Mercurial > repos > jesse-erdmann > tapdance
changeset 0:1437a2df99c0
Uploaded
| author | jesse-erdmann |
|---|---|
| date | Fri, 09 Dec 2011 11:56:56 -0500 |
| parents | |
| children | 034eb7e37be4 |
| files | lib/Fisher_clean.pl lib/Report.pl lib/TAP2.pl lib/TAP4.pl lib/TAPDANCE.pl lib/cis_finder.pl lib/cis_summary.txt lib/config.pl lib/convert_nr_2_annot.pl lib/feature_finder.pl lib/feature_finder_methods.pl lib/insert_vis.R lib/list2tab.pl lib/list_projects.pl lib/matrix2fisher.pl lib/mm9.bed lib/project_man.pl lib/project_test.pl lib/shuffle.pl lib/tapdance_base_config.pl lib/util.pl lib/visualize.pl list_projects.xml tapdance.xml tapdance_runner.pl util.pl |
| diffstat | 26 files changed, 41607 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/Fisher_clean.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,124 @@ +#this is a script to automate data workup following Fishers exact test association analyses +# This script takes the R_result and the names file and then generates +#4 4xls spreadsheets +# 3 images +@name; +@sub_name; +@result; +@sub_result; +$count = 0; +unless (-d "results/Assoc") { + mkdir("results/Assoc"); +} +open OUT1, "> results/Assoc/Associations.xls"; +open OUT2, "> results/Assoc/Ann_cis_list.txt"; +open OUT3, "> results/Assoc/Ann_cis_table.xls"; +print OUT3 "Event1\tEvent2\tFET Pvalue\tBonferroni Significance\tBH 20%FDR Significancei\n"; +open OUT4, "> results/Assoc/Cis_cis_list.txt"; +open OUT5, "> results/Assoc/Cis_cis_table.xls"; +print OUT5 "Event1\tEvent2\tFET Pvalue\tBonferroni Significance\tBH 20%FDR Significance\n"; +open OUT6, "> results/Assoc/Ann_ann_list.txt"; +open OUT7, "> results/Assoc/Ann_Ann_table.xls"; +print OUT7 "Event1\tEvent2\tFET Pvalue\tBonferroni Significance\tBH 20%FDR Significance\n"; +open SOURCE, "< results/Assoc/R_result.txt"; +@tableAnnCis; +@tableAnnAnn; +@tableCisCis; +while (defined($line = <SOURCE>)) { +$count++; +chomp $line; +@result= split(/\t/, $line); +@sub_result= split(/\s=\s|\s<\s/, $result[1]); +print $sub_result[1]; +$pval[$count]= $sub_result[1]; +} +$count = 0; +open SOURCE, "< results/Assoc/Fisher_pre_named.txt"; +while (defined($line = <SOURCE>)) { +$count++; +chomp $line; +@name= split(/\t/, $line); +@sub_name= split(/__/, $name[0]); +print OUT1 "$line\t$pval[$count]\n"; +if (($sub_name[1] =~m/descriptor/) and ($sub_name[0] !~ m/descriptor/)) { +$viewpval= -(log($pval[$count])/log(10)); +print OUT2 "$sub_name[1]\t$sub_name[0]\t$viewpval\n"; +if ($pval[$count] < 0.05) { +$data4table = "$sub_name[1]\t$sub_name[0]\t$pval[$count]\n"; +push(@tableAnnCis, $data4table); +} +} + + +if (($sub_name[1] !~m/descriptor/) and ($sub_name[0] !~ m/descriptor/)) { +$viewpval= -log($pval[$count]); +print OUT4 "$sub_name[1]\t$sub_name[0]\t$viewpval\n"; +print OUT4 "$sub_name[0]\t$sub_name[1]\t$viewpval\n"; +if ($pval[$count] < 0.05) { +$data4table = "$sub_name[1]\t$sub_name[0]\t$pval[$count]\n"; +push(@tableCisCis, $data4table); +} +} + +if (($sub_name[1] =~m/descriptor/) and ($sub_name[0] =~ m/descriptor/)) { +$viewpval= -log($pval[$count]); +print OUT6 "$sub_name[1]\t$sub_name[0]\t$viewpval\n"; +print OUT6 "$sub_name[0]\t$sub_name[1]\t$viewpval\n"; +if ($pval[$count] < 0.05) { +$data4table = "$sub_name[1]\t$sub_name[0]\t$pval[$count]\n"; +push(@tableAnnAnn, $data4table); +} +} + + +} +@sortedAnnCis = sort { (split '\t', $a)[2] <=> (split '\t', $b)[2] } @tableAnnCis; +@sortedCisCis = sort { (split '\t', $a)[2] <=> (split '\t', $b)[2] } @tableCisCis; +@sortedAnnAnn = sort { (split '\t', $a)[2] <=> (split '\t', $b)[2] } @tableAnnAnn; + +open SOURCE, "< FISH/multi_test.txt"; +while (defined($line = <SOURCE>)) { +chomp $line; +@name=split(/\t/, $line); +$corrAnnCis = $name[2]; +$corrCisCis = $name[3]; +$corrAnnAnn = $name[4]; +} + +$pos = 1; +foreach (@sortedAnnCis) { +$bonf = 0.05/$corrAnnCis; +$fdr = ($pos/$corrAnnCis)*0.20; +$pos++; +chomp $_; +print OUT3 "$_\t$bonf\t$fdr\n"; +} +$pos = 1; + +foreach (@sortedCisCis) { +$bonf = 0.05/$corrCisCis; +$fdr = ($pos/$corrCisCis)*0.20; +$pos++; +chomp $_; +print OUT5 "$_\t$bonf\t$fdr\n"; +} +$pos =1; +foreach (@sortedAnnAnn) { +$bonf = 0.05/$corrAnnAnn; +$fdr = ($pos/$corrAnnAnn)*0.20; +$pos++; +chomp $_; +print OUT7 "$_\t$bonf\t$fdr\n"; +} + + +close OUT7; +close OUT6; +close OUT5; +close OUT4; +close OUT3; +close OUT2; +close OUT1; +system ("perl lib/list2tab.pl 1 2 3 0 results/Assoc/Ann_cis_list.txt > results/Assoc/Ann_cis_matrix.txt"); +system ("perl lib/list2tab.pl 1 2 3 0 results/Assoc/Cis_cis_list.txt > results/Assoc/Cis_cis_matrix.txt"); +system ("perl lib/list2tab.pl 1 2 3 0 results/Assoc/Ann_ann_list.txt > results/Assoc/Ann_ann_matrix.txt");
