000414181"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	290648	290757	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; exon_id "ENSE00001690275"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	CDS	290648	290757	.	+	0	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; exon_number "3"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; protein_id "ENSP00000414181"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	five_prime_utr	283734	284187	.	+	.	gene_id "ENSG00000182378"; gene_version "13"; transcript_id "ENST00000448477"; transcript_version "6"; gene_name "PLCXD1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022693"; havana_gene_version "5"; transcript_name "PLCXD1-004"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000058881"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2 (assigned to previous version 5)";
+X	ensembl_havana	gene	304529	318819	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3";
+X	havana	transcript	304529	312463	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	311419	312463	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00001866313"; exon_version "2"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	307732	307880	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "2"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00003604694"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	307360	307512	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "3"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00003552346"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	304529	305197	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000485332"; transcript_version "7"; exon_number "4"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000467781"; havana_transcript_version "1"; exon_id "ENSE00001878585"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	ensembl_havana	transcript	304750	318819	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	318439	318819	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003711516"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	318439	318787	.	-	0	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	start_codon	318785	318787	.	-	0	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "1"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	316914	317051	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "2"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003733507"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	316914	317051	.	-	2	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "2"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	315229	315299	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "3"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003733593"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	315229	315299	.	-	2	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "3"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	314890	315020	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "4"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003714129"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	314890	315020	.	-	0	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "4"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	314150	314217	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "5"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003449454"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	314150	314217	.	-	1	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "5"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	312766	312924	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "6"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00001793174"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	312766	312924	.	-	2	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "6"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	311419	311627	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "7"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00001288218"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	311419	311627	.	-	2	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "7"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	307732	307880	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "8"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003654058"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	307732	307880	.	-	0	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "8"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	307360	307512	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00003581203"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	307360	307512	.	-	1	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	exon	304750	305197	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "10"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; exon_id "ENSE00001797294"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	CDS	305077	305197	.	-	1	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "10"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; protein_id "ENSP00000316598"; protein_version "5"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	stop_codon	305074	305076	.	-	0	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; exon_number "10"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	five_prime_utr	318788	318819	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	ensembl_havana	three_prime_utr	304750	305073	.	-	.	gene_id "ENSG00000178605"; gene_version "13"; transcript_id "ENST00000326153"; transcript_version "9"; gene_name "GTPBP6"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000022694"; havana_gene_version "3"; transcript_name "GTPBP6-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS75943"; havana_transcript "OTTHUMT00000058882"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 8)";
+X	havana	gene	320990	321851	.	+	.	gene_id "ENSG00000226179"; gene_version "6"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1";
+X	havana	transcript	320990	321851	.	+	.	gene_id "ENSG00000226179"; gene_version "6"; transcript_id "ENST00000391707"; transcript_version "7"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; transcript_name "LINC00685-001"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTHUMT00000055574"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	havana	exon	320990	321248	.	+	.	gene_id "ENSG00000226179"; gene_version "6"; transcript_id "ENST00000391707"; transcript_version "7"; exon_number "1"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; transcript_name "LINC00685-001"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTHUMT00000055574"; havana_transcript_version "1"; exon_id "ENSE00001675006"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	havana	exon	321683	321851	.	+	.	gene_id "ENSG00000226179"; gene_version "6"; transcript_id "ENST00000391707"; transcript_version "7"; exon_number "2"; gene_name "LINC00685"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTHUMG00000021049"; havana_gene_version "1"; transcript_name "LINC00685-001"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTHUMT00000055574"; havana_transcript_version "1"; exon_id "ENSE00001778583"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 6)";
