changeset 25:2ecf82136986

Define defuse.results.tsv ext as subclass of tabular, add defuse_results_to_vcf to generate vcf form DeFuse results
author Jim Johnson <jj@umn.edu>
date Fri, 09 Aug 2013 11:19:26 -0500
parents 2cbb285cc54e
children 8f0775c43739
files datatypes_conf.xml defuse.xml defuse_results_to_vcf.py defuse_results_to_vcf.xml test-data/mm10_results.filtered.tsv test-data/mm10_results.filtered.vcf
diffstat 6 files changed, 425 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Wed Aug 07 12:00:42 2013 -0500
+++ b/datatypes_conf.xml	Fri Aug 09 11:19:26 2013 -0500
@@ -2,5 +2,6 @@
 <datatypes>
     <registration>
         <datatype extension="defuse.conf" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="true"/>
+        <datatype extension="defuse.results.tsv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true"/>
     </registration>
 </datatypes>
--- a/defuse.xml	Wed Aug 07 12:00:42 2013 -0500
+++ b/defuse.xml	Fri Aug 09 11:19:26 2013 -0500
@@ -86,8 +86,8 @@
   <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
     <filter>keep_output == True</filter>
   </data>
-  <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
-  <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
+  <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
+  <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
   <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
     <filter>do_get_reads == True</filter>
   </data>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/defuse_results_to_vcf.py	Fri Aug 09 11:19:26 2013 -0500
@@ -0,0 +1,236 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                         University of Minnesota
+#         Copyright 2012, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#  James E Johnson
+#  Jesse Erdmann
+#
+#------------------------------------------------------------------------------
+"""
+
+
+"""
+This tool takes the defuse results.tsv  tab-delimited file as input and creates a Variant Call Format file as output.
+"""
+
+import sys,re,os.path
+import optparse
+from optparse import OptionParser
+
+"""
+http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42
+
+5. INFO keys used for structural variants
+When the INFO keys reserved for encoding structural variants are used for imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each alelle (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles).
+The following INFO keys are reserved for encoding structural variants. In general, when these keys are used by imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each alelle (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles).
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+For precise variants, END is POS + length of REF allele - 1, and the for imprecise variants the corresponding best estimate.
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+Value should be one of DEL, INS, DUP, INV, CNV, BND. This key can be derived from the REF/ALT fields but is useful for filtering.
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+One value for each ALT allele. Longer ALT alleles (e.g. insertions) have positive values, shorter ALT alleles (e.g. deletions) have negative values.
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+For precise variants, the consensus sequence the alternate allele assembly is derivable from the REF and ALT fields. However, the alternate allele assembly file may contain additional information about the characteristics of the alt allele contigs.
+##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
+##INFO=<ID=METRANS,Number=4,Type=String,Description="Mobile element transduction info of the form CHR,START,END,POLARITY">
+##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation">
+##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR">
+##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the length of the inserted material between breakends">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
+##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
+##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">
+##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">
+##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment">
+##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency">
+6. FORMAT keys used for structural variants
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood for imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel with respect to the genome's ancestor">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+These keys are analogous to GT/GQ/GL and are provided for genotyping imprecise events by copy number (either because there is an unknown number of alternate alleles or because the haplotypes cannot be determined). CN specifies the integer copy number of the variant in this sample. CNQ is encoded as a phred quality -10log_10p(copy number genotype call is wrong). CNL specifies a list of log10 likelihoods for each potential copy number, starting from zero. When possible, GT/GQ/GL should be used instead of (or in addition to) these keys.
+
+Specifying Complex Rearrangements with Breakends
+An arbitrary rearrangement event can be summarized as a set of novel adjacencies.
+Each adjacency ties together 2 breakends. The two breakends at either end of a novel adjacency are called mates.
+There is one line of VCF (i.e. one record) for each of the two breakends in a novel adjacency. A breakend record is identified with the tag SYTYPE=BND" in the INFO field. The REF field of a breakend record indicates a base or sequence s of bases beginning at position POS, as in all VCF records. The ALT field of a breakend record indicates a replacement for s. This "breakend replacement" has three parts:
+the string t that replaces places s. The string t may be an extended version of s if some novel bases are inserted during the formation of the novel adjacency.
+The position p of the mate breakend, indicated by a string of the form "chr:pos". This is the location of the first mapped base in the piece being joined at this novel adjacency.
+The direction that the joined sequence continues in, starting from p. This is indicated by the orientation of square brackets surrounding p.
+These 3 elements are combined in 4 possible ways to create the ALT. In each of the 4 cases, the assertion is that s is replaced with t, and then some piece starting at position p is joined to t. The cases are:
+REF   ALT    Meaning
+s     t[p[   piece extending to the right of p is joined after t
+s     t]p]   reverse comp piece extending left of p is joined after t
+s     ]p]t   piece extending to the left of p is joined before t
+s     [p[t   reverse comp piece extending right of p is joined before t
+
+Examples:
+#CHROM POS    ID     REF ALT           QUAL FILT INFO
+2      321681 bnd_W  G   G]17:198982]  6    PASS SVTYPE=BND;MATEID=bnd_Y
+2      321682 bnd_V  T   ]13:123456]T  6    PASS SVTYPE=BND;MATEID=bnd_U
+13     123456 bnd_U  C   C[2:321682[   6    PASS SVTYPE=BND;MATEID=bnd_V
+13     123457 bnd_X  A   [17:198983[A  6    PASS SVTYPE=BND;MATEID=bnd_Z
+17     198982 bnd_Y  A   A]2:321681]   6    PASS SVTYPE=BND;MATEID=bnd_W
+17     198983 bnd_Z  C   [13:123457[C  6    PASS SVTYPE=BND;MATEID=bnd_X
+"""
+
+vcf_header =  """\
+##fileformat=VCFv4.1
+##source=defuse
+##reference=%s
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
+##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction">
+##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SPLICESCORE,Number=1,Type=Integer,Description="number of nucleotides similar to GTAG at fusion splice">
+##INFO=<ID=GENE,Number=2,Type=String,Description="Gene Names at each breakend">
+##INFO=<ID=GENEID,Number=2,Type=String,Description="Gene IDs at each breakend">
+##INFO=<ID=ORF,Number=0,Type=Flag,Description="fusion combines genes in a way that preserves a reading frame">
+##INFO=<ID=EXONBND,Number=0,Type=Flag,Description="fusion splice at exon boundaries">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO\
+"""
+
+def cmp_alphanumeric(s1,s2):
+  if s1 == s2:
+    return 0
+  a1 = re.findall("\d+|[a-zA-Z]+",s1)
+  a2 = re.findall("\d+|[a-zA-Z]+",s2)
+  for i in range(min(len(a1),len(a2))):
+    if a1[i] == a2[i]:
+      continue
+    if a1[i].isdigit() and a2[i].isdigit():
+      return int(a1[i]) - int(a2[i])
+    return 1 if a1[i] >  a2[i] else -1
+  return len(a1) - len(a2)
+
+def __main__():
+  # VCF functions
+  chr_dict = dict()
+  def add_vcf_line(chr,pos,id,line):
+    if chr not in chr_dict:
+      pos_dict = dict()
+      chr_dict[chr] = pos_dict
+    if pos not in chr_dict[chr]:
+      id_dict = dict()
+      chr_dict[chr][pos] = id_dict
+    chr_dict[chr][pos][id] = line
+
+  def write_vcf():
+    print >> outputFile, vcf_header % (refname)
+    for chr in sorted(chr_dict.keys(),cmp=cmp_alphanumeric):
+      for pos in sorted(chr_dict[chr].keys()):
+        for id in chr_dict[chr][pos]:
+          print >> outputFile, chr_dict[chr][pos][id]
+  #Parse Command Line
+  parser = optparse.OptionParser()
+  # files
+  parser.add_option( '-i', '--input', dest='input', help='The input defuse results.tsv file (else read from stdin)' )
+  parser.add_option( '-o', '--output', dest='output', help='The output vcf file (else write to stdout)' )
+  parser.add_option( '-r', '--reference', dest='reference', default=None, help='The genomic reference id' )
+  (options, args) = parser.parse_args()
+
+  # results.tsv input 
+  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
+  # vcf output 
+  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
+
+  refname = options.reference if options.reference else 'unknown'
+
+  svtype = 'SVTYPE=BND'
+  filt = 'PASS'
+  columns = []
+  try:
+    for linenum,line in enumerate(inputFile):
+      ## print >> sys.stderr, "%d: %s\n" % (linenum,line)
+      fields = line.strip().split('\t')
+      if line.startswith('cluster_id'):
+        columns = fields
+        ## print >> sys.stderr, "columns: %s\n" % columns
+        continue
+      cluster_id = fields[columns.index('cluster_id')]
+      gene_chromosome1 = fields[columns.index('gene_chromosome1')]
+      gene_chromosome2 = fields[columns.index('gene_chromosome2')]
+      genomic_strand1 = fields[columns.index('genomic_strand1')]
+      genomic_strand2 = fields[columns.index('genomic_strand2')]
+      gene1 = fields[columns.index('gene1')]
+      gene2 = fields[columns.index('gene2')]
+      gene_info = 'GENEID=%s,%s' % (gene1,gene2)
+      gene_name1 = fields[columns.index('gene_name1')]
+      gene_name2 = fields[columns.index('gene_name2')]
+      gene_name_info = 'GENE=%s,%s' % (gene_name1,gene_name2)
+      genomic_break_pos1 = int(fields[columns.index('genomic_break_pos1')])
+      genomic_break_pos2 = int(fields[columns.index('genomic_break_pos2')])
+      breakpoint_homology = int(fields[columns.index('breakpoint_homology')])
+      homlen = 'HOMLEN=%s' % breakpoint_homology
+      orf = fields[columns.index('orf')] == 'Y'
+      exonboundaries = fields[columns.index('exonboundaries')] == 'Y'
+      read_through = fields[columns.index('read_through')] == 'Y'
+      span_count = int(fields[columns.index('span_count')])
+      splitr_count = int(fields[columns.index('splitr_count')])
+      splice_score = int(fields[columns.index('splice_score')])
+      probability = fields[columns.index('probability')] if columns.index('probability') else '.'
+      splitr_sequence = fields[columns.index('splitr_sequence')]
+      split_seqs = splitr_sequence.split('|')
+      mate_id1 = "bnd_%s_1" % cluster_id
+      mate_id2 = "bnd_%s_2" % cluster_id
+      ref1 = split_seqs[0][-1]
+      ref2 = split_seqs[1][0]
+      b1 = '[' if genomic_strand1 == '+' else ']'
+      b2 = '[' if genomic_strand2 == '+' else ']'
+      alt1 = "%s%s%s:%d%s" %  (ref1,b2,gene_chromosome2,genomic_break_pos2,b2) 
+      alt2 = "%s%s:%d%s%s" %  (b1,gene_chromosome1,genomic_break_pos1,b1,ref2) 
+      #TODO evaluate what should be included in the INFO field
+      info = ['DP=%d' % (span_count + splitr_count),'SPLITCNT=%d' % splitr_count,'SPANCNT=%d' % span_count,gene_name_info,gene_info,homlen,'SPLICESCORE=%d' % splice_score]
+      if orf:
+        info.append('ORF')
+      if exonboundaries:
+        info.append('EXONBND')
+      info1 = [svtype,'MATEID=%s' % mate_id2] + info
+      info2 = [svtype,'MATEID=%s' % mate_id1] + info
+      qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.'
+      vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) )
+      vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) )
+      add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1)
+      add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2)
+    write_vcf()
+  except Exception, e:
+    print >> sys.stderr, "failed: %s" % e
+    exit(1)
+
+if __name__ == "__main__" : __main__()
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/defuse_results_to_vcf.xml	Fri Aug 09 11:19:26 2013 -0500
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="0.6.1">
+  <description>generate a VCF from a DeFuse Results file</description>
+  <requirements>
+    <requirement type="package" version="0.6.1">defuse</requirement>
+  </requirements>
+  <command interpreter="python">defuse_results_to_vcf.py  --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
+  </command>
+  <inputs>
+    <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> 
+  </inputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <outputs>
+    <data name="vcf" metadata_source="input_file" format="vcf"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
+      <output name="vcf" file="mm10_results.filtered.vcf"/>
+    </test>
+  </tests>
+  <help>
+**Defuse Results to VCF**
+
+Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file.   
+
+This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file.   