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/Report.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,262 @@ +require 'config.pl'; + + + +$sth = $dbh->prepare("drop table if exists lib_m_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table lib_m_$proj select distinct library, sum(number) as total from illumina4dec2_$proj group by library"); +$sth->execute; +$sth = $dbh->prepare("update lib_m_$proj set library = left(library,LENGTH(library)-2) where library like '%-L'"); +$sth->execute; +$sth = $dbh->prepare("update lib_m_$proj set library = left(library,LENGTH(library)-2) where library like '%-R'"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists lib_mappable_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table lib_mappable_$proj select library, sum(total) as total from lib_m_$proj group by library"); +$sth->execute; + +print "completed mapping!!!"; + +### +#Generate a report describing the mapping. +### + +open OUT, "> results/project_summary.txt"; +print OUT "Summary of project $proj\n\nA.Report of project based counts \n"; + +$sth = $dbh->prepare("select count(*) from illumina_raw_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Seqeunces\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_decoded_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Sequences that map to a barcode\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Sequences with a barcode that also have an IRDR\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'idR';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Ideal Right linker sequences\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'idL';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Ideal left linkersequences\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'good';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of good sequences\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'bam';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Bamh1 sequence Artifact (removed)\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'noTA';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of sequences removed because of lack of TA sequence)\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'min';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of sequences removed because of sequence length < 24)\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina4dec2_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of unique seqeunces pryor to mapping\n"; +} + +$sth = $dbh->prepare("select sum(number) from bowtie_$proj;"); +$sth->execute; +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total SUM of seqeunces that mapped\n"; +} + +$sth = $dbh->prepare("select count(*) from bowtie_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Number of unique sequences that mapped\n"; +} + +$sth = $dbh->prepare("select count(*) from bowtie_lib_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Number of distinct locations mapped\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_hist_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Number of distinct regions mapped\n"; +} +close OUT; + +#report part B +open OUT, ">> results/project_summary.txt"; +print OUT"\n\nB. Library counts associated with project $proj\n"; + +%sequence=''; +%barcode_count=''; +%IRDR_count=''; +%IRDR_good=''; +%IRDR_unique=''; +%map_count=''; +%map_total=''; +%nr_count=''; +@library=''; + +$sth = $dbh->prepare("select * from barcode_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $sequence{$row[1]} = $row[0]; + push(@library,$row[1]); +} + +$sth = $dbh->prepare("select library, count(id) from illumina_decoded_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $barcode_count{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(id) from illumina_without_IRDR_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $IRDR_count{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, sum(number) from