+X	ensembl_havana	gene	333963	386955	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3";
+X	ensembl_havana	transcript	333963	386710	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	386368	386710	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00001912068"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	386368	386691	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	start_codon	386689	386691	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	361405	361590	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003653358"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	361405	361590	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	347590	347693	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003509428"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	347590	347693	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	347234	347336	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003492683"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	347234	347336	.	-	1	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	346701	346775	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003489026"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	346701	346775	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	346174	346260	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003574906"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	346174	346260	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	345516	345672	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003687848"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	345516	345672	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	341883	341931	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003511595"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	341883	341931	.	-	2	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	341307	341396	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "9"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003587700"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	341307	341396	.	-	1	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "9"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	340765	340940	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "10"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003668507"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	340765	340940	.	-	1	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "10"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	338778	338896	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "11"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003622978"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	338778	338896	.	-	2	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "11"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	338604	338710	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "12"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00003501875"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	338604	338710	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "12"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	exon	333963	334517	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "13"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; exon_id "ENSE00001844596"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	CDS	334370	334517	.	-	1	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "13"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; protein_id "ENSP00000375080"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	stop_codon	334367	334369	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; exon_number "13"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	five_prime_utr	386692	386710	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	ensembl_havana	three_prime_utr	333963	334366	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000390665"; transcript_version "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14104"; havana_transcript "OTTHUMT00000055577"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 7)";
+X	havana	transcript	334235	341711	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	341307	341711	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00001918099"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	340765	340940	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	338778	338896	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00003592960"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	338604	338710	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00003534283"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	334235	334517	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000479438"; transcript_version "6"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-008"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354555"; havana_transcript_version "1"; exon_id "ENSE00001489278"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	transcript	334239	347324	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	347234	347324	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00001716328"; exon_version "2"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	346701	346775	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003571094"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	346174	346260	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003477290"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	345516	345672	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003641725"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	341307	341931	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00001915623"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	340765	340940	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	338778	338896	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00003592960"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	exon	334239	338710	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477110"; transcript_version "6"; exon_number "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-003"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055583"; havana_transcript_version "2"; exon_id "ENSE00001815257"; exon_version "1"; transcript_support_level "1 (assigned to previous version 5)";
+X	havana	transcript	338613	345629	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; transcript_support_level "3 (assigned to previous version 5)";