+
+.. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
+.. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_results.filtered.tsv	Fri Aug 09 11:19:26 2013 -0500
@@ -0,0 +1,46 @@
+cluster_id	splitr_sequence	splitr_count	splitr_span_pvalue	splitr_pos_pvalue	splitr_min_pvalue	adjacent	altsplice	break_adj_entropy1	break_adj_entropy2	break_adj_entropy_min	breakpoint_homology	breakseqs_estislands_percident	cdna_breakseqs_percident	deletion	est_breakseqs_percident	eversion	exonboundaries	expression1	expression2	gene1	gene2	gene_align_strand1	gene_align_strand2	gene_chromosome1	gene_chromosome2	gene_end1	gene_end2	gene_location1	gene_location2	gene_name1	gene_name2	gene_start1	gene_start2	gene_strand1	gene_strand2	genome_breakseqs_percident	genomic_break_pos1	genomic_break_pos2	genomic_strand1	genomic_strand2	interchromosomal	interrupted_index1	interrupted_index2	inversion	library_name	max_map_count	max_repeat_proportion	mean_map_count	min_map_count	num_multi_map	num_splice_variants	orf	read_through	repeat_proportion1	repeat_proportion2	span_count	span_coverage1	span_coverage2	span_coverage_max	span_coverage_min	splice_score	splicing_index1	splicing_index2	probability
+8647	GTGCTCCTGCTGCCAGGCGCAGCTGGGCGACATTGGCACGTCCTGTTACACCAAGAGCGGCATGATCCTTTGCAGAAATGACTACATTAGGT|GAAGATTGTAAAAAATTGACATCAGAAATATTTACAGAAATAGATACCTGTTTGAATAAAGTTAGAGATGAAATTTTTGCTAAACTTCAACCGAAGCTTAGATGCACATTAGGTGACATGGAAAGTCCTGTGTTTGCACTTCCTG	4	0.849232794977309	0.875860929877954	0.794775556794258	N	N	3.72551845106187	3.02448896101185	3.02448896101185	1	0.0366733649981732	0	N	0	N	Y	2482	2085	ENSMUSG00000028266	ENSMUSG00000041264	+	-	3	5	144205220	149215434	coding	coding	Lmo4	Uspl1	144188530	149184350	-	+	0	144201813	149198645	-	-	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	5	0.831776131589327	0.982288003019777	0.982288003019777	0.831776131589327	4	-	-	0.950339354539546
+12095	CTTCCAGGGTCCCCCGAGCCTAATGGATGCCGAGACAGACGAGGGCATGGACTATACAGGCTGTAGCCCTGGAGCGGCGTCCTCAGAGTCTTCCACCATGGACCGTAGCTGTTCCAGCACCC|CTGGCCCTTGACATCTAGCACCCCTTCACCCTCTTCCTGGGGACCCAGCAGGTGGTATGTGGCCGTGGAGCCCTCCGGGCTGTGGCTGTCCTTCCCAGGAGAGGATGACGTAGACTCGTTGCTGACAGGGGAGATGTCACTGCTGC	6	0.869976758916331	0.907802910133282	0.774396849342807	Y	Y	3.64400585547602	3.28189243439864	3.28189243439864	0	0.983667499542934	0	Y	0	N	N	0	1453	ENSMUSG00000086606	ENSMUSG00000028975	-	+	4	4	148948914	149099876	intron	coding	Gm13205	Pex14	148947492	148960535	-	-	0	148948907	148961548	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	5	0.760481034595956	1.02189639023832	1.02189639023832	0.760481034595956	4	-	-	0.976704594819493
+4068	CGACACGCCGGGGCTGGCTGAGGAAAACAAAACGAAGCCCCTGGAGACCCGGCTTATCTCAGAGACCACAGCTATTTGCAAACCAGAGCAGGTGGCCAAACAAATTGTCAAAGATGCCATA|TACCGTTCCCCAGCTGAAGAGTTCTGAATCCACGCCGGATCCTTCTCAACAGTCTGTTTTACGGGAACTTTTATTAACCACTCCTTCCCCGTGATGCAGTTCTGAATCCTCCCTGTAGCAGGGGGTCTTCACTCATGCCTGAAGATGTTTCTTTTCC	8	1	0.541521196503195	0.26082452496772	N	Y	3.46128890676658	3.81976875220098	3.46128890676658	2	0	0	N	0.794128973014604	N	N	775	35409	ENSMUSG00000009905	ENSMUSG00000022816	+	-	1	16	106759742	37836514	coding	intron	Kdsr	Fstl1	106720410	37776873	-	+	0.00358422939068104	106734547	37799068	-	-	Y	-	-	N	dataset_6344_files	4	1	1.81818181818182	1	4	1	N	N	0	1	11	0.974366325576069	1.17240826166877	1.17240826166877	0.974366325576069	4	-	-	0.913877182950088
+12868	GCGGTCTCGGCTCCAGCGGCAGTAGCAGCGGCGCCGGTCCCGTGTGCAGGAGCTCCTTTGCGGCCCAGTTTCTTGGCCATCGCCTGCTCTCCCCACAGCGCCAGGACGAGTCCCGTGCGCGTCCGTCCGCGGAGGTCTTTCTCATCTCGCTCGGCTGCGGGAAATCGGGCTGAAGCGACTGAGTCCGCGATGGAGA|AAACTTTAGAAACTGTTCCTTTGGAGAGGAAAAAGAGAGAAAAGGAAAACTT	69	1	0.439895614069599	0.332872660216425	N	Y	3.30124852419771	2.96787791690762	2.96787791690762	0	0.0997837503861599	0.00401606425702794	N	0.540315106580167	N	N	41631	0	ENSMUSG00000004980	ENSMUSG00000085456	+	+	6	10	51469894	73327027	coding	intron	Hnrnpa2b1	Gm15398	51460434	73201399	-	-	0.0997837503861599	51467295	73201702	-	-	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	41	1.14864322933764	0.720872647377417	1.14864322933764	0.720872647377417	1	-	-	0.520098627306064
+5160	TACGGATTCATTCAGTGTTCAGAACGGCAAGCTAGACTTTTCTTCCACTGTTCACAATATAATGGCAACCTCCAAGACTTAAAAGTAGGAGATGATGTTGAATTTGAAGTATCATCTGACCGGAGGACTGGGAAACCTATTGCTATTAAATTGGTGAAGATAAAACCAGAAATACATCCTGAAGAACGAATGAACGGAC|AAGAAGTATTTTATCTGACTTACACCCCTGAAGATGTGGAAGGGAAAGTTCAGC	33	1	0.767323324767952	0.471361574015707	N	Y	3.3022815939676	3.55553920790569	3.3022815939676	91	0.944663167104112	0.00393700787401585	N	0.944663167104112	N	N	10681	0	ENSMUSG00000068823	ENSMUSG00000087940	+	-	3	18	103058189	28309891	coding	upstream	Csde1	SNORA17	103020546	28309760	+	+	0	103040040	28188917	+	-	Y	-	-	N	dataset_6344_files	2	0	1.03333333333333	1	1	1	N	N	0	0	30	1.1011131646754	0.67334258271517	1.1011131646754	0.67334258271517	3	-	-	0.835626866413202
+8748	GGGGTAGATCACCTTCCGAGGGTCTCCATGGGTCCAGGCTATGATGCCCACAGCCACATAGCCTACGATGGCCAGGAAGAGCAACACACAGCAAATGACATCTGTGCATCCCCTGTTGTAAATGGGTCCTTTGAAGGTGGGGTCGTATTTCTGAGGCGTCCC|ATAGACTGCGTCCTTCCGATCGTCCTCCATGGCCTCAACCGAGGAGAGCTGAGTCCGAAGCCAGCGCGACCCCAACCCAAGCGGGCGGGAGACACCGCGCGCTGCTGGCCCCGCC	51	1	0.844316325604616	0.871821260113135	Y	Y	3.29447165365238	3.73336824417043	3.29447165365238	2	0	0	Y	0.991335627150454	N	N	6343	2	ENSMUSG00000057193	ENSMUSG00000003309	-	-	9	9	21355025	21312333	coding	upstream	Slc44a2	Ap1m2	21337828	21295457	+	-	0	21337962	21320850	-	+	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	52	1.3070767782118	0.958522970688653	1.3070767782118	0.958522970688653	2	-	-	0.74403558965543
+11169	CCACATCTGACAGAACTTGCCACTGTGCCTGCAACCTTGTCTGAGAGGAACCCTTCTCTG|AGGATGGACACTTCTCACACTACAAAGTCCTGTTTGCTGATTCTTCTTGTGGCCCTACTGTGTGCAGAAAGAGCTCAGGGACTGGAGTGTTACCAGTGCTATGGAGTCCCATTTGAGACTTCTTGCCCATCAATTACCTGCCCCTACCCTGATGGAGTCTGTGTTACTCAGGAGGCAGCAGTTATTGTGGATTCTCAAACAAGGAAAGTAAAGAACAATCTTTGCTTACCC	410	1	0.87136611677351	0.978590093310325	Y	Y	3.45293525254824	3.55976477294109	3.45293525254824	0	0	0.152910958904109	Y	0.966780821917808	N	Y	1416	5049	ENSMUSG00000079018	ENSMUSG00000075602	+	-	15	15	75048837	74997634	utr5p	utr5p	Ly6c1	Ly6a	75045017	74994878	-	-	0	75048442	74996568	-	+	N	-	-	N	dataset_6344_files	2	0	1.53082191780822	1	155	2	Y	Y	0	0	292	0.728794324821125	1.49719703686079	1.49719703686079	0.728794324821125	4	-	-	0.93076564160702
+12600	CTAAAATCGCCAAGCCTGTCAAGTTTGAGCTTTCTGGCTGCACCAGTGTGAAGACATACAGGGCTAAGTTCTGCGGGGTGTGCACAGACGGCCGCTGCTGCACACCGCACAGAACCACCACTCTGCCAGTGGAGTTCAAATGCCCCGATGGCGAGATCATGAAAAAGAATATGATGTTCATCAAG|CCCTGCCCCTGCCATTACCACTGTTCTGGGGTCCCTGGCATGCTCCCATTAC	1	1	0.820229055260519	0.873212995139997	N	N	3.28548615724827	3.17936818462789	3.17936818462789	0	0.482950872656755	0.482950872656755	N	0.482950872656755	N	N	7298	2735	ENSMUSG00000019997	ENSMUSG00000015133	+	+	10	7	24598683	66388350	coding	intron	Ctgf	Lrrk1	24595442	66226912	+	-	0.482950872656755	24597524	66355922	+	-	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	5	1.02981806768202	0.41192722707281	1.02981806768202	0.41192722707281	3	-	-	0.58275607356487
+1855	CCTGGTCACACAGCTCTCCTAGGAAGCGCGTCTCCAATGACTCGTTTGTCAACCCCAGGTGTCTTCCACGTTGTGGTTTCAACTTCATAATTCTCTGAAGTCTTATTCAT|CTCTTTGTCAAGCCCACGGCGTCAGCCTCTGACACGAGGGCGGGCGTCCTCGCCTCCGGGGTGAAAGAGGGGCGCAGCGGGCCGCCCCTCCCCCCCGCCCCCCTACGACACGCGGGGCCCTGCCTCGGGCGACCTGTTGGCAGGGCGCGTCACGTGACGCGGCGGGCCGCGCCGTCCCC	4	0.769054178023969	0.159736089157399	0.42467594723228	Y	Y	3.40528677690917	3.51935717616377	3.40528677690917	0	0.981880877742947	0	Y	0.0487460815047023	N	N	0	8476	ENSMUSG00000097162	ENSMUSG00000039361	-	-	7	7	90129474	90209447	intron	upstream	AC130210.1	Picalm	90124858	90130232	-	+	0	90125032	90129872	+	-	N	-	-	N	dataset_6344_files	1	0.23489932885906	1	1	0	1	N	Y	0	0.23489932885906	9	0.887227873695282	1.18032993911247	1.18032993911247	0.887227873695282	4	-	-	0.949188379753168