illumina4dec2_$proj group by library;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $IRDR_good{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(number) from illumina4dec2_$proj group by library;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $IRDR_unique{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, sum(number) from bowtie_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $map_count{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(id) from bowtie_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $map_total{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(chromo) from bowtie_lib_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $map_nr{$row[0]} = $row[1]; +} + +print OUT "Library\tBarcode Sequence\tBarcode\tIRDR\tMappable\tUnique mappable\tTotal map\tUnique map\tNR map"; +foreach $item (@library) { +print OUT "$item\t$sequence{$item}\t$barcode_count{$item}\t$IRDR_count{$item}\t$IRDR_good{$item}\t$IRDR_unique{$item}\t$map_count{$item}\t$map_total{$item}\t$map_nr{$item}\n"; +} +close OUT; + +open OUT, ">> results/project_summary.txt"; +print OUT "\n\nC. Regions associated with project $proj\n"; + +%mappable=''; +%name=''; +%count01=''; +%count001=''; +%count0001=''; +%count0=''; +@library=''; + +$sth = $dbh->prepare("select * from lib_count_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $name{$row[0]} = $row[1]; + push(@library,$row[0]); +} + +$sth = $dbh->prepare("select * from lib_mappable_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $mappable{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > .01 group by A.library order by chromo,start+0"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $count01{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > .001 group by A.library order by chromo,start+0"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $count001{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > .0001 group by A.library order by chromo,start+0"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $count0001{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > 0 group by A.library order by chromo,start+0"); +$sth->execute; + +print OUT "Library\tTotal mappable\ttotal map\tLocations >0.01\tLocations >0.001\tLocations >0.0001\t All mapped Locations"; +while ((@row) = $sth->fetchrow_array) { + $count0{$row[0]} = $row[1]; +} + +foreach $item (@library) { +print OUT "$item\t$mappable{$item}\t$name{$item}\t$count01{$item}\t$count001{$item}\t$count0001{$item}\t$count0{$item}\n"; +} +close OUT; + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/TAP2.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,321 @@ +#This is the TAp2.pl script +#The goal of this is to count the number of CIS present in a NR set +# one file is required nr.txt sorted in chromosome order! +# Aaron Lyman Sarver Oct 21, 2010 +# This script takes over following the bowtie mapping and generates CIS. +# Update NOV15,2010 to pass library information through +#$Fully modified december 1 2010i +#Fully modifed May 1 2010 +use File::Copy; +require 'config.pl'; +require 'lib/feature_finder_methods.pl'; +my $path = $0; +$path =~ s/\/\w*\.pl$//g; +require "$path/project_man.pl"; +unless(-d "CIS") { + mkdir("CIS"); +} + +open CIS, "> results/summary_CIS_$proj.txt"; +close CIS; + +#generate required tables +$sth = $dbh->prepare("drop table if exists cis_result_final_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table cis_result_final_$proj (chromo varchar(20), start int, stop int, name varchar(20), number varchar(20), size varchar(20), pvalue double, total varchar(20), pvaluetotal double,region varchar(20), pvalueregion double, library_name varchar(5000), strand int, gene_name varchar(1000), type varchar(20))"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists sort_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table sort_$proj (chromo varchar(20), start int, stop int, name varchar(20), number varchar(20), size varchar(20), pvalue double, total varchar(20), pvaluetotal double,region varchar(20), pvalueregion double, library_name varchar(5000), strand int, gene_name varchar(1000), type varchar(20))"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists sort2_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table