+X	havana	exon	345516	345629	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00001890387"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)";
+X	havana	exon	341883	341931	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00003555172"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)";
+X	havana	exon	341307	341396	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00003689816"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)";
+X	havana	exon	340765	340940	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)";
+X	havana	exon	338613	338896	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000468169"; transcript_version "6"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-006"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055585"; havana_transcript_version "1"; exon_id "ENSE00001951758"; exon_version "1"; transcript_support_level "3 (assigned to previous version 5)";
+X	havana	transcript	340765	345626	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	345516	345626	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00001888244"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	341883	342237	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00001815626"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	341307	341396	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00003689816"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	340765	340940	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000484364"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-004"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055580"; havana_transcript_version "1"; exon_id "ENSE00003553826"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	transcript	341911	346514	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	346174	346514	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; exon_id "ENSE00001896157"; exon_version "1"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	345516	345672	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; exon_id "ENSE00003641725"; exon_version "1"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	exon	341911	341931	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000477636"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-005"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000055581"; havana_transcript_version "1"; exon_id "ENSE00001911121"; exon_version "1"; transcript_support_level "5 (assigned to previous version 5)";
+X	havana	transcript	344896	386955	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	386368	386955	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00001912680"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	362255	362332	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00001847312"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	361405	361590	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003585491"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	347590	347693	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003475055"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	347234	347336	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "5"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003606316"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	346701	346775	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003571094"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	346174	346260	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "7"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00003477290"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	exon	344896	345672	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000445792"; transcript_version "7"; exon_number "8"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-007"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354554"; havana_transcript_version "1"; exon_id "ENSE00001950030"; exon_version "1"; transcript_support_level "2 (assigned to previous version 6)";
+X	havana	transcript	346637	361516	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	361405	361516	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00001916804"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	347590	347693	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00003475055"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	347234	347336	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00003606316"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	346637	346775	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000496630"; transcript_version "6"; exon_number "4"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-010"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354557"; havana_transcript_version "1"; exon_id "ENSE00001851476"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	transcript	346720	347838	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	347590	347838	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; exon_id "ENSE00001843788"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	347234	347336	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; exon_id "ENSE00003606316"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	exon	346720	346775	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000475859"; transcript_version "6"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-009"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTHUMT00000354556"; havana_transcript_version "1"; exon_id "ENSE00001849084"; exon_version "1"; transcript_support_level "2 (assigned to previous version 5)";
+X	havana	transcript	347611	374044	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	exon	373532	374044	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; exon_id "ENSE00001489321"; exon_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	CDS	373532	373771	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; protein_id "ENSP00000371038"; protein_version "4"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	start_codon	373769	373771	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "1"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	exon	361405	361590	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; exon_id "ENSE00003653358"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	CDS	361405	361590	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "2"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; protein_id "ENSP00000371038"; protein_version "4"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	exon	347611	347693	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; exon_id "ENSE00001877883"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	CDS	347611	347693	.	-	0	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; exon_number "3"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; protein_id "ENSP00000371038"; protein_version "4"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