+1870	CTGGGTCAAGAGCCGGAGGGACAGGACCAGAGCACCCCTTACGCCAGAACTAGCTCTCCTTGTTCCTACTGGGTGACCTCATCTCGCCACGCCTCCTCAGGTGAACACCCGGGCTGGTAACGTCACTTCCTGC|CAGGGTTTCACTATGTAGACCCTGGTCGGCCTGGAACTCTATAGACCAGACTGGCCTCGAGCTCAGATCCGTCCCCCTCTGCTGTCCCAGCACGGGGATTAAGAACGCGCCACCACTACAGCTGACCGGA	2	0.788660184540219	0.550050944563454	0.182990959521483	Y	Y	3.63552422018169	3.63193049733206	3.63193049733206	4	0	0	Y	0	N	N	1543	697	ENSMUSG00000044786	ENSMUSG00000003444	-	+	7	7	28379255	28392708	downstream	intron	Zfp36	Med29	28376784	28386146	-	-	0	28376683	28392166	+	-	N	-	-	N	dataset_6344_files	1	0.869158878504673	1	1	0	1	N	Y	0	0.869158878504673	8	1.08526980978798	0.847619486476743	1.08526980978798	0.847619486476743	1	-	-	0.841318537051835
+3153	CAGAGCTATGTAGAAAGACCCTGTCTGGTAAGTAAATAAAAACATAGCCAGGCATGGTGGCAATCAGCAGGTAGATTGGAGTTTGAGGTCATCCTGGTCTGGAGAGTGAGTTCCAGGAGAGCCAAGATTACACAAACCC|TGTCTTTTTCTTTCTTTCTGTTGTTGTTGTTGCTGTTCCTGCTGCTGCTGCTGTTTTGCTTTTCATGACAGGGTTTCTCTGTGTCTCTGTGCAACTTTGGCTATCCTGGAATTCACACTGTAGACCAGGCTGGCCTTGAATTCACACAGATCCATCTG	16	1	0.656277930324132	0.671834466829468	Y	Y	3.40740634961144	2.41484814640267	2.41484814640267	0	0.9928298971561	0	Y	0.985659794312201	N	N	0	30	ENSMUSG00000097379	ENSMUSG00000047786	-	-	17	17	17395303	17459387	intron	intron	AC154200.1	Lix1	17389943	17402672	-	+	0	17395298	17411818	+	-	N	-	-	N	dataset_6344_files	1	0.709459459459459	1	1	0	1	N	Y	0.685314685314685	0.709459459459459	25	1.13279987445023	1.17240826166877	1.17240826166877	1.13279987445023	1	-	-	0.81041504882724
+11596	GCCGGAGCAGATCAGGCTGAAAGTTGGTGGTGTGGACCCAAAGCAGCTAGCCGTCTATGAAGAGTTTGCACGAAATGTGCCTGGCTTCTTACCTACAAATGACTTAAGTCAGCCTACAGGGTTTTTAGCTCAGCCCATGAA|GTTTCTGGATCAAGATGTGAGCTTTCAGCTGTTGCTTGAGCATCATGCCTGCCTGCCTGCCACCACGCTCTCGGCCAGGATAGTGATGGATTCCTTCCCTCGGACTATAAGCCCCAAATGAACCCTTCCTTCTATGAGTTGCCT	8	0.974101244860941	0.684001003266195	0.530048089286902	N	Y	3.49640736351508	3.32783191248938	3.32783191248938	0	0	0	Y	0	N	N	6004	544	ENSMUSG00000036550	ENSMUSG00000036564	+	+	8	8	95807462	95715119	coding	intron	Cnot1	Ndrg4	95719451	95676980	-	+	0	95739809	95682960	-	+	N	-	-	N	dataset_6344_files	1	1	1	1	0	1	N	N	0	1	16	1.12487819700652	1.17240826166877	1.17240826166877	1.12487819700652	1	-	-	0.873952352979217
+3783	CTCTGTTCGTGCATCCCTGGGATATGCAGATGGATGGACGAATGGCCAAATACTGGCTGCCTTGGCTCGTAGGTTTGTGCTGGACTAGGGTTGGGAACACAGCACCAACTCTTGGGTTTTTTCTGTTATCCATGGAATTCTGTTCT|TTTCTTTCCGAGTGACCCCCACTTTACGGCGTCTCCCAATGACAAGAGGCGCAGAGCATTGTGGTCCCGCGGGTCCGAGA	2	0.867750583125795	0.425502304916607	0.692249690893423	Y	Y	3.22804973003685	3.42048008240514	3.22804973003685	0	0	0	Y	0.987555066079295	N	N	0	752	ENSMUSG00000026348	ENSMUSG00000026349	+	-	1	1	127767564	127808061	intron	upstream	Acmsd	Ccnt2	127729413	127774164	+	+	0	127753955	127773930	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	6	1.02189639023832	0.649577550384046	1.02189639023832	0.649577550384046	3	-	-	0.711778687837589
+4912	TAACAGAACAAGAGCAATGTGCTAGAATAGAAGACCAGAAAATGAAATGGTGGAGTTTGA|GGCTGGATAGACAGTTTGAAAGGTAAGTATTGAAAAACACTTGAATTTGGGTCAGTACAAAGGGACATGCAGAGACTTTGAATCATCAAAACTCCAGCATGCATTGTCTTACGGATGTTTAGATAGGTGTGTTTTGGACAACACTCTGGGTTCTTGTAATGATGTTGATCAAATGTCTGAG	15	1	0.895469718833858	0.922600375157455	N	Y	3.29868787111796	3.36447795254773	3.29868787111796	0	0.933608815426997	0	N	0.933608815426997	N	N	0	0	ENSMUSG00000088422	ENSMUSG00000053332	+	-	5	1	79639109	161038539	downstream	intron	7SK	Gas5	79638815	161034422	-	+	0.933608815426997	79638354	161036831	-	-	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	5	0.459457291735057	0.808011099258204	0.808011099258204	0.459457291735057	1	-	-	0.592482164323654
+5141	TCTTATCTCTGTGTTGGTGTGCTTCTCTGTTTGATGACAGAGCAGGGTCTTGCTGAACTGCACCTACTGGAGTAGGCAACTGTTTACCAATCCAGTCATATTCATAATCAAACATATACCCTTTTCGATCAAACAAGTCAGTAAAAAGCTTTCTTAGGTAATCATAGTCTGGCTTTTCAAAAAAATCCAGCCTTCGTACGTAACGGAGAT|ACGTTGCCATTTCTGGGAAGTTCTCACACAACACTTCTATTGGTGTGGCTCGTTT	9	1	0.853164221793603	0.997416520640376	N	Y	3.60831833727406	3.59847695253922	3.59847695253922	266	0.981886534518113	0.981886534518113	N	0.981886534518113	N	N	2227	0	ENSMUSG00000073563	ENSMUSG00000083798	-	+	18	X	53955684	53418967	coding	intron	Csnk1g3	Gm14584	53862113	53418331	+	+	0	53932206	53418862	-	+	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	17	1.2040949714436	0.990209680463485	1.2040949714436	0.990209680463485	2	-	-	0.788432447586541
+1886	CGCGGGGCGCCCGCCGGCTCACACTCCCGCGCTCTCTCTCCGGGTTTGGCGGCCGCCAGGAGGAGGAAGAGGAGGAGGAGGAGAAGAAGAAGGAGGAGGAGTGGAGCGAGCGCAGAAG|TAGCTGCTGCTGCTGGTGGTGACAATGTCAAATAACGGCGTAGACATCCAGGACAAACCCCCAGCCCCTCCGATGAGAAACACCAGCACTATGATTGGAGCCGGCAGCAAAGACACTGGAACCCTAAACCACGGCTCCAAACCTCTGCCTCCAAACCCAGAGGAG	18	1	0.708948431161152	0.783431002546196	Y	Y	2.65454686157692	3.52101274054962	2.65454686157692	0	0.983110527572213	0	Y	0.983110527572213	N	N	16	2476	ENSMUSG00000042797	ENSMUSG00000030774	-	-	7	7	97738247	97912381	upstream	utr5p	Aqp11	Pak1	97726379	97842935	-	+	0	97788974	97854436	+	-	N	-	-	N	dataset_6344_files	1	0.366666666666667	1	1	0	1	N	Y	0.366666666666667	0	18	0.950601293244945	1.29915510076809	1.29915510076809	0.950601293244945	4	-	-	0.970255256454431
+9297	GTGCTGGGCAGGAAGTCCCGGGCCAGGCAGCCCATGGCCACCAGATTCTTATCAGACAGGGGGCTCTCGCAGGAGACGAGGGGGAAGACATTTGGGAAGGACTGACTCT|CATTTGCGGTGCCTGGTTTCGGAGAGGTCCAGAGTCTTTGTGTGGAATTGTTCCTTCAAAGCCACCGAGGCTGGCTGGTCCATGAGCAGCCAGGTGGATGGGTGGCAGAAGCC	20	0.318065745640931	0.64026046146514	0.56228459372928	N	Y	3.05166433869594	3.43614916339873	3.05166433869594	0	0	0	Y	0.990866828485621	N	N	1488	0	ENSMUSG00000076617	ENSMUSG00000092748	-	+	12	12	113422730	113425227	coding	upstream	Ighm	AC073553.3	113418950	113425150	-	-	0	113422730	113426655	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	6	0.665420905271462	0.879306196251575	0.879306196251575	0.665420905271462	4	-	-	0.831715391282697
+5326	GTACACTGTAGCTGTCTTCAGACACACCAGAAGAGGGAGTCAGATCTTGTTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCC|GAGTTACACAGTTTTAATGACTTCCTTACTTCTCATGATCTCTATACTGTTTAACTTTCCTCGGTGTGTTTTTAAGTCTTTGCTATCTTGTTCTAGTTTTTTGCAAGAATCACGAAAATGATTCTTGGATTTCCAGACTCTTCCTTTTGAAAGCTG	7	1	0.607242467201396	0.755062684986217	N	Y	3.49744043328497	3.49528100778935	3.49528100778935	9	0.960654062340317	0	N	0.967211718616931	N	N	2963	0	ENSMUSG00000039671	ENSMUSG00000073647	+	+	2	18	165899016	4198969	utr3p	downstream	Zmynd8	Gm10557	165784152	4198216	-	-	0.00979390223130638	165827729	4198107	-	-	Y	-	-	N	dataset_6344_files	476	0.993464052287582	298.461538461538	168	13	1	N	N	0.993464052287582	0	13	1.21201664888731	1.34668516543034	1.34668516543034	1.21201664888731	1	-	-	0.536685629613134
+1721	CGTACCTCCCTCCCAGCAACCGGCCTGGCGGCAGCGCGGCTACAAAACTGAGGAGGCGGAGCCGAGACGGAGTCGGTACTGCGCTCTGACTCCTAGACCAGGTTTAAGTTTTTGAAGTTGAAGTAGGTCTACACAGTAGGAACCCATGTCTTTTCTTGTAAGTAAACCAGAGCGCATTA|GGGCCAATGAGGCGAGCTCAGAGTCCATAGCATTGTTCTCCAAACCA	8	0.903915350299452	0.697638501162383	0.785699237375327	N	Y	3.65384724021086	3.68527868815389	3.65384724021086	142	0.936451401255975	0.343331146311745	N	0.936451401255975	N	N	800	0	ENSMUSG00000069631	ENSMUSG00000087034	+	+	11	5	106202168	60232198	coding	upstream	Strada	Cbfa2t2-ps1	106163330	60231482	-	+	0	106187103	60176541	-	+	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	5	0.879306196251575	0.475300646622473	0.879306196251575	0.475300646622473	1	-	-	0.738431070020728