sort2_$proj (chromo varchar(20), start int, stop int, name varchar(20), number varchar(20), size varchar(20), pvalue double, total varchar(20), pvaluetotal double,region varchar(20), pvalueregion double, library_name varchar(5000), strand int, gene_name varchar(1000), type varchar(20))"); +$sth->execute; + +#load concatamer information from file +$sth = $dbh->prepare("drop table if exists chromo_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table chromo_$proj (chromo varchar(20) ) "); +$sth->execute; +$sth = $dbh->prepare("load DATA local INFILE 'data/chromo.tab' INTO TABLE chromo_$proj "); +$sth->execute; +$sth = $dbh->prepare("select distinct chromo from chromo_$proj"); +$sth->execute; +print "10.3 - Loaded concatamer chromo\n"; +#generate donor exclusion portion of the SQL query +@exclude; +$query_chromo= ''; +while ((@row) = $sth->fetchrow_array) { + push (@exclude,$row[0]); + print "\n$row[0]"; +} +print @exclude; +foreach $desc(@exclude) { + $query_chromo = $query_chromo."and chromo != '".$desc."' "; +} +print $query_chromo; + +#10.4 load library metadata +$sth = $dbh->prepare("drop table if exists metadata_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table metadata_$proj (library varchar(20), descriptor varchar(20), type varchar (20) ) "); +$sth->execute; +$sth = $dbh->prepare("load DATA local INFILE 'data/metadata.tab' INTO TABLE metadata_$proj "); +$sth->execute; +$sth = $dbh->prepare("select distinct descriptor from metadata_$proj where type = 'cis'"); +$sth->execute; +print "10.4 - Loaded metadata\n"; + +#10.2 load the feature hash +print "10.2 - Loading features...\n"; +my ($feature_file, $window, $fchrom, $fstart, $fend, $debug) = ($annotation_file, 20000, 0, 1, 2, 1); +my $feature_hash_ref = &feature_index(\$feature_file, \$window, \$fchrom, \$fstart, \$fend, \$debug); +print "10.2 - Features loaded.\n"; + +#generate metadata based library portion of the SQL query +@descriptors; +$query_definition = ''; +while ((@row) = $sth->fetchrow_array) { + push (@descriptors,$row[0]); + print "\n$row[0]"; +} +print @descriptors; +foreach $desc(@descriptors) { + $query_definition = ''; + $query = "select distinct library from metadata_$proj where descriptor = '$desc'"; +#print "\n$query\n"; + $sth = $dbh->prepare("$query"); + $sth->execute; + + while ((@row) = $sth->fetchrow_array) { + $query_definition = $query_definition."or A.library = '$row[0]' "; +#print "$row[0]"; + } + print "\n$desc\n"; +#print "$query_definition\n"; +#setup the looping featured + @options = (''); + foreach $library(@options) { + @percent =("$library_percent"); + foreach $percent(@percent) { + +#11.1 query to select regions of interest + $sth = $dbh->prepare("select chromo, start, A.library,count, count/total,orient from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > $percent $query_chromo and (1=2 $query_definition) +order by chromo,start+0 ;"); + $sth->execute; + + unless(-d "results") { + mkdir("results"); + } + unless(-d "results/$desc") { + mkdir("results/$desc"); + } + + open OUT, "> CIS/nr.txt"; + $name = "$desc-nr-$proj-$percent"; + open OUT2, "> results/$desc/$name.txt"; + open OUT3, "> results/$desc/$name.BED"; + print OUT3 "track type ='BED' name='$name' description='$name Insertions' visibility=2 itemRgb='On'"; + while ((@row) = $sth->fetchrow_array) { + print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]"; + $start = $row[1]-50; + $stop = $row[1]+50; + print OUT2 "\n$row[0]\t$start\t$stop\t$row[2]\t$row[3]\t$row[4]\t$row[5]"; + print OUT3 "\n$row[0]\t$start\t$stop\t$row[2]\t$row[3]\t$row[5]\t$start\t$stop\t159,0,197"; + } + close OUT; + +#11.2 Anotate the inserts from the .txt file + my ($interval_file, $out_file, $req_res_type, $direction, $interval_cols, $feature_cols, $display_distance) = ("results/$desc/$name.txt", "results/$desc/$name.ann.txt", "ALL", "BOTH", "1:2:3:4:10", "1:2:3:4:6", 0); + &process_intervals(\$interval_file, \$out_file, $feature_hash_ref, \$req_res_type, \$direction, \$window, \$html, \$cturl, \$db, \$interval_cols, \$feature_cols, \$debug, \$display_distance); + unlink("results/$desc/$name.txt"); + #generate a list of gense with high density inserts + #if (($percent == '0.01') and ($library eq 'library')) { + #system("perl