+X	havana	five_prime_utr	373772	374044	.	-	.	gene_id "ENSG00000167393"; gene_version "17"; transcript_id "ENST00000381625"; transcript_version "9"; gene_name "PPP2R3B"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000021052"; havana_gene_version "3"; transcript_name "PPP2R3B-002"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTHUMT00000055578"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "5 (assigned to previous version 8)";
diff -r 000000000000 -r 9f4ea174ce3d test-data/GRCh38_X400k.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GRCh38_X400k.tsv	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,62 @@
+#CHROM	POS	REF	ALT	ANN[*].EFFECT	ANN[*].GENE	ANN[*].FEATUREID	DP	DPR	ANN[*].CDS_POS	ANN[*].HGVS_C	ANN[*].HGVS_P	ANN[*].AA_POS	ANN[*].BIOTYPE
+X	284201	T	C	missense_variant	PLCXD1	ENST00000381657	693	1,598	14	n.14T>C	p.Val5Ala	5	ensembl_havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000399012	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000430923	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000445062	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000429181	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000381663	693	1,598	14	n.14T>C	p.Val5Ala	5	ensembl
+X	284201	T	C	missense_variant	PLCXD1	ENST00000443019	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000415337	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000447472	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	284201	T	C	missense_variant	PLCXD1	ENST00000448477	693	1,598	14	n.14T>C	p.Val5Ala	5	havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000381657	21	3,10	247	n.246_247insC	p.Lys83fs	83	ensembl_havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000399012	21	3,10	247	n.246_247insC	p.Lys83fs	83	havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000430923	21	3,10	247	n.246_247insC	p.Lys83fs	83	havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000445062	21	3,10	247	n.246_247insC	p.Lys83fs	83	havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000381663	21	3,10	247	n.246_247insC	p.Lys83fs	83	ensembl
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000415337	21	3,10	247	n.246_247insC	p.Lys83fs	83	havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000447472	21	3,10	247	n.246_247insC	p.Lys83fs	83	havana
+X	288851	G	GC	frameshift_variant	PLCXD1	ENST00000448477	21	3,10	247	n.246_247insC	p.Lys83fs	83	havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000381657	910	130,681	312	n.312C>G	p.Asp104Glu	104	ensembl_havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000399012	910	130,681	312	n.312C>G	p.Asp104Glu	104	havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000484611	910	130,681	404	n.404C>G	p.Thr135Ser	135	havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000430923	910	130,681	312	n.312C>G	p.Asp104Glu	104	havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000381663	910	130,681	312	n.312C>G	p.Asp104Glu	104	ensembl
+X	290695	C	G	missense_variant	PLCXD1	ENST00000415337	910	130,681	312	n.312C>G	p.Asp104Glu	104	havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000447472	910	130,681	312	n.312C>G	p.Asp104Glu	104	havana
+X	290695	C	G	missense_variant	PLCXD1	ENST00000448477	910	130,681	312	n.312C>G	p.Asp104Glu	104	havana
+X	299221	G	C	missense_variant	PLCXD1	ENST00000381657	18	3,13	858	n.858G>C	p.Glu286Asp	286	ensembl_havana
+X	299221	G	C	missense_variant	PLCXD1	ENST00000399012	18	3,13	858	n.858G>C	p.Glu286Asp	286	havana
+X	299221	G	C	missense_variant	PLCXD1	ENST00000381663	18	3,13	858	n.858G>C	p.Glu286Asp	286	ensembl
+X	307850	G	C	missense_variant	GTPBP6	ENST00000485332	24	7,8	1076	n.1076C>G	p.Pro359Arg	359	havana
+X	307850	G	C	missense_variant	GTPBP6	ENST00000326153	24	7,8	1156	n.1156C>G	p.His386Asp	386	ensembl_havana
+X	311500	C	CAT	frameshift_variant	GTPBP6	ENST00000485332	56	11,22	963	n.963_964insAT	p.Gly322fs	321	havana
+X	311500	C	CAT	frameshift_variant	GTPBP6	ENST00000326153	56	11,22	1043	n.1043_1044insAT	p.Asp349fs	348	ensembl_havana
+X	334496	A	G	missense_variant	PPP2R3B	ENST00000477110	159	52,60	5545	n.5545T>C	p.Cys1849Arg	1849	havana
+X	334496	A	G	missense_variant	PPP2R3B	ENST00000479438	159	52,60	829	n.829T>C	p.Cys277Arg	277	havana
+X	338625	G	A	missense_variant	PPP2R3B	ENST00000390665	308	146,132	1556	n.1556C>T	p.Ala519Val	519	ensembl_havana
+X	338625	G	A	missense_variant	PPP2R3B	ENST00000468169	308	146,132	701	n.701C>T	p.Ala234Val	234	havana
+X	338627	A	G	missense_variant	PPP2R3B	ENST00000477110	301	0,271	1414	n.1414T>C	p.Cys472Arg	472	havana
+X	338627	A	G	missense_variant	PPP2R3B	ENST00000479438	301	0,271	784	n.784T>C	p.Cys262Arg	262	havana
+X	338856	A	G	missense_variant	PPP2R3B	ENST00000468169	517	15,390	470	n.470T>C	p.Leu157Pro	157	havana
+X	340856	CTG	C	frameshift_variant	PPP2R3B	ENST00000477110	17	0,11	1118	n.1118_1119delCA	p.Ala373fs	373	havana
+X	340856	CTG	C	frameshift_variant	PPP2R3B	ENST00000390665	17	0,11	1258	n.1258_1259delCA	p.Gln420fs	420	ensembl_havana
+X	340856	CTG	C	frameshift_variant	PPP2R3B	ENST00000479438	17	0,11	488	n.488_489delCA	p.Ala163fs	163	havana
+X	340856	CTG	C	frameshift_variant	PPP2R3B	ENST00000468169	17	0,11	336	n.336_337delCA	p.Ser112fs	112	havana
+X	340856	CTG	C	frameshift_variant	PPP2R3B	ENST00000484364	17	0,11	639	n.639_640delCA	p.Ser213fs	213	havana
+X	340928	C	CA	frameshift_variant	PPP2R3B	ENST00000477110	65	0,50	1047	n.1047_1048insT	p.Val350fs	349	havana
+X	340928	C	CA	frameshift_variant	PPP2R3B	ENST00000390665	65	0,50	1187	n.1187_1188insT	p.Trp396fs	396	ensembl_havana
+X	340928	C	CA	frameshift_variant	PPP2R3B	ENST00000479438	65	0,50	417	n.417_418insT	p.Val140fs	139	havana
+X	340928	C	CA	frameshift_variant	PPP2R3B	ENST00000468169	65	0,50	265	n.265_266insT	p.Gly89fs	89	havana
+X	340928	C	CA	frameshift_variant	PPP2R3B	ENST00000484364	65	0,50	568	n.568_569insT	p.Gly190fs	190	havana
+X	341347	A	C,G	missense_variant	PPP2R3B	ENST00000477110	48	0,20,15	995	n.995T>G	p.Leu332Arg	332	havana
+X	341347	A	C,G	missense_variant	PPP2R3B	ENST00000477110	48	0,20,15	995	n.995T>C	p.Leu332Pro	332	havana
+X	341347	A	C,G	missense_variant	PPP2R3B	ENST00000390665	48	0,20,15	1135	n.1135T>G	p.Trp379Gly	379	ensembl_havana
+X	341347	A	C,G	missense_variant	PPP2R3B	ENST00000390665	48	0,20,15	1135	n.1135T>C	p.Trp379Arg	379	ensembl_havana
+X	341347	A	C,G	missense_variant	PPP2R3B	ENST00000479438	48	0,20,15	365	n.365T>G	p.Leu122Arg	122	havana
+X	341347	A	C,G	missense_variant	PPP2R3B	ENST00000479438	48	0,20,15	365	n.365T>C	p.Leu122Pro	122	havana
+X	345580	G	A	missense_variant	PPP2R3B	ENST00000390665	6	0,4	972	n.972C>T	p.Trp324Cys	324	ensembl_havana
+X	345580	G	A	missense_variant	PPP2R3B	ENST00000468169	6	0,4	50	n.50C>T	p.Gly17Val	17	havana
+X	345580	G	A	missense_variant	PPP2R3B	ENST00000484364	6	0,4	47	n.47C>T	p.Gly16Val	16	havana
+X	345580	G	A	missense_variant	PPP2R3B	ENST00000477636	6	0,4	434	n.434C>T	p.Gly145Val	145	havana