+1027	GCGGCAGCCGGTTCGGGCGGGCGGCATCATGGACGAGAAGTTGTTCACCAAGGAGCTGGACCAGTGGATCGAGCAGCTGAACGAGTGCAAGCAGCTCTCCGAGTCCCAGGTCAAGAGCCTCTGCGAGAAG|TGCTGCCTTTGACAGAGATGACATGCTTATACCATGCGGGTGGCACGAAGCTGTGAAGTGGTGATGACGGGGATGAGCTTGGACATCCTACGAGAGTGGCAAAGGTGAAGCAAGCCCAGGTGCTGGCTGTGCAAGG	2	1	0.148625497007208	0.21082086276253	N	N	3.33524062522047	3.43039601505348	3.33524062522047	3	0	0	N	0	N	N	10063	1785	ENSMUSG00000020349	ENSMUSG00000035021	+	+	11	12	52127778	55014348	coding	intron	Ppp2ca	Baz1a	52098681	54892989	+	-	0	52099150	54980379	+	-	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	10	0.942679615801238	1.07734813234427	1.07734813234427	0.942679615801238	4	-	-	0.83438414122479
+7746	AAAGGGAGTCGAGACTGCCTTCTGCGCGCGCCCGGCTTTGCGCGCCTCCGCCACCAGATGTGGGGGGATGGGAGGCCCCCTCCGCGGCCCCTTCCCCACCCAGCCCAGAAAGCTGAACTGGCAAG|AGGCAATTTGAAACAAGCCACTCCAACCTCTTTTTCAAAGTTATAGGAGGTTCCCTGTCTTGAAGTCTCCTGCCTTGGATTTTCTGAGGTGCTGCTATTCTGGGCAACTATCAAAATCCTACCTGTTAAAACATGATGGATTAGAGAAAAAAAACAACCCAC	26	1	0.707412664952061	0.861438628736582	Y	Y	3.14574680596571	3.22961716614005	3.14574680596571	0	0	0	Y	0	N	N	0	0	ENSMUSG00000087658	ENSMUSG00000087626	+	-	6	6	52162119	52174059	intron	intron	Gm15051	Gm15050	52156902	52172881	+	+	0	52158684	52173634	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	20	1.02189639023832	1.23578168121843	1.23578168121843	1.02189639023832	2	-	-	0.746044848941682
+8762	GGGGGCGGGGCTGAGCGCGGCCGCAGCCATTTTGGTGGAAGAGAAACAATAGGACGGAAGCGTCGCGGGACTGGGCTGTGGCCGCAG|AGTGTCCTGGCCTGCACAAACCGAGGAGCTGAGATCAAACAGGTGGCTGTAAGGACAGACAGTGAACGGAGGGCAAGCCGGCCTCTGGACCCCGCTGCCTCCCCTTTCTCCCTGCTGCTCGTGTCCAGAGGATGAGCCCAGCCTTCAGGACCATGGACGTGGAGCCCCGCACCAAGGGCATCC	28	0.498252441818171	0.890426951441059	0.30351938174741	Y	Y	3.55041790174621	3.58424216889964	3.55041790174621	0	0.977096322687365	0.0380455528693218	Y	0.977096322687365	N	N	0	714	ENSMUSG00000088626	ENSMUSG00000032599	-	-	9	9	108795388	108806333	downstream	utr5p	SNORA28	Ip6k2	108795243	108795994	-	+	0	108783870	108796064	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	8	0.705029292490001	1.27539006843697	1.27539006843697	0.705029292490001	4	-	-	0.953988239876003
+13800	GATTGTTAGGGATGGGTCCTTGGTCAGCTGTCCAGAATGCTAGAGCTTCGTCCTCCTGGGAGATGGTTTCAGTCCTTACCCCCAGGACTCTGATGAGATCCTGAGGGAATCCACCCTCTGCTGATGGCCCAGTGAAAGCC|AGGCTCCGTGGCTTTACAGTGGATGGGATCTGGGAGAGTAGAGGGAAGGTTCTAGAACCCTGAAACCAGACCACTCTATTAGCGAACTCACAGCTGCCTTGTGGTGTAGAC	3	0.978409273957491	0.969552944230377	0.898574822628826	N	Y	3.329991337985	3.51679652308403	3.329991337985	0	0	0	Y	0	N	N	575	443	ENSMUSG00000053799	ENSMUSG00000024987	+	-	19	19	37683245	37701528	intron	upstream	Exoc6	Cyp26a1	37550418	37697808	+	+	0	37678397	37696729	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	12	0.839697809033035	0.855541163920451	0.855541163920451	0.839697809033035	1	-	-	0.80116231284735
+5983	CCATGTCAAACCACCATCCACGGCTGTCGTCCTCGAAGTGCAGGTAGTCCATCCTGTGAGCGCCGTGCGGGAACTGCCTCCGTGTCACTGGGGCGGCGCGCCTGTGGAAT|CCTCCGAAGAGATGGAATCCTTTCCTGCAGCTCGGCAAGGGCCACTTCGCAGAGCTGGATTTCTGAAAGCTTTGCTTGATTTTCAAATATTCTTTAGTAAAGAATGTCTTTGTGGCATTGTTC	1	1	1	0.945022483912395	Y	Y	3.49015970162987	3.55334927718654	3.49015970162987	0	0.990947940947941	0.00427350427350426	Y	0.990947940947941	N	N	0	60	ENSMUSG00000021718	ENSMUSG00000021720	+	+	13	13	105121782	105271039	downstream	intron	4933425L06Rik	Rnf180	105082122	105149352	+	-	0	105131562	105167527	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	5	0.78424606692708	0.974366325576069	0.974366325576069	0.78424606692708	1	-	-	0.813708699275449
+12092	TGCCCAATGAGCTGCTGGCACTCAGCACAGGTGTTGGCGAAGGTGTTGTCATAGCACGGAACGCAGTAGGGGCCACTGTCTGTCTGGATGTATTTGCGGCCGTACAAGGACTCGTTGCATTTTGCACAGTCAAATGCCTCGCTCATGGTGGCGGTGCCCAGTGAGC|CCTCAAACTCAAGAAGCCCCATCTCAGTCGGTCTTCTTACTTTGCAAGAGTTTTCAAAGGACTGCGCTGGGTCTCTTCTGCCAAGCGGCTCATGGCTTCCTCTGGGTGCTGAATCATTCTCTGGTGCCTGCAACCACAAGACCTCCTTCC	2	1	0.16313785091306	0.240986946418107	Y	Y	3.43784458057793	3.48805370929674	3.43784458057793	0	0.99335436382755	0.00315457413249232	Y	0	N	N	2072	0	ENSMUSG00000032643	ENSMUSG00000088067	-	-	4	4	124708611	124697607	utr5p	downstream	Fhl3	U6	124700701	124697505	+	-	0	124705614	124696071	-	+	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	9	1.21993832633101	1.18825161655618	1.21993832633101	1.18825161655618	1	-	-	0.736022708835765
+11605	CTCCACACCACAGCGTCACCGATGTCCAGCGCTTTCGAGCCGGCACACAGCTGTTGCAGAAGACTACAGGGGTGGGATCCGAGCTGGGAATGTAGAAGGAGGAACAGCGGCCAAAACAGAGATGATTAAGGACCCGGGCACTTGTGCAACCAGGCCTGGAGATCACCTGC|GCCGTACGGACTAAAGCAGCGCGGCGCTCCTCCGCTCCCCGGCCGGAGGCCCCCGGTGTTTCCGCCGCGCAGGCAGCGCCGTAGCCAGCCCCGCTGCCGCGAGGACCCACAGCCAAG	11	0.982340211125991	0.568397069242315	0.586452494205497	Y	Y	3.57167229721571	3.28292550416853	3.28292550416853	0	0	0	Y	0.770032051282051	N	N	167	2428	ENSMUSG00000053226	ENSMUSG00000033751	-	-	8	8	84822823	84835482	intron	utr5p	Dand5	Gadd45gip1	84815405	84831522	-	+	0	84816537	84832174	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	12	1.26746839099326	0.990209680463485	1.26746839099326	0.990209680463485	2	-	-	0.758045795414889
+7456	AAATTCTGGAGTCAGTTCTGGAGACATAGATAGCTCCCAAATTATAACCAACCCTCTTCCTCCCGTGGCCTCCCCTCCTCCTGCATCTAAAGCAAAGGAAGTTTCCGATGGGGAAAATCTCGAGCAAGATCTATGTACGTTCTTGATATCAAGAGCCTGTAAGAACTCAACACTGGCTAATTATTTATACTGG|TCACTTTTACTCTGCTATTCCCCTATCTATGCTCCGAAAATCATTCTGACTCCTGCAATGACCCCTATTACCCAGATTTTGAAGATACTCCCTGCTATCTACTCAGCTCTGAAGACTTG	9	1	0.674019218743678	0.827309111200933	N	N	3.64400585547602	3.3012485241977	3.3012485241977	0	0	0	N	0	N	N	1791	0	ENSMUSG00000033628	ENSMUSG00000056822	+	-	18	16	30348126	19487830	coding	downstream	Pik3c3	Olfr166	30272747	19486793	+	+	0	30311220	19493776	+	-	Y	-	-	N	dataset_6344_files	1	1	1	1	0	1	N	N	0	1	10	1.37837187520517	0.942679615801238	1.37837187520517	0.942679615801238	1	-	-	0.745013975183866
+2385	CGGGACGGGGCGGGGCCGGCGAACTTCTGTGCCTCACTGTCCCCGGACACTGAGGGACACCGGGCAGGCAGCTGGCACCATGAAGATCTGGACTTCGGAGCACGTCTTTGAC|TACATCCGGTTTTCCCAGATCTGTGCAAAAGCAGTGAGGGATGCCCTGAAGACCGAGTTCAAAGCGAACGCTGAGAAGACTTCGGGCAGCAGCATAAAAATTGTGAAAGTCTCGAAGAAGGAGTAGCTGAATCTGAAGCCTGAAGTGCTGAGTCTTGAA	7	1	0.168340481582645	0.162692865850249	Y	Y	3.69784855983781	3.60831833727406	3.60831833727406	0	0	0	Y	0	N	Y	3085	3617	ENSMUSG00000016257	ENSMUSG00000016252	+	-	2	2	174473081	174464105	coding	coding	Slmo2	Atp5e	174465067	174461072	-	-	0	174472832	174462629	-	+	N	-	-	N	dataset_6344_files	2	0.190909090909091	1.2	1	1	1	Y	Y	0.190909090909091	0	5	0.871384518807867	1.29915510076809	1.29915510076809	0.871384518807867	4	-	-	0.7622459420951
+13923	AGACTGTTGAGAAGGATTCAACTGCCGAATTCAGAACTCATCAGCTGGGGAACGACGGTGATAAAGGTTCCCGTAAAGCAGACTGTTGAGAAGGATTCAACTGCCGAATTCAGAACTCATCAG|CCAGAGTCGGCGCTCTCCGGCGAGCTATCCCCTTCTCACCACACTCTGAGAACGGAGCTTGGTGCCGGCTCGGCCGCCTCCGCCAATTCCGGGTCCCTCTTCA	4	0.0503617839630236	0.900541946891923	0.647988756014038	N	Y	3.6988816296077	3.47080361183081	3.47080361183081	0	0.980668063812497	0	N	0.980668063812497	N	N	590	367	ENSMUSG00000046079	ENSMUSG00000051671	-	-	5	8	105832436	126425434	intron	upstream	Lrrc8d	1810063B05Rik	105699969	126422501	+	+	0	105728723	126422269	-	-	Y	-	-	N	dataset_6344_files	10	0.968503937007874	8	4	7	1	N	N	0.968503937007874	0	7	0.974366325576069	0.617890840609215	0.974366325576069	0.617890840609215	4	-	-	0.812231785796686