lib/convert_nr_2_annot.pl results/$desc/$name.txt results/$desc/$name.ingenuity.txt"); + #} + + $count = 0; + open SOURCE, "< CIS/nr.txt"; + while (defined($line = <SOURCE>)) { + $count++; + } + @libSizes =(); + open CIS, ">> results/summary_CIS_$proj.txt"; + print "\n\n11.3 - $name Total number of NR regions $count\n"; + print CIS "\n\n$name\nExcluded chromosomes $query_chromo\nTotal number of NR regions $count\n"; + print CIS "CIS analyses calculate window sizes based on NR count\n"; + +#11.4 Ideal window size calculation + $n = 10000; + $f = 3; + while ($n < 300000) { + $stat =poissonBonf($n,$count,$f); + if ($stat > 0.05) { + $nf=$n-1000; + $stat2=poissonBonf($nf,$count,$f); + if ($stat2 < 0.05) { + print "$stat2\t$nf\t$f\n"; + print CIS "$stat2\t$nf\t$f\n"; + unshift(@libSizes, $nf); + } + $f=$f+1; + } + $n = $n+1000; + } + $nf='301000'; + unshift(@libSizes, $nf); + print @libSizes; + print CIS @libsizes; + close CIS; + if ($count < 2000) { + @libSizes =('301000','200000','100000','50000','25000','12500'); + } + if ($count > 200000) { + @libSizes =('301000','200000','100000','50000','25000','12500'); + } + +#11.5 + foreach $lib(@libSizes) { + +#11.5 call the cis_finder.pl script to calculate the CIS. + system("perl lib/cis_finder.pl $lib"); + print "\n$lib\n"; + + +#11.6 call the feature_finder.pl script to annotat the CIS regions + my ($interval_file, $out_file, $req_res_type, $direction, $interval_cols, $feature_cols, $display_distance) = ("CIS/cis$lib.txt", "CIS/final_cis_named_$lib.txt", "ALL", "BOTH", "1:2:3:4:10", "1:2:3:4:6", 0); + &process_intervals(\$interval_file, \$out_file, $feature_hash_ref, \$req_res_type, \$direction, \$window, \$html, \$cturl, \$db, \$interval_cols, \$feature_cols, \$debug, \$display_distance); + } + +#load the results into the database.and resolve overlap + $sth = $dbh->prepare("delete from sort_$proj"); + $sth->execute; + $sth = $dbh->prepare("delete from sort2_$proj"); + $sth->execute; + +#11.7 + foreach $lib(@libSizes) { + $sth = $dbh->prepare("load DATA local INFILE 'CIS/final_cis_named_$lib.txt' INTO TABLE sort2_$proj"); +$sth->execute; + resolve_cis(); +} + +#MOve and rename CIS to cis_result_final table + $filename = $desc."_".$percent.$library; + $query2 = "delete from cis_result_final_$proj where type= '$filename'"; + print "\n$query2\n"; + $sth = $dbh->prepare("$query2"); + $sth->execute; + $sth = $dbh->prepare("insert into cis_result_final_$proj select * from sort_$proj"); + $sth->execute; + $query3 = "update cis_result_final_$proj set type = '$filename' where type is NULL"; + print "$query3"; + $sth = $dbh->prepare("$query3"); + $sth->execute; + +#Export CIS list to the results subdirectory + $query4 = "select number,CONCAT(chromo,':',start,'-',stop)as pos, total, pvaluetotal,number, pvalue,region,pvalueregion,gene_name,library_name,strand from cis_result_final_$proj where type = '$filename' and pvalueregion < '$CIS_region_pvalue' and pvaluetotal < '$CIS_total_pvalue' and pvalue < '$CIS_library_pvalue' and gene_name not like '%BAD%' order by pvalueregion;"; + $sth = $dbh->prepare("$query4"); + $sth->execute; + open CIS, "> results/$desc/cis_$name.xls"; + print CIS "$filename\nnumber\tpos\t#inserts\tpvalueinsert#\t#library\tpvaluelibrary#\t#regions\tpvalueregion#\tgene_name\tlibrary_name\tnumber of inserts drive transcription on positive strand"; + while ((@row) = $sth->fetchrow_array) { + print CIS "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]\t$row[9]\t$row[10]\t$row[11]\t"; + } + close CIS; + + + open SOURCE, "< results/$desc/cis_$name.xls"; + open CIS, "> results/$desc/plot_$name.wig"; + print CIS "track type=wiggle_0 name=\"$proj.$filename\" description=\"$proj.