+X	345580	G	A	missense_variant	PPP2R3B	ENST00000445792	6	0,4	1314	n.1314C>T	p.Trp438Cys	438	havana
diff -r 000000000000 -r 9f4ea174ce3d test-data/GRCh38_X400k_ANN.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GRCh38_X400k_ANN.vcf	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,85 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.2+htslib-1.2.1
+##samtoolsCommand=samtools mpileup -f /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa --BCF --output-tags DP,DPR,DV,DP4,INFO/DPR,SP --output /panfs/roc/galaxy/GALAXYP/files/000/144/dataset_144978.dat localbam_0.bam
+##reference=file:///panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa
+##contig=<ID=1,length=248956422>
+##contig=<ID=2,length=242193529>
+##contig=<ID=3,length=198295559>
+##contig=<ID=4,length=190214555>
+##contig=<ID=5,length=181538259>
+##contig=<ID=6,length=170805979>
+##contig=<ID=7,length=159345973>
+##contig=<ID=8,length=145138636>
+##contig=<ID=9,length=138394717>
+##contig=<ID=10,length=133797422>
+##contig=<ID=11,length=135086622>
+##contig=<ID=12,length=133275309>
+##contig=<ID=13,length=114364328>
+##contig=<ID=14,length=107043718>
+##contig=<ID=15,length=101991189>
+##contig=<ID=16,length=90338345>
+##contig=<ID=17,length=83257441>
+##contig=<ID=18,length=80373285>
+##contig=<ID=19,length=58617616>
+##contig=<ID=20,length=64444167>
+##contig=<ID=21,length=46709983>
+##contig=<ID=22,length=50818468>
+##contig=<ID=X,length=156040895>
+##contig=<ID=Y,length=57227415>
+##contig=<ID=MT,length=16569>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes 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=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
+##bcftools_callVersion=1.3+htslib-1.3
+##bcftools_callCommand=call -m --variants-only --output-type b --threads 1 input.bcf
+##bcftools_viewVersion=1.3+htslib-1.3
+##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets ^Mt --output-type v --threads 1 input.bcf
+##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets X --output-type v --threads 1 input.vcf.gz
+##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --regions X:1-400000 --output-type v --threads 1 input.vcf.gz
+##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -no CDS -no CHROMOSOME_LARGE_DELETION -no CODON_CHANGE -no CODON_INSERTION -no CODON_CHANGE_PLUS_CODON_INSERTION -no CODON_DELETION -no CODON_CHANGE_PLUS_CODON_DELETION -no DOWNSTREAM -no EXON -no EXON_DELETED -no GENE -no INTERGENIC -no INTERGENIC_CONSERVED -no INTRAGENIC -no INTRON -no INTRON_CONSERVED -no MICRO_RNA -no NON_SYNONYMOUS_START -no NON_SYNONYMOUS_STOP -no RARE_AMINO_ACID -no SPLICE_SITE_ACCEPTOR -no SPLICE_SITE_DONOR -no SPLICE_SITE_REGION -no SPLICE_SITE_BRANCH -no SPLICE_SITE_BRANCH_U12 -no STOP_LOST -no START_GAINED -no START_LOST -no STOP_GAINED -no SYNONYMOUS_CODING -no SYNONYMOUS_START -no SYNONYMOUS_STOP -no REGULATION -no UPSTREAM -no UTR_3_PRIME -no UTR_3_DELETED -no UTR_5_PRIME -no UTR_5_DELETED -no NEXT_PROT -stats /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148016.dat GRCh38.78 /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148008.dat "
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
+##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' ">
+##SnpSiftVersion="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani"
+##SnpSiftCmd="SnpSift filter -f /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148015.dat -e /panfs/roc/galaxy/GALAXYP/job_working_directory/000/126/126606/tmpTp3aAM"
+##FILTER=<ID=SnpSift,Description="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani, Expression used: ( ANN[*].EFFECT has 'missense_variant' | ANN[*].EFFECT has 'frameshift_variant')">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	localbam_0.bam
+X	284201	.	T	C	219.0	.	DP=693;VDB=0.999766;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.382033;BQB=1;MQ0F=0.001443;DPR=1,598;AC=2;AN=2;DP4=1,0,425,173;MQ=17;ANN=C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|2/7|n.14T>C|p.Val5Ala|528/5507|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|3/8|n.14T>C|p.Val5Ala|311/5287|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|2/5|n.14T>C|p.Val5Ala|77/587|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000445062|havana|3/4|n.14T>C|p.Val5Ala|305/555|14/-1|5/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000429181|havana|3/4|n.14T>C|p.Val5Ala|301/469|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|2/8|n.14T>C|p.Val5Ala|258/1863|14/-1|5/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000443019|havana|2/3|n.14T>C|p.Val5Ala|74/284|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|2/5|n.14T>C|p.Val5Ala|59/579|14/-1|5/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|2/5|n.14T>C|p.Val5Ala|77/587|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|1/3|n.14T>C|p.Val5Ala|468/828|14/-1|5/-1||WARNING_TRANSCRIPT_INCOMPLETE	GT:PL:DP:DV:SP:DP4:DPR	1/1:246,255,0:599:598:0:1,0,425,173:1,598
+X	288851	.	G	GC	30.4966	.	DP=21;VDB=0.0115453;SGB=-0.670168;RPB=0.597928;MQB=1;BQB=0.968368;MQ0F=0;DPR=3,10;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,10,0;MQ=20;ANN=GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|3/7|n.246_247insC|p.Lys83fs|761/5507|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|4/8|n.246_247insC|p.Lys83fs|544/5287|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|3/5|n.246_247insC|p.Lys83fs|310/587|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000445062|havana|4/4|n.246_247insC|p.Lys83fs|538/555|247/-1|83/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|3/8|n.246_247insC|p.Lys83fs|491/1863|247/-1|83/-1||,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|3/5|n.246_247insC|p.Lys83fs|292/579|247/-1|83/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|3/5|n.246_247insC|p.Lys83fs|310/587|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE,GC|frameshift_variant|HIGH|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|2/3|n.246_247insC|p.Lys83fs|701/828|247/-1|83/-1||WARNING_TRANSCRIPT_INCOMPLETE	GT:PL:DP:DV:SP:DP4:DPR	0/1:64,0,15:13:10:0:3,0,10,0:3,10
+X	290695	.	C	G	114.0	.	DP=910;VDB=0.336517;SGB=-0.693147;RPB=0.479982;MQB=0.997299;MQSB=0.999049;BQB=0.555736;MQ0F=0.010989;DPR=130,681;AC=2;AN=2;DP4=72,58,392,289;MQ=18;ANN=G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|4/7|n.312C>G|p.Asp104Glu|826/5507|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|5/8|n.312C>G|p.Asp104Glu|609/5287|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000484611|havana|4/5|n.404C>G|p.Thr135Ser|404/540|404/-1|135/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000430923|havana|4/5|n.312C>G|p.Asp104Glu|375/587|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|4/8|n.312C>G|p.Asp104Glu|556/1863|312/-1|104/-1||,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000415337|havana|4/5|n.312C>G|p.Asp104Glu|357/579|312/-1|104/-1||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000447472|havana|4/5|n.312C>G|p.Asp104Glu|375/587|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000448477|havana|3/3|n.312C>G|p.Asp104Glu|766/828|312/-1|104/-1||WARNING_TRANSCRIPT_INCOMPLETE	GT:PL:DP:DV:SP:DP4:DPR	1/1:141,210,0:811:681:2:72,58,392,289:130,681