+11177	ATCTGACAGAACTTGCCACTGTGCCTGCAACCTTGTCTGAGAGGAA|CCCTTCTCTGAGGATGGACACTTCTCACACTACAAAGTCCTGTTTGCTGATTCTTCTTGTGGCCCTACTGTGTGCAGAAAGAGCTCAGGGACTGGAGTGTTACCAGTGCTATGGAGTCCCATTTGAGACTTCTTGCCCATCAATTACCTGCCCCTACCCTGATGGAGTCTGTGTTACTCAGGAGGCAGCAGTTATTGTGGATTCTCAAACAAGGA	434	0.873359569934578	0.121885088610831	0.552181129473186	Y	Y	3.55081912933034	3.43784458057793	3.43784458057793	0	0	0.00381679389312994	Y	0.956687686691006	N	Y	1416	5049	ENSMUSG00000079018	ENSMUSG00000075602	+	-	15	15	75048837	74997634	utr5p	utr5p	Ly6c1	Ly6a	75045017	74994878	-	-	0	75048442	74996568	-	+	N	-	-	N	dataset_6344_files	2	0	1.65079365079365	1	41	2	Y	Y	0	0	63	0.665420905271462	1.36252852031776	1.36252852031776	0.665420905271462	4	-	-	0.566839236883877
+3839	GTCACAGCCACCAATGTGTCAGCCCATGGAAGCCAAGCTAACTCGCCCTCTACTCCCAACTCAGCGGGTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGATACAGTGACGGACTCGCAGCCAGTCAGATGTACAGTCCGCAGGGCATCAGT|GATATGTCAAGAACCTACTGATCCTCACAAGAACCTACTGTCTCTCTTCTCTTGACTGAAAACAAAAGTCTTCTTCTACCTGACCCGTGGCCTGACTTCTGGAAGAATGCATATGGACTTTCGAAGAAGTCAGAGGATATCTGCTGGCCACTTGTATCAGACAAAACAAGGCTGGTGAGCA	13	1	0.804385830976137	0.0961220231684031	Y	Y	3.42779550918039	3.49697642496855	3.42779550918039	0	0	0	Y	0.993649362117881	N	N	3895	0	ENSMUSG00000052534	ENSMUSG00000093538	+	+	1	1	168432270	168122465	coding	intron	Pbx1	Gm20711	168153527	168115244	-	+	0	168183530	168121480	-	+	N	-	-	N	dataset_6344_files	1	0.745098039215686	1	1	0	1	N	Y	0	0.745098039215686	16	1.29915510076809	1.21201664888731	1.29915510076809	1.21201664888731	4	-	-	0.97679698937665
+66	CTGAGAACGAGGAGCAGGAAGAACACACCAGCATGGGCGCGTTCAACGATCCGTTCCTGGCTCAGCCCCCCGATGAAGATTCACATTCCAGTTTTCCTGATGGTGAACAAATAGACCCTGAAAATCTCCACTTCAACCCTGATGAAGGAGGTGGA|AGACTGCTTGTTCTTGGAACCCAGCAGCCATACTGTGAGGAAGTCCAAACCAGCCAACCTGGAGAGACGGCATGCACAGGGTCCCACGGATA	13	0.719595391393931	0.399734668051015	0.808813953308524	Y	Y	3.39487633072086	3.67849247003875	3.39487633072086	0	0	0	Y	0.989174263674614	N	N	1514	627	ENSMUSG00000018548	ENSMUSG00000046442	+	+	11	11	87220683	87359023	coding	intron	Trim37	Ppm1e	87127077	87226906	+	-	0	87218328	87250589	+	-	N	-	-	N	dataset_6344_files	1	1	1	1	0	1	N	Y	0	1	11	0.863462841364159	0.689185937602586	0.863462841364159	0.689185937602586	1	-	-	0.615916282680748
+11601	GGCACTGGGAACCCGAGCGCAGCTTGGACAAGTGGACTGCACGCAGCGCCTGCCTGGTCTTTCACACTTCTCTGGGGACCTCAGGAGAGGAAGGAAGACTTTTGGATATGG|GGTGCTTCGAGTGCTGCATTAAATGCCTGGGAGGTATTCCCTATGCTTCTCTGATTGCAACCATCCTGCTGTATGCAGGCGTTGCCCTGTTCTGTGGCTGTGGCCATGAAGCCCTTTCTGGAACAGTCAACATTCTGCAGACCTACTTTGAGTTGGCAAGGACTGCTG	45	1	0.903984782676282	0.890308208832683	Y	Y	3.25993583872649	3.64553343878587	3.25993583872649	0	0	0	Y	0.991023166023166	N	N	195	2438	ENSMUSG00000039375	ENSMUSG00000031517	-	-	8	8	54887184	55060877	intron	coding	Wdr17	Gpm6a	54629055	54954728	-	+	0	54779650	55037328	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	33	0.887227873695282	1.25162503610584	1.25162503610584	0.887227873695282	4	-	-	0.961094875436964
+11202	CAAACACGTCCTGGAGCAAGGCCTCCACAGCCACGGGGTCCCCATCCAGGGTCCTGAGTGGTTTTGAGTCAGCCATCAGGATGAAATCTTCCAGCTCAGGAGGGCTCAGAGAAGGATCAGACGAGCTGGTGACAAGGTACACAATGGACTTTTCAGAATAGGG|CTGGACTGCTTATTCCTTTAGAAGCAAGGTCTCTTCCCCAACCTGGGGCTCTAATTTTCTCAGTTAAGGTGGAATCCAGCAAGTCCAGGGGATTCTCCAGTCTCCACCTTTGTCAGAGCAGGCTTGTTAACC	21	1	0.362314658679907	0.288186846563607	Y	Y	3.57167229721571	3.6035982586987	3.57167229721571	0	0	0	Y	0.984899672399672	N	N	1306	3566	ENSMUSG00000023044	ENSMUSG00000046897	-	-	15	15	102189043	102215606	utr5p	upstream	Csad	Zfp740	102176998	102203648	-	+	0	102188962	102202444	+	-	N	-	-	N	dataset_6344_files	1	0.961240310077519	1	1	0	3	N	Y	0	0.961240310077519	10	1.21993832633101	1.02189639023832	1.21993832633101	1.02189639023832	4	-	-	0.973142113883806
+9292	GGAGGTATCAAAGGACTTTTCAAAGGCGGTGATATGTCTAAGAATGTGAGTCAGTCACAGATGGCAAAATTAAACCAACAAATGGCCAAAATGATGGACCCACGAGTTCTTCATCACATG|GGAGGAGGAGGAGGAAGAAGAAAATAGGATGTCAGAAGAAGCAGAAAGACAATACCAACAAAACAAGCTGCAGGCCGATTCCATTGTACAGACAGACCAACCAGAAACAGTGTCGTCCAGCTTTGTAAATATTAATTTTGAAATGGAGGAAGACTGTGAAGCAATTAAG	13	0.627587070077396	0.568913321228002	0.464690965079815	N	Y	3.57233464462502	2.71992636785275	2.71992636785275	0	0	0	Y	0.368850574712644	N	Y	1463	391	ENSMUSG00000073079	ENSMUSG00000094103	+	-	12	12	55112891	55214076	coding	intron	Srp54c	1700047I17Rik2	55089202	55199533	+	+	0	55111181	55213840	+	-	N	-	-	N	dataset_6344_files	9	0	9	9	9	1	N	N	0	0	9	0.93475793835753	1.17240826166877	1.17240826166877	0.93475793835753	4	-	-	0.529926984288339
+8690	CTGGAGGAAAGCACCGCAGGTCTGAGCAGCCCTGAGCCGGGCAGGGTGGGGGCAGTGGCTAAGGCCTAGCTGGGGACGATTTAAAGGTATCGCGCCACCCAGCCACACCCCACAGGCCAGGCGAGGGTGCCACCCCCGGAGATCAGAGGTCATTGCTGGCGTTCAGA|GCCTAGGAAGTGGGCTGCGTTTCAGGGGGAAGTCCATGATCACCACGTGGCAACATGCAAGCGGGTGCTG	4	0.685704457350918	0.684620189710687	0.966832507460471	N	Y	3.58424216889964	3.53768019619294	3.53768019619294	39	0.98577430972389	0.260264105642257	N	0.260264105642257	N	N	4781	556	ENSMUSG00000032000	ENSMUSG00000016409	+	-	9	X	7873186	37150746	utr5p	intron	Birc3	Nkap	7848699	37126795	-	+	0	7872842	37143984	-	-	Y	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	N	0	0	5	0.831776131589327	0.712950969933709	0.831776131589327	0.712950969933709	1	-	-	0.520824161374586
+11497	CCTTTCCAGCGAGGTTCCAAGTTCTTAGTCTGGTGCCGGCGTACCCACACGGCGTCACCGACACGGAAGGGGTGTGGTATCACTGGCTGATCTAGCTGGTCCTGATAAGCAGCGGCCAGCGGCTTCCAGACCTCTCGTTGTACTGCTTGGAGGGCCTGTAAGTGAG|CTTCTCTTCTGGAAGTCGGACCAATTCACCTCAAGCACCAGAGCTTGAATTCATGATCATCCTGGACACAGCACTCATCAGGACCGCGCCGCGGCTGA	67	0.883499713768307	0.731092666993054	0.679758623906517	N	Y	3.66336194527509	3.6508225788147	3.6508225788147	0	0.0444358875625721	0	N	0.94917212167886	N	N	0	1604	ENSMUSG00000096832	ENSMUSG00000039007	-	+	5	15	23711061	33594552	downstream	intron	SNORD93	Pgcp	23710991	33083129	-	+	0	23703360	33221484	+	+	Y	-	-	N	dataset_6344_files	76	1	38.7730061349693	5	163	1	N	N	1	0	163	1.34668516543034	0.760481034595956	1.34668516543034	0.760481034595956	4	-	-	0.903135577741999
+8726	GAGCAAGCTGACAGCTGAGCAGAAGCTGAGCATGGACACCTTCAGATCCAACTCAGCGGACATCATTCTTTCTGCAGGGCGGCAAGAGCTCAAGAGCAAGCCAAGGCTGATAAGCATGAAGAGGATGGAGATGAGGAACAAGGCTCTGGAGTACTGGAGATAAT|CATGTCAGTTCGGCCGCGCAGGCGGGCTGCGTCGTCCTCGACGAGGCCTTTCGACGCTACCGTAACCTGCTCTTCGGTTCCGGCTCTTGGCCCCGACCCAGCTTCTCAAGTGAGTCACTGCCC	3	0.70117526311829	0.321035960603558	0.664396670389762	Y	Y	3.42949092635959	3.29652844562235	3.29652844562235	0	0	0	Y	0	N	N	44	8769	ENSMUSG00000049526	ENSMUSG00000025232	-	-	9	9	59525501	59565105	coding	coding	Tmem202	Hexa	59518686	59539667	-	+	0	59520238	59539868	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	5	1.02981806768202	0.744637679708541	1.02981806768202	0.744637679708541	4	-	-	0.931447658206354
+5020	CAAACCATCATTTGTATTTTTCAAACTGTCTATCGAGCCTCAAACTCC|ACCATTTCATTTTCTGGTCTTCTATTCTAGCACCTACAACAAACAAATAGTTAAAGCTGCCCGGTTAGGCCCCTGACTCAGCACTTAAGATGGGGGAACCAGAGTCCACCAAATAGGGGGTAAATGCGTTAACGACCACTAGCTCCCACATATCAAAAACCAGCCTCCTCAGATACGCAGAAACAATGCCCTGACTTCAGAC	27	0.772639018637575	0.542772921402035	0.769655490407199	N	Y	3.43152237077921	3.41592783769912	3.41592783769912	0	0.89624833997344	0	N	0.584993359893758	N	N	0	0	ENSMUSG00000088422	ENSMUSG00000053332	-	+	5	1	79639109	161038539	downstream	intron	7SK	Gas5	79638815	161034422	-	+	0.89624833997344	79638362	161036581	+	+	Y	-	-	N	dataset_6344_files	1	0	1	1	0	3	N	N	0	0	9	0.52283071128472	1.06942645490056	1.06942645490056	0.52283071128472	1	-	-	0.818668251983994
+3184	CATTGGAGCTGTGGTGGCTTTTGTGATGAAGAGAAGGAGAAACACAGGTGGAAAAGGAGGGGACTATGCTCTGGCTCCAG|AGAACAGCGCCTGATGTTCCCTGTGAGCCTATGGGCTCAATGTGAAGAATTGTGGAGCCCAGCCTTCGCCTACACACCAGGACCCTGTCTCTGCATTGCCCTGTGTTCCCTTCCACCGCCAACCTTCCGGGTCTGCAGTGGAAACTAAGGGTTCTTTGGAAAGTCGG	40	1	0.843266171585359	0.786568876550746	N	Y	3.49424793801946	3.684245618384	3.49424793801946	0	0	0.551814516129032	Y	0.950201612903226	N	Y	23545	2145	ENSMUSG00000073411	ENSMUSG00000035929	+	-	17	17	35267499	35385290	coding	utr3p	H2-D1	H2-Q4	35262730	35379617	+	+	0	35266514	35383995	+	-	N	-	-	N	dataset_6344_files	4	0.22972972972973	2.57142857142857	2	7	1	N	N	0	0.22972972972973	7	0.562439098503259	1.03773974512573	1.03773974512573	0.562439098503259	4	-	-	0.85501289117385