$filename\" visibility=full autoScale=off"; + while (defined($line = <SOURCE>)) { + chomp $line; + @field= split(/\t/, $line); + @chromo=split(/:|-/, $field[1]); + + if ($field[1] =~ m/chr/) { + if ($field[7] < 1.0e-100) { + $field[7] = 1.0e-100;} + + $log= -(log($field[7])/log(10)); + print CIS "\n$chromo[0]\t$chromo[1]\t$chromo[2]\t$log"; + } + } + close CIS; + +#11.11 Generate the cis summary file of top 25 library CIS + $query4 = "select number,CONCAT(chromo,':',start,'-',stop)as pos, total, pvaluetotal,number, pvalue,region,pvalueregion,gene_name,library_name,strand from cis_result_final_$proj where type = '$filename' and pvalueregion < '$CIS_region_pvalue' and pvaluetotal < '$CIS_total_pvalue' and pvalue < '$CIS_library_pvalue' and gene_name not like '%BAD%' order by pvalueregion;"; + print "$query4"; + $sth = $dbh->prepare("$query4"); + $sth->execute; + open CIS, ">> results/summary_CIS_$proj.txt"; + print CIS "\n\n$filename\nnumber\tpos\t#inserts\tpvalueinsert#\t#library\tpvaluelibrary#\t#regions\tpvalueregion#\tgene_name\tlibrary_name\t+strand\t"; + while ((@row) = $sth->fetchrow_array) { + print CIS "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]\t$row[9]\t$row[10]\t$row[11]\t"; + } + close CIS; + +#generate matrix and carry out association analyses + if (($desc eq 'all') and ($percent == 0.0001) ) { + print "\n\n Starting Association analyses for $name"; + mkdir "FISH"; + mkdir "results/Assoc"; + system ('perl lib/visualize.pl'); + copy("FISH/cis4cluster.txt", "results/Assoc/cis4cluster.txt") or die "Unable to copy file: $!\n"; + #system ('module load R'); + system ('perl lib/matrix2fisher.pl FISH/cis4cluster.txt'); + copy("FISH/R_result.txt", "results/Assoc/R_result.txt") or die "Unable to copy file: $!\n"; + copy("FISH/Fisher_pre_named.txt", "results/Assoc/Fisher_pre_named.txt") or die "Unable to copy file: $!\n"; + system ('perl lib/Fisher_clean.pl'); + } + + }#close the threshhold loop + }#close the libraries loop +}#close the metadata loop + +&set_project_status($proj, 0, 1); + +exit(0); + +sub resolve_cis { + $sth = $dbh->prepare("delete from A using sort_$proj A, sort2_$proj B where A.chromo = B.chromo and A.start <= B.start and A.stop >= B.start and A.pvalue > B.pvalue"); + $sth->execute; + + $sth = $dbh->prepare("delete from A using sort_$proj A, sort2_$proj B where A.chromo = B.chromo and A.start <= B.stop and A.stop >= B.stop and A.pvalue > B.pvalue"); + $sth->execute; + $sth = $dbh->prepare("delete from B using sort_$proj A, sort2_$proj B where A.chromo = B.chromo and A.start <= B.start and A.stop >= B.start and A.pvalue < B.pvalue; "); + $sth->execute; + $sth = $dbh->prepare("delete from B using sort_$proj A, sort2_$proj B where A.chromo = B.chromo and A.start <= B.stop and A.stop >= B.stop and A.pvalue <= + B.pvalue; "); + $sth->execute; + + $sth = $dbh->prepare("insert into sort_$proj select * from sort2_$proj"); + $sth->execute; + + $sth = $dbh->prepare("delete from sort2_$proj"); + $sth->execute; +} + +sub poisson { + return ((($_[1]/(2393726033/$_[0]))**($_[2]))*(2.71828**-($_[1]/(2393726033/$_[0 + ])))/(fac($_[2]))); +} + +sub poissonBonf { + return (((($_[1]/(2393726033/$_[0]))**($_[2]))*(2.71828**-($_[1]/(2393726033/$_[ + 0])))/(fac($_[2])))*$_[1]); +} + +sub fac { + my ($n) = @_; + + if ($n < 2) { + return $n; + } + else { + return $n * fac($n-1); + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/TAP4.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,128 @@ +#This is the TAp2.pl script +#The goal of this is to count the number of CIS present in a NR set +# one file is required nr.txt sorted in chromosome order! +# Aaron Lyman Sarver Oct 21, 2010 +# This script takes over following the bowtie mapping and generates CIS. +# Update NOV15,2010 to pass library information through +#$Fully modified december 1 2010i + +require 'config.pl'; +require 'lib/feature_finder_methods.pl'; +my $path = $0; +$path =~ s/\/\w*\.pl$//g; +require "$path/project_man.pl"; +unless (-d "CIS") { + mkdir("CIS"); +} +unless (-d "results") { + mkdir("results"); +} + +$proj_all = $proj."_all"; + +$sth = $dbh->prepare("drop table if exists lib_mappable_$proj_all"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists lib_mappable_$proj"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists illumina_hist_$proj_all"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists illumina_hist_$proj"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists bowtie_lib_$proj_all"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists bowtie_lib_$proj"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists metadata_$proj_all"); +$sth->execute; + + +open DIN, "< data/meta.tab"; +@met; +while (defined($line = <DIN>)) { + chomp $line; + @field= split(/\t/, $line); + push (@met,$line); +} + +$proj_all = $proj."