+X	299221	.	G	C	77.0	.	DP=18;VDB=0.00122481;SGB=-0.683931;RPB=0.169694;MQB=1;MQSB=1;BQB=0.560355;MQ0F=0;DPR=3,13;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,9,4;MQ=20;ANN=C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381657|ensembl_havana|7/7|n.858G>C|p.Glu286Asp|1372/5507|858/-1|286/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000399012|havana|8/8|n.858G>C|p.Glu286Asp|1155/5287|858/-1|286/-1||,C|missense_variant|MODERATE|PLCXD1|ENSG00000182378|transcript|ENST00000381663|ensembl|7/8|n.858G>C|p.Glu286Asp|1102/1863|858/-1|286/-1||	GT:PL:DP:DV:SP:DP4:DPR	0/1:110,0,10:16:13:3:1,2,9,4:3,13
+X	307850	.	G	C	40.3947	.	DP=24;VDB=0.351291;SGB=-0.651104;RPB=0.511891;MQB=1;MQSB=1;BQB=0.720273;MQ0F=0;DPR=7,8;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,6,2;MQ=20;ANN=C|missense_variant|MODERATE|GTPBP6|ENSG00000178605|transcript|ENST00000485332|havana|2/4|n.1076C>G|p.Pro359Arg|1076/2016|1076/-1|359/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|missense_variant|MODERATE|GTPBP6|ENSG00000178605|transcript|ENST00000326153|ensembl_havana|8/10|n.1156C>G|p.His386Asp|1188/1907|1156/-1|386/-1||	GT:PL:DP:DV:SP:DP4:DPR	0/1:73,0,69:15:8:0:5,2,6,2:7,8
+X	311500	.	C	CAT	59.0	.	DP=56;VDB=0.625112;SGB=-0.692562;RPB=0.999818;MQB=0.915545;MQSB=0.982508;BQB=0.929674;MQ0F=0;DPR=11,22;ICB=1;HOB=0.5;AC=1;AN=2;DP4=11,0,19,3;MQ=18;ANN=CAT|frameshift_variant|HIGH|GTPBP6|ENSG00000178605|transcript|ENST00000485332|havana|1/4|n.963_964insAT|p.Gly322fs|963/2016|963/-1|321/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CAT|frameshift_variant|HIGH|GTPBP6|ENSG00000178605|transcript|ENST00000326153|ensembl_havana|7/10|n.1043_1044insAT|p.Asp349fs|1075/1907|1043/-1|348/-1||	GT:PL:DP:DV:SP:DP4:DPR	0/1:92,0,40:33:22:3:11,0,19,3:11,22
+X	334496	.	A	G	30.4121	.	DP=159;VDB=0.0384616;SGB=-0.693147;RPB=0.000107797;MQB=0.271035;MQSB=0.730753;BQB=0.124283;MQ0F=0.0880503;DPR=52,60;ICB=1;HOB=0.5;AC=1;AN=2;DP4=48,4,58,3;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|8/8|n.5545T>C|p.Cys1849Arg|5545/5802|5545/-1|1849/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|5/5|n.829T>C|p.Cys277Arg|829/1090|829/-1|277/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	0/1:63,0,72:113:61:2:48,4,58,3:52,60
+X	338625	.	G	A	74.0	.	DP=308;VDB=6.22534e-11;SGB=-0.693147;RPB=0.0585974;MQB=0.956346;MQSB=0.973687;BQB=0.279044;MQ0F=0.0681818;DPR=146,132;ICB=1;HOB=0.5;AC=1;AN=2;DP4=122,24,108,24;MQ=16;ANN=A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|12/13|n.1556C>T|p.Ala519Val|1575/2151|1556/-1|519/-1||,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|5/5|n.701C>T|p.Ala234Val|701/713|701/-1|234/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	0/1:107,0,99:278:132:1:122,24,108,24:146,132
+X	338627	.	A	G	190.0	.	DP=301;VDB=1.9745e-09;SGB=-0.693147;MQSB=0.973119;MQ0F=0.0697674;DPR=0,271;AC=2;AN=2;DP4=0,0,229,42;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|8/8|n.1414T>C|p.Cys472Arg|1414/5802|1414/-1|472/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|4/5|n.784T>C|p.Cys262Arg|784/1090|784/-1|262/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	1/1:217,255,0:271:271:0:0,0,229,42:0,271
+X	338856	.	A	G	182.0	.	DP=517;VDB=0.238596;SGB=-0.693147;RPB=0.857702;MQB=0.810962;MQSB=0.0368774;BQB=0.944745;MQ0F=0.0135397;DPR=15,390;AC=2;AN=2;DP4=7,8,244,146;MQ=16;ANN=G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|5/5|n.470T>C|p.Leu157Pro|470/713|470/-1|157/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	1/1:209,255,0:405:390:6:7,8,244,146:15,390
+X	340856	.	CTG	C	107.0	.	DP=17;VDB=3.781e-05;SGB=-0.676189;MQSB=0.8618;MQ0F=0;DPR=0,11;AC=2;AN=2;DP4=0,0,6,5;MQ=18;ANN=C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|6/8|n.1118_1119delCA|p.Ala373fs|1119/5802|1118/-1|373/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|10/13|n.1258_1259delCA|p.Gln420fs|1278/2151|1258/-1|420/-1||,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|2/5|n.488_489delCA|p.Ala163fs|489/1090|488/-1|163/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|4/5|n.336_337delCA|p.Ser112fs|337/713|336/-1|112/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|4/4|n.639_640delCA|p.Ser213fs|640/732|639/-1|213/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	1/1:134,33,0:11:11:0:0,0,6,5:0,11
+X	340928	.	C	CA	181.0	.	DP=65;VDB=2.0017e-11;SGB=-0.693147;MQSB=0.996914;MQ0F=0;DPR=0,50;AC=2;AN=2;DP4=0,0,21,29;MQ=19;ANN=CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|6/8|n.1047_1048insT|p.Val350fs|1047/5802|1047/-1|349/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|10/13|n.1187_1188insT|p.Trp396fs|1206/2151|1187/-1|396/-1||,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|2/5|n.417_418insT|p.Val140fs|417/1090|417/-1|139/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|4/5|n.265_266insT|p.Gly89fs|265/713|265/-1|89/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,CA|frameshift_variant|HIGH|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|4/4|n.568_569insT|p.Gly190fs|568/732|568/-1|190/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	1/1:208,151,0:50:50:0:0,0,21,29:0,50
+X	341347	.	A	C,G	170.0	.	DP=48;VDB=0.802018;SGB=-0.693136;MQSB=0.969233;MQ0F=0;DPR=0,20,15;AC=2;AN=2;DP4=0,0,20,15;MQ=19;ANN=C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|5/8|n.995T>G|p.Leu332Arg|995/5802|995/-1|332/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477110|havana|5/8|n.995T>C|p.Leu332Pro|995/5802|995/-1|332/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|9/13|n.1135T>G|p.Trp379Gly|1154/2151|1135/-1|379/-1||,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|9/13|n.1135T>C|p.Trp379Arg|1154/2151|1135/-1|379/-1||,C|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|1/5|n.365T>G|p.Leu122Arg|365/1090|365/-1|122/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,G|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000479438|havana|1/5|n.365T>C|p.Leu122Pro|365/1090|365/-1|122/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS	GT:PL:DP:DV:SP:DP4:DPR	1/1:197,105,0:35:35:0:0,0,20,15:0,20,15
+X	345580	.	G	A	41.8455	.	DP=6;VDB=0.910845;SGB=-0.556411;MQSB=1;MQ0F=0;DPR=0,4;AC=2;AN=2;DP4=0,0,3,1;MQ=20;ANN=A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000390665|ensembl_havana|7/13|n.972C>T|p.Trp324Cys|991/2151|972/-1|324/-1||WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000468169|havana|1/5|n.50C>T|p.Gly17Val|50/713|50/-1|17/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000484364|havana|1/4|n.47C>T|p.Gly16Val|47/732|47/-1|16/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000477636|havana|2/3|n.434C>T|p.Gly145Val|434/519|434/-1|145/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME,A|missense_variant|MODERATE|PPP2R3B|ENSG00000167393|transcript|ENST00000445792|havana|8/8|n.1314C>T|p.Trp438Cys|1314/1998|1314/-1|438/-1||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME	GT:PL:DP:DV:SP:DP4:DPR	1/1:69,12,0:4:4:0:0,0,3,1:0,4