+9158	CCGAATTTCAACCTCCTTATCAACAGTGGGATCTTCAAAGAGTTGTACCCTGAAGTTGCTCTTTCTCAGTGGAGTCCCACACTCAGGACAGTTTCCAGCTCCTCTTACAAACAGTAAGTCCACACAACTCTCACAC|CTTCCCCACCAGCCTGGTCCGGCTGCCCACCTCTCCCCGCCCCCCACCTCGCTTCCCTACCGGGGTGGTAGGGGGGACGACGGTGGCAACGAGCGGGCGGGGGATCCTCCC	5	1	0.770112168741176	0.964592797110167	Y	Y	3.1490579347374	3.11232376639641	3.11232376639641	0	0	0	Y	0	N	N	1882	677	ENSMUSG00000021103	ENSMUSG00000034460	-	-	12	12	73273988	73114037	coding	intron	Mnat1	Six4	73123717	73099609	+	-	0	73168000	73112254	-	+	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	5	1.0060530353509	0.78424606692708	1.0060530353509	0.78424606692708	4	-	-	0.934413835802699
+1851	GCTGCAGGTGGGCTTATTCTACCATTGCTACTGTTCTGTCTTTGAAGATGTTCTTTATAGCATACTGAACACATGCCATTTGTACGAGGGTTTCCATAAAATCCGCAGCCAGTGGAGCAAAGCATAGGTGCTTGGCTGTGATTAGTTTCTTGAGCCATGTTCTTCTGTTGCA|CACCTGGCGGCGGCCCTCTCCGCCGGACGCGCTGCCGCCGCCGCCTCTCGCCGCCGCTGAGAGTGAGGACAGGTGAGGCCGCCAAACCCCCACTCGCTCCCGGCCCGCCGCCGCCGGCCCTCCGTCCGC	21	0.826443478467522	0.547250352165575	0.543160934834641	Y	Y	3.38908332958226	2.95732075160099	2.95732075160099	0	0	0	Y	0.992273730684327	N	N	1944	1	ENSMUSG00000030629	ENSMUSG00000085236	-	-	7	7	84679361	84776549	utr5p	intron	Zfand6	2610206C17Rik	84615054	84689640	-	+	0	84634406	84689743	+	-	N	-	-	N	dataset_6344_files	2	0.159420289855072	1.04878048780488	1	2	1	N	Y	0	0.159420289855072	41	1.14864322933764	1.09319148723169	1.14864322933764	1.09319148723169	1	-	-	0.715005473321084
+9962	CTGCGGCCCGCCGGGTCCCGGAGCCCACTGCCCCAGCACCCCGCGCTCGGCGCCCGCAGACGGCGCGGACCTCAGCGCGCACTTATGGGCTCGTTACCAGGACATGCGGAGGCTGGTGCACG|ACCTTCTGCCCCCTGAGGTCTGCAGCCTCCTAAACCCAGCAGCTATTTATGCCAACAATGAGATCAGCCTGAGTGACGTCGAAGTCTATGGCTTTGACTACGACTACACGCTGGCCCAGTATGCGGATGCACTGCACCCTGAGATCTTCAATGCTGCCCGGGACATCTTGATAGAGC	93	0.0971360740885943	0.213119196903586	0.467950871740144	Y	Y	3.71720464963688	3.27448372166755	3.27448372166755	0	0.983661202185792	0	Y	0.991830601092896	N	N	211	4122	ENSMUSG00000058351	ENSMUSG00000071547	-	-	14	14	31128930	31139121	upstream	upstream	2010107H07Rik	Nt5dc2	31088869	31134853	-	+	0	31131376	31134739	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	33	1.1011131646754	0.808011099258204	1.1011131646754	0.808011099258204	4	-	-	0.743419539119423
+12549	TTGGAGATGCCAGTACCATGAGATGACCACCAAGAGCAGCAGCAGCAGTGGAGTACAGGCATCTGGAGCCTAGAGGATGACACATGTGCTACAAAGGGCCTGGCTGGAGAAGTGACCCAAGCCCTTGGAGGAGCCCAGAAGATC|GTCCATCCTGATAAAAATCACCATCCCCGGGCTGAGGAGGCCTTCAAAATTTTGCGGGCAGCTTGGGACATTGTCAGCAACCCAGAGAGGCGGAAGGAATATGAGATGAAACGGAT	18	1	0.96278392593137	0.394484707065412	N	Y	3.2808195118354	3.46448140203209	3.2808195118354	1	0.965649359228432	0	N	0.974237019421324	N	Y	1732	2437	ENSMUSG00000039307	ENSMUSG00000025354	+	-	11	10	121222655	128819446	utr5p	coding	Hexdc	Dnajc14	121204433	128805676	+	+	0	121206748	128814038	+	-	Y	-	-	N	dataset_6344_files	3	0.993103448275862	1.72222222222222	1	11	1	N	N	0.993103448275862	0	18	1.14864322933764	0.879306196251575	1.14864322933764	0.879306196251575	4	-	-	0.927135541379163
+3179	CTGGAGCAGTCCCCGTGACGCCGGGTGGCGACTGGCTCCCGGGTCTGAGGGGCTTCTGCTTGTCAGGTTCT|AGATATGTGCTGACTAGCAGGCTCACGTGCACAGTGTGGAGGATAAGCTATATCTTACAAAATGGGATTTGGGAGTGACCTGAAGAACTCACAGGAAGCTGTGTTAAAGTTGCAAGACTGGGAACTACGGTTGCTGGAGACAGTGAAGAAATTTATGGCTCTGAG	10	1	0.557528435226891	0.364482194613623	Y	Y	3.15741158895574	3.54759612884129	3.15741158895574	0	0.985974921257503	0	Y	0.873774291317525	N	N	10	1325	ENSMUSG00000045506	ENSMUSG00000000127	-	-	17	17	63863791	64139494	upstream	upstream	A930002H24Rik	Fer	63863300	63896018	-	+	0	63864053	63896016	+	-	N	-	-	N	dataset_6344_files	1	0	1	1	0	1	N	Y	0	0	7	0.499065678953596	1.12487819700652	1.12487819700652	0.499065678953596	3	-	-	0.767822892174251
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm10_results.filtered.vcf	Fri Aug 09 11:19:26 2013 -0500
@@ -0,0 +1,106 @@
+##fileformat=VCFv4.1
+##source=defuse
+##reference=mm10
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
+##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction">
+##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SPLICESCORE,Number=1,Type=Integer,Description="number of nucleotides similar to GTAG at fusion splice">
+##INFO=<ID=GENE,Number=2,Type=String,Description="Gene Names at each breakend">
+##INFO=<ID=GENEID,Number=2,Type=String,Description="Gene IDs at each breakend">
+##INFO=<ID=ORF,Number=0,Type=Flag,Description="fusion combines genes in a way that preserves a reading frame">
+##INFO=<ID=EXONBND,Number=0,Type=Flag,Description="fusion splice at exon boundaries">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	106734547	bnd_4068_1	A	A]16:37799068]	233	PASS	SVTYPE=BND;MATEID=bnd_4068_2;DP=19;SPLITCNT=8;SPANCNT=11;GENE=Kdsr,Fstl1;GENEID=ENSMUSG00000009905,ENSMUSG00000022816;HOMLEN=2;SPLICESCORE=4
+1	127753955	bnd_3783_1	T	T]1:127773930]	181	PASS	SVTYPE=BND;MATEID=bnd_3783_2;DP=8;SPLITCNT=2;SPANCNT=6;GENE=Acmsd,Ccnt2;GENEID=ENSMUSG00000026348,ENSMUSG00000026349;HOMLEN=0;SPLICESCORE=3
+1	127773930	bnd_3783_2	T	[1:127753955[T	181	PASS	SVTYPE=BND;MATEID=bnd_3783_1;DP=8;SPLITCNT=2;SPANCNT=6;GENE=Acmsd,Ccnt2;GENEID=ENSMUSG00000026348,ENSMUSG00000026349;HOMLEN=0;SPLICESCORE=3
+1	161036581	bnd_5020_2	A	[5:79638362[A	208	PASS	SVTYPE=BND;MATEID=bnd_5020_1;DP=36;SPLITCNT=27;SPANCNT=9;GENE=7SK,Gas5;GENEID=ENSMUSG00000088422,ENSMUSG00000053332;HOMLEN=0;SPLICESCORE=1
+1	161036831	bnd_4912_2	G	]5:79638354]G	151	PASS	SVTYPE=BND;MATEID=bnd_4912_1;DP=20;SPLITCNT=15;SPANCNT=5;GENE=7SK,Gas5;GENEID=ENSMUSG00000088422,ENSMUSG00000053332;HOMLEN=0;SPLICESCORE=1
+1	168121480	bnd_3839_2	G	]1:168183530]G	249	PASS	SVTYPE=BND;MATEID=bnd_3839_1;DP=29;SPLITCNT=13;SPANCNT=16;GENE=Pbx1,Gm20711;GENEID=ENSMUSG00000052534,ENSMUSG00000093538;HOMLEN=0;SPLICESCORE=4
+1	168183530	bnd_3839_1	T	T[1:168121480[	249	PASS	SVTYPE=BND;MATEID=bnd_3839_2;DP=29;SPLITCNT=13;SPANCNT=16;GENE=Pbx1,Gm20711;GENEID=ENSMUSG00000052534,ENSMUSG00000093538;HOMLEN=0;SPLICESCORE=4
+2	165827729	bnd_5326_1	C	C]18:4198107]	136	PASS	SVTYPE=BND;MATEID=bnd_5326_2;DP=20;SPLITCNT=7;SPANCNT=13;GENE=Zmynd8,Gm10557;GENEID=ENSMUSG00000039671,ENSMUSG00000073647;HOMLEN=9;SPLICESCORE=1
+2	174462629	bnd_2385_2	T	]2:174472832]T	194	PASS	SVTYPE=BND;MATEID=bnd_2385_1;DP=12;SPLITCNT=7;SPANCNT=5;GENE=Slmo2,Atp5e;GENEID=ENSMUSG00000016257,ENSMUSG00000016252;HOMLEN=0;SPLICESCORE=4;ORF;EXONBND
+2	174472832	bnd_2385_1	C	C[2:174462629[	194	PASS	SVTYPE=BND;MATEID=bnd_2385_2;DP=12;SPLITCNT=7;SPANCNT=5;GENE=Slmo2,Atp5e;GENEID=ENSMUSG00000016257,ENSMUSG00000016252;HOMLEN=0;SPLICESCORE=4;ORF;EXONBND
+3	103040040	bnd_5160_1	C	C]18:28188917]	213	PASS	SVTYPE=BND;MATEID=bnd_5160_2;DP=63;SPLITCNT=33;SPANCNT=30;GENE=Csde1,SNORA17;GENEID=ENSMUSG00000068823,ENSMUSG00000087940;HOMLEN=91;SPLICESCORE=3
+3	144201813	bnd_8647_1	T	T]5:149198645]	242	PASS	SVTYPE=BND;MATEID=bnd_8647_2;DP=9;SPLITCNT=4;SPANCNT=5;GENE=Lmo4,Uspl1;GENEID=ENSMUSG00000028266,ENSMUSG00000041264;HOMLEN=1;SPLICESCORE=4;EXONBND
+4	124696071	bnd_12092_2	C	]4:124705614]C	187	PASS	SVTYPE=BND;MATEID=bnd_12092_1;DP=11;SPLITCNT=2;SPANCNT=9;GENE=Fhl3,U6;GENEID=ENSMUSG00000032643,ENSMUSG00000088067;HOMLEN=0;SPLICESCORE=1
+4	124705614	bnd_12092_1	C	C[4:124696071[	187	PASS	SVTYPE=BND;MATEID=bnd_12092_2;DP=11;SPLITCNT=2;SPANCNT=9;GENE=Fhl3,U6;GENEID=ENSMUSG00000032643,ENSMUSG00000088067;HOMLEN=0;SPLICESCORE=1
+4	148948907	bnd_12095_1	C	C]4:148961548]	249	PASS	SVTYPE=BND;MATEID=bnd_12095_2;DP=11;SPLITCNT=6;SPANCNT=5;GENE=Gm13205,Pex14;GENEID=ENSMUSG00000086606,ENSMUSG00000028975;HOMLEN=0;SPLICESCORE=4
+4	148961548	bnd_12095_2	C	[4:148948907[C	249	PASS	SVTYPE=BND;MATEID=bnd_12095_1;DP=11;SPLITCNT=6;SPANCNT=5;GENE=Gm13205,Pex14;GENEID=ENSMUSG00000086606,ENSMUSG00000028975;HOMLEN=0;SPLICESCORE=4
+5	23703360	bnd_11497_1	G	G[15:33221484[	230	PASS	SVTYPE=BND;MATEID=bnd_11497_2;DP=230;SPLITCNT=67;SPANCNT=163;GENE=SNORD93,Pgcp;GENEID=ENSMUSG00000096832,ENSMUSG00000039007;HOMLEN=0;SPLICESCORE=4
+5	60176541	bnd_1721_2	G	]11:106187103]G	188	PASS	SVTYPE=BND;MATEID=bnd_1721_1;DP=13;SPLITCNT=8;SPANCNT=5;GENE=Strada,Cbfa2t2-ps1;GENEID=ENSMUSG00000069631,ENSMUSG00000087034;HOMLEN=142;SPLICESCORE=1
+5	79638354	bnd_4912_1	A	A]1:161036831]	151	PASS	SVTYPE=BND;MATEID=bnd_4912_2;DP=20;SPLITCNT=15;SPANCNT=5;GENE=7SK,Gas5;GENEID=ENSMUSG00000088422,ENSMUSG00000053332;HOMLEN=0;SPLICESCORE=1
+5	79638362	bnd_5020_1	C	C[1:161036581[	208	PASS	SVTYPE=BND;MATEID=bnd_5020_2;DP=36;SPLITCNT=27;SPANCNT=9;GENE=7SK,Gas5;GENEID=ENSMUSG00000088422,ENSMUSG00000053332;HOMLEN=0;SPLICESCORE=1
+5	105728723	bnd_13923_1	G	G]8:126422269]	207	PASS	SVTYPE=BND;MATEID=bnd_13923_2;DP=11;SPLITCNT=4;SPANCNT=7;GENE=Lrrc8d,1810063B05Rik;GENEID=ENSMUSG00000046079,ENSMUSG00000051671;HOMLEN=0;SPLICESCORE=4
+5	149198645	bnd_8647_2	G	]3:144201813]G	242	PASS	SVTYPE=BND;MATEID=bnd_8647_1;DP=9;SPLITCNT=4;SPANCNT=5;GENE=Lmo4,Uspl1;GENEID=ENSMUSG00000028266,ENSMUSG00000041264;HOMLEN=1;SPLICESCORE=4;EXONBND
+6	51467295	bnd_12868_1	A	A]10:73201702]	132	PASS	SVTYPE=BND;MATEID=bnd_12868_2;DP=110;SPLITCNT=69;SPANCNT=41;GENE=Hnrnpa2b1,Gm15398;GENEID=ENSMUSG00000004980,ENSMUSG00000085456;HOMLEN=0;SPLICESCORE=1
+6	52158684	bnd_7746_1	G	G]6:52173634]	190	PASS	SVTYPE=BND;MATEID=bnd_7746_2;DP=46;SPLITCNT=26;SPANCNT=20;GENE=Gm15051,Gm15050;GENEID=ENSMUSG00000087658,ENSMUSG00000087626;HOMLEN=0;SPLICESCORE=2
+6	52173634	bnd_7746_2	A	[6:52158684[A	190	PASS	SVTYPE=BND;MATEID=bnd_7746_1;DP=46;SPLITCNT=26;SPANCNT=20;GENE=Gm15051,Gm15050;GENEID=ENSMUSG00000087658,ENSMUSG00000087626;HOMLEN=0;SPLICESCORE=2
+7	28376683	bnd_1870_1	C	C]7:28392166]	214	PASS	SVTYPE=BND;MATEID=bnd_1870_2;DP=10;SPLITCNT=2;SPANCNT=8;GENE=Zfp36,Med29;GENEID=ENSMUSG00000044786,ENSMUSG00000003444;HOMLEN=4;SPLICESCORE=1
+7	28392166	bnd_1870_2	C	[7:28376683[C	214	PASS	SVTYPE=BND;MATEID=bnd_1870_1;DP=10;SPLITCNT=2;SPANCNT=8;GENE=Zfp36,Med29;GENEID=ENSMUSG00000044786,ENSMUSG00000003444;HOMLEN=4;SPLICESCORE=1
+7	66355922	bnd_12600_2	C	[10:24597524[C	148	PASS	SVTYPE=BND;MATEID=bnd_12600_1;DP=6;SPLITCNT=1;SPANCNT=5;GENE=Ctgf,Lrrk1;GENEID=ENSMUSG00000019997,ENSMUSG00000015133;HOMLEN=0;SPLICESCORE=3
+7	84634406	bnd_1851_1	A	A]7:84689743]	182	PASS	SVTYPE=BND;MATEID=bnd_1851_2;DP=62;SPLITCNT=21;SPANCNT=41;GENE=Zfand6,2610206C17Rik;GENEID=ENSMUSG00000030629,ENSMUSG00000085236;HOMLEN=0;SPLICESCORE=1
+7	84689743	bnd_1851_2	C	[7:84634406[C	182	PASS	SVTYPE=BND;MATEID=bnd_1851_1;DP=62;SPLITCNT=21;SPANCNT=41;GENE=Zfand6,2610206C17Rik;GENEID=ENSMUSG00000030629,ENSMUSG00000085236;HOMLEN=0;SPLICESCORE=1
+7	90125032	bnd_1855_1	T	T]7:90129872]	242	PASS	SVTYPE=BND;MATEID=bnd_1855_2;DP=13;SPLITCNT=4;SPANCNT=9;GENE=AC130210.1,Picalm;GENEID=ENSMUSG00000097162,ENSMUSG00000039361;HOMLEN=0;SPLICESCORE=4
+7	90129872	bnd_1855_2	C	[7:90125032[C	242	PASS	SVTYPE=BND;MATEID=bnd_1855_1;DP=13;SPLITCNT=4;SPANCNT=9;GENE=AC130210.1,Picalm;GENEID=ENSMUSG00000097162,ENSMUSG00000039361;HOMLEN=0;SPLICESCORE=4
+7	97788974	bnd_1886_1	G	G]7:97854436]	247	PASS	SVTYPE=BND;MATEID=bnd_1886_2;DP=36;SPLITCNT=18;SPANCNT=18;GENE=Aqp11,Pak1;GENEID=ENSMUSG00000042797,ENSMUSG00000030774;HOMLEN=0;SPLICESCORE=4
+7	97854436	bnd_1886_2	T	[7:97788974[T	247	PASS	SVTYPE=BND;MATEID=bnd_1886_1;DP=36;SPLITCNT=18;SPANCNT=18;GENE=Aqp11,Pak1;GENEID=ENSMUSG00000042797,ENSMUSG00000030774;HOMLEN=0;SPLICESCORE=4
+8	54779650	bnd_11601_1	G	G]8:55037328]	245	PASS	SVTYPE=BND;MATEID=bnd_11601_2;DP=78;SPLITCNT=45;SPANCNT=33;GENE=Wdr17,Gpm6a;GENEID=ENSMUSG00000039375,ENSMUSG00000031517;HOMLEN=0;SPLICESCORE=4
+8	55037328	bnd_11601_2	G	[8:54779650[G	245	PASS	SVTYPE=BND;MATEID=bnd_11601_1;DP=78;SPLITCNT=45;SPANCNT=33;GENE=Wdr17,Gpm6a;GENEID=ENSMUSG00000039375,ENSMUSG00000031517;HOMLEN=0;SPLICESCORE=4
+8	84816537	bnd_11605_1	C	C]8:84832174]	193	PASS	SVTYPE=BND;MATEID=bnd_11605_2;DP=23;SPLITCNT=11;SPANCNT=12;GENE=Dand5,Gadd45gip1;GENEID=ENSMUSG00000053226,ENSMUSG00000033751;HOMLEN=0;SPLICESCORE=2
+8	84832174	bnd_11605_2	G	[8:84816537[G	193	PASS	SVTYPE=BND;MATEID=bnd_11605_1;DP=23;SPLITCNT=11;SPANCNT=12;GENE=Dand5,Gadd45gip1;GENEID=ENSMUSG00000053226,ENSMUSG00000033751;HOMLEN=0;SPLICESCORE=2
+8	95682960	bnd_11596_2	G	]8:95739809]G	222	PASS	SVTYPE=BND;MATEID=bnd_11596_1;DP=24;SPLITCNT=8;SPANCNT=16;GENE=Cnot1,Ndrg4;GENEID=ENSMUSG00000036550,ENSMUSG00000036564;HOMLEN=0;SPLICESCORE=1
+8	95739809	bnd_11596_1	A	A[8:95682960[	222	PASS	SVTYPE=BND;MATEID=bnd_11596_2;DP=24;SPLITCNT=8;SPANCNT=16;GENE=Cnot1,Ndrg4;GENEID=ENSMUSG00000036550,ENSMUSG00000036564;HOMLEN=0;SPLICESCORE=1
+8	126422269	bnd_13923_2	C	]5:105728723]C	207	PASS	SVTYPE=BND;MATEID=bnd_13923_1;DP=11;SPLITCNT=4;SPANCNT=7;GENE=Lrrc8d,1810063B05Rik;GENEID=ENSMUSG00000046079,ENSMUSG00000051671;HOMLEN=0;SPLICESCORE=4
+9	7872842	bnd_8690_1	A	A]X:37143984]	132	PASS	SVTYPE=BND;MATEID=bnd_8690_2;DP=9;SPLITCNT=4;SPANCNT=5;GENE=Birc3,Nkap;GENEID=ENSMUSG00000032000,ENSMUSG00000016409;HOMLEN=39;SPLICESCORE=1
+9	21320850	bnd_8748_2	A	]9:21337962]A	189	PASS	SVTYPE=BND;MATEID=bnd_8748_1;DP=103;SPLITCNT=51;SPANCNT=52;GENE=Slc44a2,Ap1m2;GENEID=ENSMUSG00000057193,ENSMUSG00000003309;HOMLEN=2;SPLICESCORE=2
+9	21337962	bnd_8748_1	C	C[9:21320850[	189	PASS	SVTYPE=BND;MATEID=bnd_8748_2;DP=103;SPLITCNT=51;SPANCNT=52;GENE=Slc44a2,Ap1m2;GENEID=ENSMUSG00000057193,ENSMUSG00000003309;HOMLEN=2;SPLICESCORE=2
+9	59520238	bnd_8726_1	T	T]9:59539868]	237	PASS	SVTYPE=BND;MATEID=bnd_8726_2;DP=8;SPLITCNT=3;SPANCNT=5;GENE=Tmem202,Hexa;GENEID=ENSMUSG00000049526,ENSMUSG00000025232;HOMLEN=0;SPLICESCORE=4
+9	59539868	bnd_8726_2	C	[9:59520238[C	237	PASS	SVTYPE=BND;MATEID=bnd_8726_1;DP=8;SPLITCNT=3;SPANCNT=5;GENE=Tmem202,Hexa;GENEID=ENSMUSG00000049526,ENSMUSG00000025232;HOMLEN=0;SPLICESCORE=4
+9	108783870	bnd_8762_1	G	G]9:108796064]	243	PASS	SVTYPE=BND;MATEID=bnd_8762_2;DP=36;SPLITCNT=28;SPANCNT=8;GENE=SNORA28,Ip6k2;GENEID=ENSMUSG00000088626,ENSMUSG00000032599;HOMLEN=0;SPLICESCORE=4
+9	108796064	bnd_8762_2	A	[9:108783870[A	243	PASS	SVTYPE=BND;MATEID=bnd_8762_1;DP=36;SPLITCNT=28;SPANCNT=8;GENE=SNORA28,Ip6k2;GENEID=ENSMUSG00000088626,ENSMUSG00000032599;HOMLEN=0;SPLICESCORE=4
+10	24597524	bnd_12600_1	G	G]7:66355922]	148	PASS	SVTYPE=BND;MATEID=bnd_12600_2;DP=6;SPLITCNT=1;SPANCNT=5;GENE=Ctgf,Lrrk1;GENEID=ENSMUSG00000019997,ENSMUSG00000015133;HOMLEN=0;SPLICESCORE=3
+10	73201702	bnd_12868_2	A	]6:51467295]A	132	PASS	SVTYPE=BND;MATEID=bnd_12868_1;DP=110;SPLITCNT=69;SPANCNT=41;GENE=Hnrnpa2b1,Gm15398;GENEID=ENSMUSG00000004980,ENSMUSG00000085456;HOMLEN=0;SPLICESCORE=1
+10	128814038	bnd_12549_2	G	[11:121206748[G	236	PASS	SVTYPE=BND;MATEID=bnd_12549_1;DP=36;SPLITCNT=18;SPANCNT=18;GENE=Hexdc,Dnajc14;GENEID=ENSMUSG00000039307,ENSMUSG00000025354;HOMLEN=1;SPLICESCORE=4;EXONBND
+11	52099150	bnd_1027_1	G	G]12:54980379]	212	PASS	SVTYPE=BND;MATEID=bnd_1027_2;DP=12;SPLITCNT=2;SPANCNT=10;GENE=Ppp2ca,Baz1a;GENEID=ENSMUSG00000020349,ENSMUSG00000035021;HOMLEN=3;SPLICESCORE=4