diff -r 000000000000 -r 9f4ea174ce3d test-data/GRCh38_X400k_EFF.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GRCh38_X400k_EFF.vcf	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,85 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.2+htslib-1.2.1
+##samtoolsCommand=samtools mpileup -f /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa --BCF --output-tags DP,DPR,DV,DP4,INFO/DPR,SP --output /panfs/roc/galaxy/GALAXYP/files/000/144/dataset_144978.dat localbam_0.bam
+##reference=file:///panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/seq/GRCh38_canon.fa
+##contig=<ID=1,length=248956422>
+##contig=<ID=2,length=242193529>
+##contig=<ID=3,length=198295559>
+##contig=<ID=4,length=190214555>
+##contig=<ID=5,length=181538259>
+##contig=<ID=6,length=170805979>
+##contig=<ID=7,length=159345973>
+##contig=<ID=8,length=145138636>
+##contig=<ID=9,length=138394717>
+##contig=<ID=10,length=133797422>
+##contig=<ID=11,length=135086622>
+##contig=<ID=12,length=133275309>
+##contig=<ID=13,length=114364328>
+##contig=<ID=14,length=107043718>
+##contig=<ID=15,length=101991189>
+##contig=<ID=16,length=90338345>
+##contig=<ID=17,length=83257441>
+##contig=<ID=18,length=80373285>
+##contig=<ID=19,length=58617616>
+##contig=<ID=20,length=64444167>
+##contig=<ID=21,length=46709983>
+##contig=<ID=22,length=50818468>
+##contig=<ID=X,length=156040895>
+##contig=<ID=Y,length=57227415>
+##contig=<ID=MT,length=16569>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes 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=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
+##bcftools_callVersion=1.3+htslib-1.3
+##bcftools_callCommand=call -m --variants-only --output-type b --threads 1 input.bcf
+##bcftools_viewVersion=1.3+htslib-1.3
+##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets ^Mt --output-type v --threads 1 input.bcf
+##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --targets X --output-type v --threads 1 input.vcf.gz
+##bcftools_viewCommand=view --exclude 'DP < 5 || DPR[1] < 3 || MIN(DV/DP)<0.33' --regions X:1-400000 --output-type v --threads 1 input.vcf.gz
+##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -i vcf -o vcf -classic -formatEff -no-downstream -no-intergenic -no-intron -no-upstream -no-utr -no CDS -no CHROMOSOME_LARGE_DELETION -no CODON_CHANGE -no CODON_INSERTION -no CODON_CHANGE_PLUS_CODON_INSERTION -no CODON_DELETION -no CODON_CHANGE_PLUS_CODON_DELETION -no DOWNSTREAM -no EXON -no EXON_DELETED -no GENE -no INTERGENIC -no INTERGENIC_CONSERVED -no INTRAGENIC -no INTRON -no INTRON_CONSERVED -no MICRO_RNA -no NON_SYNONYMOUS_START -no NON_SYNONYMOUS_STOP -no RARE_AMINO_ACID -no SPLICE_SITE_ACCEPTOR -no SPLICE_SITE_DONOR -no SPLICE_SITE_REGION -no SPLICE_SITE_BRANCH -no SPLICE_SITE_BRANCH_U12 -no STOP_LOST -no START_GAINED -no START_LOST -no STOP_GAINED -no SYNONYMOUS_CODING -no SYNONYMOUS_START -no SYNONYMOUS_STOP -no REGULATION -no UPSTREAM -no UTR_3_PRIME -no UTR_3_DELETED -no UTR_5_PRIME -no UTR_5_DELETED -no NEXT_PROT -stats /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148027.dat GRCh38.78 /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148008.dat "
+##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_Rank  | Genotype [ | 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' ">
+##SnpSiftVersion="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani"
+##SnpSiftCmd="SnpSift filter -f /panfs/roc/galaxy/GALAXYP/files/000/148/dataset_148026.dat -e /panfs/roc/galaxy/GALAXYP/job_working_directory/000/126/126614/tmpzEvowV"
+##FILTER=<ID=SnpSift,Description="SnpSift 4.1l (build 2015-10-03), by Pablo Cingolani, Expression used: ( EFF[*].EFFECT has 'NON_SYNONYMOUS_CODING' | EFF[*].EFFECT has 'FRAME_SHIFT')">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	localbam_0.bam
+X	284201	.	T	C	219.0	.	DP=693;VDB=0.999766;SGB=-0.693147;RPB=1;MQB=1;MQSB=0.382033;BQB=1;MQ0F=0.001443;DPR=1,598;AC=2;AN=2;DP4=1,0,425,173;MQ=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|ensembl_havana||ENST00000381657|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000399012|3|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000430923|2|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000445062|3|C|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000429181|3|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|ensembl||ENST00000381663|2|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000443019|2|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000415337|2|C|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000447472|2|C|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V5A||PLCXD1|havana||ENST00000448477|1|C|WARNING_TRANSCRIPT_INCOMPLETE)	GT:PL:DP:DV:SP:DP4:DPR	1/1:246,255,0:599:598:0:1,0,425,173:1,598
+X	288851	.	G	GC	30.4966	.	DP=21;VDB=0.0115453;SGB=-0.670168;RPB=0.597928;MQB=1;BQB=0.968368;MQ0F=0;DPR=3,10;ICB=1;HOB=0.5;AC=1;AN=2;DP4=3,0,10,0;MQ=20;EFF=FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|ensembl_havana||ENST00000381657|3|GC),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000399012|4|GC),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000430923|3|GC|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000445062|4|GC|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|ensembl||ENST00000381663|3|GC),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000415337|3|GC|WARNING_TRANSCRIPT_NO_STOP_CODON),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000447472|3|GC|WARNING_TRANSCRIPT_INCOMPLETE),FRAME_SHIFT(HIGH||aaa/Caaa|K83Q?||PLCXD1|havana||ENST00000448477|2|GC|WARNING_TRANSCRIPT_INCOMPLETE)	GT:PL:DP:DV:SP:DP4:DPR	0/1:64,0,15:13:10:0:3,0,10,0:3,10
+X	290695	.	C	G	114.0	.	DP=910;VDB=0.336517;SGB=-0.693147;RPB=0.479982;MQB=0.997299;MQSB=0.999049;BQB=0.555736;MQ0F=0.010989;DPR=130,681;AC=2;AN=2;DP4=72,58,392,289;MQ=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|ensembl_havana||ENST00000381657|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000399012|5|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aGc|T135S||PLCXD1|havana||ENST00000484611|4|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000430923|4|G|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|ensembl||ENST00000381663|4|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000415337|4|G|WARNING_TRANSCRIPT_NO_STOP_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000447472|4|G|WARNING_TRANSCRIPT_INCOMPLETE),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D104E||PLCXD1|havana||ENST00000448477|3|G|WARNING_TRANSCRIPT_INCOMPLETE)	GT:PL:DP:DV:SP:DP4:DPR	1/1:141,210,0:811:681:2:72,58,392,289:130,681