+11	87218328	bnd_66_1	A	A]11:87250589]	157	PASS	SVTYPE=BND;MATEID=bnd_66_2;DP=24;SPLITCNT=13;SPANCNT=11;GENE=Trim37,Ppm1e;GENEID=ENSMUSG00000018548,ENSMUSG00000046442;HOMLEN=0;SPLICESCORE=1
+11	87250589	bnd_66_2	A	[11:87218328[A	157	PASS	SVTYPE=BND;MATEID=bnd_66_1;DP=24;SPLITCNT=13;SPANCNT=11;GENE=Trim37,Ppm1e;GENEID=ENSMUSG00000018548,ENSMUSG00000046442;HOMLEN=0;SPLICESCORE=1
+11	106187103	bnd_1721_1	A	A[5:60176541[	188	PASS	SVTYPE=BND;MATEID=bnd_1721_2;DP=13;SPLITCNT=8;SPANCNT=5;GENE=Strada,Cbfa2t2-ps1;GENEID=ENSMUSG00000069631,ENSMUSG00000087034;HOMLEN=142;SPLICESCORE=1
+11	121206748	bnd_12549_1	C	C]10:128814038]	236	PASS	SVTYPE=BND;MATEID=bnd_12549_2;DP=36;SPLITCNT=18;SPANCNT=18;GENE=Hexdc,Dnajc14;GENEID=ENSMUSG00000039307,ENSMUSG00000025354;HOMLEN=1;SPLICESCORE=4;EXONBND
+12	54980379	bnd_1027_2	T	[11:52099150[T	212	PASS	SVTYPE=BND;MATEID=bnd_1027_1;DP=12;SPLITCNT=2;SPANCNT=10;GENE=Ppp2ca,Baz1a;GENEID=ENSMUSG00000020349,ENSMUSG00000035021;HOMLEN=3;SPLICESCORE=4
+12	55111181	bnd_9292_1	G	G]12:55213840]	135	PASS	SVTYPE=BND;MATEID=bnd_9292_2;DP=22;SPLITCNT=13;SPANCNT=9;GENE=Srp54c,1700047I17Rik2;GENEID=ENSMUSG00000073079,ENSMUSG00000094103;HOMLEN=0;SPLICESCORE=4;EXONBND
+12	55213840	bnd_9292_2	G	[12:55111181[G	135	PASS	SVTYPE=BND;MATEID=bnd_9292_1;DP=22;SPLITCNT=13;SPANCNT=9;GENE=Srp54c,1700047I17Rik2;GENEID=ENSMUSG00000073079,ENSMUSG00000094103;HOMLEN=0;SPLICESCORE=4;EXONBND
+12	73112254	bnd_9158_2	C	]12:73168000]C	238	PASS	SVTYPE=BND;MATEID=bnd_9158_1;DP=10;SPLITCNT=5;SPANCNT=5;GENE=Mnat1,Six4;GENEID=ENSMUSG00000021103,ENSMUSG00000034460;HOMLEN=0;SPLICESCORE=4
+12	73168000	bnd_9158_1	C	C[12:73112254[	238	PASS	SVTYPE=BND;MATEID=bnd_9158_2;DP=10;SPLITCNT=5;SPANCNT=5;GENE=Mnat1,Six4;GENEID=ENSMUSG00000021103,ENSMUSG00000034460;HOMLEN=0;SPLICESCORE=4
+12	113422730	bnd_9297_1	T	T]12:113426655]	212	PASS	SVTYPE=BND;MATEID=bnd_9297_2;DP=26;SPLITCNT=20;SPANCNT=6;GENE=Ighm,AC073553.3;GENEID=ENSMUSG00000076617,ENSMUSG00000092748;HOMLEN=0;SPLICESCORE=4
+12	113426655	bnd_9297_2	C	[12:113422730[C	212	PASS	SVTYPE=BND;MATEID=bnd_9297_1;DP=26;SPLITCNT=20;SPANCNT=6;GENE=Ighm,AC073553.3;GENEID=ENSMUSG00000076617,ENSMUSG00000092748;HOMLEN=0;SPLICESCORE=4
+13	105131562	bnd_5983_1	T	T]13:105167527]	207	PASS	SVTYPE=BND;MATEID=bnd_5983_2;DP=6;SPLITCNT=1;SPANCNT=5;GENE=4933425L06Rik,Rnf180;GENEID=ENSMUSG00000021718,ENSMUSG00000021720;HOMLEN=0;SPLICESCORE=1
+13	105167527	bnd_5983_2	C	[13:105131562[C	207	PASS	SVTYPE=BND;MATEID=bnd_5983_1;DP=6;SPLITCNT=1;SPANCNT=5;GENE=4933425L06Rik,Rnf180;GENEID=ENSMUSG00000021718,ENSMUSG00000021720;HOMLEN=0;SPLICESCORE=1
+14	31131376	bnd_9962_1	G	G]14:31134739]	189	PASS	SVTYPE=BND;MATEID=bnd_9962_2;DP=126;SPLITCNT=93;SPANCNT=33;GENE=2010107H07Rik,Nt5dc2;GENEID=ENSMUSG00000058351,ENSMUSG00000071547;HOMLEN=0;SPLICESCORE=4
+14	31134739	bnd_9962_2	A	[14:31131376[A	189	PASS	SVTYPE=BND;MATEID=bnd_9962_1;DP=126;SPLITCNT=93;SPANCNT=33;GENE=2010107H07Rik,Nt5dc2;GENEID=ENSMUSG00000058351,ENSMUSG00000071547;HOMLEN=0;SPLICESCORE=4
+15	33221484	bnd_11497_2	C	[5:23703360[C	230	PASS	SVTYPE=BND;MATEID=bnd_11497_1;DP=230;SPLITCNT=67;SPANCNT=163;GENE=SNORD93,Pgcp;GENEID=ENSMUSG00000096832,ENSMUSG00000039007;HOMLEN=0;SPLICESCORE=4
+15	74996568	bnd_11177_2	C	]15:75048442]C	144	PASS	SVTYPE=BND;MATEID=bnd_11177_1;DP=497;SPLITCNT=434;SPANCNT=63;GENE=Ly6c1,Ly6a;GENEID=ENSMUSG00000079018,ENSMUSG00000075602;HOMLEN=0;SPLICESCORE=4;ORF;EXONBND
+15	74996568	bnd_11169_2	A	]15:75048442]A	237	PASS	SVTYPE=BND;MATEID=bnd_11169_1;DP=702;SPLITCNT=410;SPANCNT=292;GENE=Ly6c1,Ly6a;GENEID=ENSMUSG00000079018,ENSMUSG00000075602;HOMLEN=0;SPLICESCORE=4;ORF;EXONBND
+15	75048442	bnd_11177_1	A	A[15:74996568[	144	PASS	SVTYPE=BND;MATEID=bnd_11177_2;DP=497;SPLITCNT=434;SPANCNT=63;GENE=Ly6c1,Ly6a;GENEID=ENSMUSG00000079018,ENSMUSG00000075602;HOMLEN=0;SPLICESCORE=4;ORF;EXONBND
+15	75048442	bnd_11169_1	G	G[15:74996568[	237	PASS	SVTYPE=BND;MATEID=bnd_11169_2;DP=702;SPLITCNT=410;SPANCNT=292;GENE=Ly6c1,Ly6a;GENEID=ENSMUSG00000079018,ENSMUSG00000075602;HOMLEN=0;SPLICESCORE=4;ORF;EXONBND
+15	102188962	bnd_11202_1	G	G]15:102202444]	248	PASS	SVTYPE=BND;MATEID=bnd_11202_2;DP=31;SPLITCNT=21;SPANCNT=10;GENE=Csad,Zfp740;GENEID=ENSMUSG00000023044,ENSMUSG00000046897;HOMLEN=0;SPLICESCORE=4
+15	102202444	bnd_11202_2	C	[15:102188962[C	248	PASS	SVTYPE=BND;MATEID=bnd_11202_1;DP=31;SPLITCNT=21;SPANCNT=10;GENE=Csad,Zfp740;GENEID=ENSMUSG00000023044,ENSMUSG00000046897;HOMLEN=0;SPLICESCORE=4
+16	19493776	bnd_7456_2	T	[18:30311220[T	189	PASS	SVTYPE=BND;MATEID=bnd_7456_1;DP=19;SPLITCNT=9;SPANCNT=10;GENE=Pik3c3,Olfr166;GENEID=ENSMUSG00000033628,ENSMUSG00000056822;HOMLEN=0;SPLICESCORE=1
+16	37799068	bnd_4068_2	T	]1:106734547]T	233	PASS	SVTYPE=BND;MATEID=bnd_4068_1;DP=19;SPLITCNT=8;SPANCNT=11;GENE=Kdsr,Fstl1;GENEID=ENSMUSG00000009905,ENSMUSG00000022816;HOMLEN=2;SPLICESCORE=4
+17	17395298	bnd_3153_1	C	C]17:17411818]	206	PASS	SVTYPE=BND;MATEID=bnd_3153_2;DP=41;SPLITCNT=16;SPANCNT=25;GENE=AC154200.1,Lix1;GENEID=ENSMUSG00000097379,ENSMUSG00000047786;HOMLEN=0;SPLICESCORE=1
+17	17411818	bnd_3153_2	T	[17:17395298[T	206	PASS	SVTYPE=BND;MATEID=bnd_3153_1;DP=41;SPLITCNT=16;SPANCNT=25;GENE=AC154200.1,Lix1;GENEID=ENSMUSG00000097379,ENSMUSG00000047786;HOMLEN=0;SPLICESCORE=1
+17	35266514	bnd_3184_1	G	G]17:35383995]	218	PASS	SVTYPE=BND;MATEID=bnd_3184_2;DP=47;SPLITCNT=40;SPANCNT=7;GENE=H2-D1,H2-Q4;GENEID=ENSMUSG00000073411,ENSMUSG00000035929;HOMLEN=0;SPLICESCORE=4;EXONBND
+17	35383995	bnd_3184_2	A	[17:35266514[A	218	PASS	SVTYPE=BND;MATEID=bnd_3184_1;DP=47;SPLITCNT=40;SPANCNT=7;GENE=H2-D1,H2-Q4;GENEID=ENSMUSG00000073411,ENSMUSG00000035929;HOMLEN=0;SPLICESCORE=4;EXONBND
+17	63864053	bnd_3179_1	T	T]17:63896016]	195	PASS	SVTYPE=BND;MATEID=bnd_3179_2;DP=17;SPLITCNT=10;SPANCNT=7;GENE=A930002H24Rik,Fer;GENEID=ENSMUSG00000045506,ENSMUSG00000000127;HOMLEN=0;SPLICESCORE=3
+17	63896016	bnd_3179_2	A	[17:63864053[A	195	PASS	SVTYPE=BND;MATEID=bnd_3179_1;DP=17;SPLITCNT=10;SPANCNT=7;GENE=A930002H24Rik,Fer;GENEID=ENSMUSG00000045506,ENSMUSG00000000127;HOMLEN=0;SPLICESCORE=3
+18	4198107	bnd_5326_2	G	]2:165827729]G	136	PASS	SVTYPE=BND;MATEID=bnd_5326_1;DP=20;SPLITCNT=7;SPANCNT=13;GENE=Zmynd8,Gm10557;GENEID=ENSMUSG00000039671,ENSMUSG00000073647;HOMLEN=9;SPLICESCORE=1
+18	28188917	bnd_5160_2	A	[3:103040040[A	213	PASS	SVTYPE=BND;MATEID=bnd_5160_1;DP=63;SPLITCNT=33;SPANCNT=30;GENE=Csde1,SNORA17;GENEID=ENSMUSG00000068823,ENSMUSG00000087940;HOMLEN=91;SPLICESCORE=3
+18	30311220	bnd_7456_1	G	G]16:19493776]	189	PASS	SVTYPE=BND;MATEID=bnd_7456_2;DP=19;SPLITCNT=9;SPANCNT=10;GENE=Pik3c3,Olfr166;GENEID=ENSMUSG00000033628,ENSMUSG00000056822;HOMLEN=0;SPLICESCORE=1
+18	53932206	bnd_5141_1	T	T[X:53418862[	201	PASS	SVTYPE=BND;MATEID=bnd_5141_2;DP=26;SPLITCNT=9;SPANCNT=17;GENE=Csnk1g3,Gm14584;GENEID=ENSMUSG00000073563,ENSMUSG00000083798;HOMLEN=266;SPLICESCORE=2
+19	37678397	bnd_13800_1	C	C]19:37696729]	204	PASS	SVTYPE=BND;MATEID=bnd_13800_2;DP=15;SPLITCNT=3;SPANCNT=12;GENE=Exoc6,Cyp26a1;GENEID=ENSMUSG00000053799,ENSMUSG00000024987;HOMLEN=0;SPLICESCORE=1
+19	37696729	bnd_13800_2	A	[19:37678397[A	204	PASS	SVTYPE=BND;MATEID=bnd_13800_1;DP=15;SPLITCNT=3;SPANCNT=12;GENE=Exoc6,Cyp26a1;GENEID=ENSMUSG00000053799,ENSMUSG00000024987;HOMLEN=0;SPLICESCORE=1
+X	37143984	bnd_8690_2	G	]9:7872842]G	132	PASS	SVTYPE=BND;MATEID=bnd_8690_1;DP=9;SPLITCNT=4;SPANCNT=5;GENE=Birc3,Nkap;GENEID=ENSMUSG00000032000,ENSMUSG00000016409;HOMLEN=39;SPLICESCORE=1
+X	53418862	bnd_5141_2	A	]18:53932206]A	201	PASS	SVTYPE=BND;MATEID=bnd_5141_1;DP=26;SPLITCNT=9;SPANCNT=17;GENE=Csnk1g3,Gm14584;GENEID=ENSMUSG00000073563,ENSMUSG00000083798;HOMLEN=266;SPLICESCORE=2