+X	299221	.	G	C	77.0	.	DP=18;VDB=0.00122481;SGB=-0.683931;RPB=0.169694;MQB=1;MQSB=1;BQB=0.560355;MQ0F=0;DPR=3,13;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,2,9,4;MQ=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E286D||PLCXD1|ensembl_havana||ENST00000381657|7|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E286D||PLCXD1|havana||ENST00000399012|8|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E286D||PLCXD1|ensembl||ENST00000381663|7|C)	GT:PL:DP:DV:SP:DP4:DPR	0/1:110,0,10:16:13:3:1,2,9,4:3,13
+X	307850	.	G	C	40.3947	.	DP=24;VDB=0.351291;SGB=-0.651104;RPB=0.511891;MQB=1;MQSB=1;BQB=0.720273;MQ0F=0;DPR=7,8;ICB=1;HOB=0.5;AC=1;AN=2;DP4=5,2,6,2;MQ=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P359R||GTPBP6|havana||ENST00000485332|2|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Gac|H386D||GTPBP6|ensembl_havana||ENST00000326153|8|C)	GT:PL:DP:DV:SP:DP4:DPR	0/1:73,0,69:15:8:0:5,2,6,2:7,8
+X	311500	.	C	CAT	59.0	.	DP=56;VDB=0.625112;SGB=-0.692562;RPB=0.999818;MQB=0.915545;MQSB=0.982508;BQB=0.929674;MQ0F=0;DPR=11,22;ICB=1;HOB=0.5;AC=1;AN=2;DP4=11,0,19,3;MQ=18;EFF=FRAME_SHIFT(HIGH||cgt/cgtAT|R321R?||GTPBP6|havana||ENST00000485332|1|CAT|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||gtg/gtATg|V348V?||GTPBP6|ensembl_havana||ENST00000326153|7|CAT)	GT:PL:DP:DV:SP:DP4:DPR	0/1:92,0,40:33:22:3:11,0,19,3:11,22
+X	334496	.	A	G	30.4121	.	DP=159;VDB=0.0384616;SGB=-0.693147;RPB=0.000107797;MQB=0.271035;MQSB=0.730753;BQB=0.124283;MQ0F=0.0880503;DPR=52,60;ICB=1;HOB=0.5;AC=1;AN=2;DP4=48,4,58,3;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C1849R||PPP2R3B|havana||ENST00000477110|8|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C277R||PPP2R3B|havana||ENST00000479438|5|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	0/1:63,0,72:113:61:2:48,4,58,3:52,60
+X	338625	.	G	A	74.0	.	DP=308;VDB=6.22534e-11;SGB=-0.693147;RPB=0.0585974;MQB=0.956346;MQSB=0.973687;BQB=0.279044;MQ0F=0.0681818;DPR=146,132;ICB=1;HOB=0.5;AC=1;AN=2;DP4=122,24,108,24;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A519V||PPP2R3B|ensembl_havana||ENST00000390665|12|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A234V||PPP2R3B|havana||ENST00000468169|5|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	0/1:107,0,99:278:132:1:122,24,108,24:146,132
+X	338627	.	A	G	190.0	.	DP=301;VDB=1.9745e-09;SGB=-0.693147;MQSB=0.973119;MQ0F=0.0697674;DPR=0,271;AC=2;AN=2;DP4=0,0,229,42;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C472R||PPP2R3B|havana||ENST00000477110|8|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C262R||PPP2R3B|havana||ENST00000479438|4|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	1/1:217,255,0:271:271:0:0,0,229,42:0,271
+X	338856	.	A	G	182.0	.	DP=517;VDB=0.238596;SGB=-0.693147;RPB=0.857702;MQB=0.810962;MQSB=0.0368774;BQB=0.944745;MQ0F=0.0135397;DPR=15,390;AC=2;AN=2;DP4=7,8,244,146;MQ=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L157P||PPP2R3B|havana||ENST00000468169|5|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	1/1:209,255,0:405:390:6:7,8,244,146:15,390
+X	340856	.	CTG	C	107.0	.	DP=17;VDB=3.781e-05;SGB=-0.676189;MQSB=0.8618;MQ0F=0;DPR=0,11;AC=2;AN=2;DP4=0,0,6,5;MQ=18;EFF=FRAME_SHIFT(HIGH||gca/|A373||PPP2R3B|havana||ENST00000477110|6|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||cag/|Q420||PPP2R3B|ensembl_havana||ENST00000390665|10|C),FRAME_SHIFT(HIGH||gca/|A163||PPP2R3B|havana||ENST00000479438|2|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||agcagt/|SS112||PPP2R3B|havana||ENST00000468169|4|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||agcagt/|SS213||PPP2R3B|havana||ENST00000484364|4|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	1/1:134,33,0:11:11:0:0,0,6,5:0,11
+X	340928	.	C	CA	181.0	.	DP=65;VDB=2.0017e-11;SGB=-0.693147;MQSB=0.996914;MQ0F=0;DPR=0,50;AC=2;AN=2;DP4=0,0,21,29;MQ=19;EFF=FRAME_SHIFT(HIGH||ctg/ctgT|L349L?||PPP2R3B|havana||ENST00000477110|6|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||tgg/tgTg|W396C?||PPP2R3B|ensembl_havana||ENST00000390665|10|CA),FRAME_SHIFT(HIGH||ctg/ctgT|L139L?||PPP2R3B|havana||ENST00000479438|2|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||ggt/gTgt|G89V?||PPP2R3B|havana||ENST00000468169|4|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),FRAME_SHIFT(HIGH||ggt/gTgt|G190V?||PPP2R3B|havana||ENST00000484364|4|CA|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	1/1:208,151,0:50:50:0:0,0,21,29:0,50
+X	341347	.	A	C,G	170.0	.	DP=48;VDB=0.802018;SGB=-0.693136;MQSB=0.969233;MQ0F=0;DPR=0,20,15;AC=2;AN=2;DP4=0,0,20,15;MQ=19;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L332R||PPP2R3B|havana||ENST00000477110|5|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L332P||PPP2R3B|havana||ENST00000477110|5|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Ggg|W379G||PPP2R3B|ensembl_havana||ENST00000390665|9|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Cgg|W379R||PPP2R3B|ensembl_havana||ENST00000390665|9|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cGg|L122R||PPP2R3B|havana||ENST00000479438|1|C|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTg/cCg|L122P||PPP2R3B|havana||ENST00000479438|1|G|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS)	GT:PL:DP:DV:SP:DP4:DPR	1/1:197,105,0:35:35:0:0,0,20,15:0,20,15
+X	345580	.	G	A	41.8455	.	DP=6;VDB=0.910845;SGB=-0.556411;MQSB=1;MQ0F=0;DPR=0,4;AC=2;AN=2;DP4=0,0,3,1;MQ=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgT|W324C||PPP2R3B|ensembl_havana||ENST00000390665|7|A|WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G17V||PPP2R3B|havana||ENST00000468169|1|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G16V||PPP2R3B|havana||ENST00000484364|1|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gTg|G145V||PPP2R3B|havana||ENST00000477636|2|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tgG/tgT|W438C||PPP2R3B|havana||ENST00000445792|8|A|WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS&WARNING_REF_DOES_NOT_MATCH_GENOME)	GT:PL:DP:DV:SP:DP4:DPR	1/1:69,12,0:4:4:0:0,0,3,1:0,4
diff -r 000000000000 -r 9f4ea174ce3d tool-data/twobit.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/twobit.loc.sample	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>	<FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1	/depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1	/depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2	/depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1	/depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2	/depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
diff -r 000000000000 -r 9f4ea174ce3d tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Jun 14 17:51:39 2018 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the 2bit format -->
+    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, path</columns>
+        <file path="tool-data/twobit.loc" />
+    </table>
+</tables>