_all"; +$var=shift(@met); + +$sth = $dbh->prepare("create table lib_mappable_$proj_all select * from lib_mappable_$var"); +$sth->execute; +$sth = $dbh->prepare("create table illumina_hist_$proj_all select * from illumina_hist_$var"); +$sth->execute; +$sth = $dbh->prepare("create table bowtie_lib_$proj_all select * from bowtie_lib_$var"); +$sth->execute; +$sth = $dbh->prepare("create table metadata_$proj_all select * from metadata_$var"); +$sth->execute; + +foreach $var(@met) { +$sth = $dbh->prepare("insert into lib_mappable_$proj_all select * from lib_mappable_$var"); +$sth->execute; +$sth = $dbh->prepare("insert into illumina_hist_$proj_all select * from illumina_hist_$var"); +$sth->execute; +$sth = $dbh->prepare("insert into bowtie_lib_$proj_all select * from bowtie_lib_$var"); +$sth->execute; +$sth = $dbh->prepare("insert into metadata_$proj_all select * from metadata_$var"); +$sth->execute; +} + +unless(-e "data/metadata.tab") { + $sth = $dbh->prepare("select library, descriptor, type from metadata_$proj_all"); + $sth->execute; + open(my $meta_out, ">", "data/metadata.tab") || die "Unable to open data/metadata.tab for output. $!\n"; + while ((@row) = $sth->fetchrow_array) { + print $meta_out join("\t", @row) . "\n"; + } + close($meta_out); +} + + +$sth = $dbh->prepare("create table lib_mappable_$proj select distinct library, sum(total) as total from lib_mappable_$proj_all group by library;"); +$sth->execute; + +$sth = $dbh->prepare("create table illumina_hist_$proj select distinct library, chromo, start, sum(count) as count,orient from illumina_hist_$proj_all group by library,chromo,start,orient;"); +$sth->execute; + +$sth = $dbh->prepare("create table bowtie_lib_$proj select distinct library,chromo, start,stop, pos, sum(count) as count,strand, orient from bowtie_lib_$proj_all group by library,chromo,start,stop,pos,strand order by chromo,start+0,orient ;"); +$sth->execute; + +$sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj"); +$sth->execute; +#7.2 +open OUT, "> results/raw_$proj.BED"; +print OUT "track type ='BED' name='raw$proj' description='all$proj' visibility=2 itemRgb='On'"; +while ((@row) = $sth->fetchrow_array) { + print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]";} +close OUT; +#7.3 +$sth = $dbh->prepare("drop table if exists convert_2_hex_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table convert_2_hex_$proj (orient varchar(5), hex varchar(20))"); +$sth->execute; +$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"A\", \"255,0,0\")"); +$sth->execute; +$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"B\", \"0,0,255\")"); +$sth->execute; +$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"U\", \"0,0,0\")"); +$sth->execute; + +$sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj where count > 9"); +### JJE +#$sth = $dbh->prepare("select chromo, start, start+1, concat(library,count),count,'+',start,start+1, hex from bowtie_lib_$proj A, convert_2_hex_$proj B where A.orient = B.orient and count > 9"); +### +$sth->execute; +open OUT, "> results/raw10_$proj.BED"; +print OUT "track type ='BED' name='raw10$proj' description='10$proj' visibility=2 itemRgb='On'"; +while ((@row) = $sth->fetchrow_array) { + print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]";} +close OUT; + +&set_project_status($proj, 1, 0); +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/TAPDANCE.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,841 @@ +# Description: Processing of transposon instertion sequences. +# Requirements perl DBI read write accessible database +# Requires a file labeled barcode.txt, and a tab delimited file contatining seqeunces. +# Should work on files of less than 40 million sequences. +# Identifies and removes barcodes, IRDR sequences and linker sequences from sequencing data, then compiles a list of non redundant sequences. +# This scripts conducts the PAPS steps 1 +# Aaron Lyman Sarver July 12 2010 +# version 3.1 December 1 2010 + +use File::Copy; +require "config.pl"; + +my $path = $0; +$path =~ s/\/\w*\.pl$//g; +print $path . "\n"; +require "$path/util.pl"; +require "$path/project_man.pl"; + +my $chrom_map_ref = &get_chrom_map(); + +print join("\t", keys %{$chrom_map_ref}) . "\n"; + +unless (-d "results") { + mkdir("results"); +} + +#Remove old data if it exists +$sth = $dbh->prepare("drop table if exists illumina_raw_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists barcode_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists illumina_decoded_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists illumina_without_IRDR_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists illumina_nr_pre_map_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists illumina4dec_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists illumina4dec2_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists illumina_blastout_$proj"); +$sth->execute; + +#1.1 Part 1 load database +print "Started PROCESSING\n Tables identified by the postfix $proj in the database"; +#Determine number of columns in seqs.tab +open(SEQS, "<", "data/seqs.tab"); +my @cols = split("\t", <SEQS>); +close(SEQS); +print join(":", @cols); +print "\n"; +if ($#cols <= 2) { + &add_default_quality(); +} +$sth = $dbh->prepare("create table illumina_raw_$proj ( id varchar(20), description varchar(20), sequence varchar(100), quality varchar(100) ) "); +$sth->execute; + +print "generated illumina_raw table\n"; + +$sth = $dbh->prepare("load DATA local INFILE 'data/seqs.tab' INTO TABLE illumina_raw_$proj "); +$sth->execute; + +print "1.1 complete - Loaded illumina_raw &r/m data/seqS.tab file \n"; + +#1.2 +$sth = $dbh->prepare("create table barcode_$proj ( seq varchar(20), library varchar(30), direction varchar(20) )"); +$sth->execute; + +print "1.2 complete - Loaded barcode from data/barcode2lib.txt\n"; + +$sth = $dbh->prepare("load DATA local INFILE 'data/barcode2lib.txt' INTO TABLE barcode_$proj"); +$sth->execute; + +print "1.2 complete - Loaded barcode from data/barcode2lib.txt\n"; + +#1.3 +$sth = $dbh->prepare("select count(*) from illumina_raw_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print $row[0]." Number of lines in raw data file\n"; +} + +$sth = $dbh->prepare("select count(distinct id) from illumina_raw_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print $row[0]." Number of unique ids in illumina raw\n"; +} +#1.4 +$sth = $dbh->prepare("select count(*) from barcode_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print $row[0]." Number of lines in barcode \n"; +} + +#2.1 map the barcodes to the sequences..migrated to functionin config.pl. +my $barcode_length = 0; +open (BARCODE, "<", "data/barcode2lib.txt") || die "Unable to open barcode to library file. $!\n"; +while (<BARCODE>) { + chomp; + my @split = split("\t", $_); + if (length($split[0]) > $barcode_length) { $barcode_length = length($split[0]); } +} +close(BARCODE); + +$sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,$barcode_length+1) as decoded_sequence, substring(quality, $barcode_length+1) as decoded_quality from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); +$sth->execute; +print "Mapped barcodes to sequences in table illumina_decoded2\n"; +print "2.1 complete - Mapped barcodes to sequences in table illumina_decoded\n"; + +#2.2 +$sth = $dbh->prepare("select distinct library, count(id) from illumina_decoded_$proj group by library;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print $row[0]."\t".$row[1]." inserts\n"; +} + +#2.3 +if (!defined($mutagens)) { + #454 + $mutagens="__GTATGTAAACTTCCGACTTCAACTG"; + #illumina data + #$mutagens = "TGTATGTAAACTTCCGACTTCAACTG"; + #illumina_2 data + #$mutagens = "___TGTATGTAAACTTCCGACTTCAACTG"; + #MULV + #$mutagens = "CCAAACCTACAGGTGGGGTCTTTCA"; +} + +my @mutagens_array = split(",", $mutagens); +my $first = 1; + +foreach my $mutagen (@mutagens_array) { + $mutagen =~ s/^\s+//; + $mutagen =~ s/\s+$//; + if ($first) { + $sql_str = "create table "; + $first = 0; + } else { + $sql_str = "insert into "; + } + $sql_str = join("", $sql_str, "illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,", length($mutagen)+1, ") as insertion_sequence, substring(decoded_quality, ", length($mutagen)+1, ") as insertion_quality, 'good' as type from illumina_decoded_$proj where decoded_sequence like '", $mutagen, "%'"); + $sth = $dbh->prepare($sql_str); + $sth->execute; +} +print "2.3 - Mapped and removed IRDR sequences, created table illumina_without_IRDR\n"; + +# 3.1 Find and Remove internal linker + +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set type = 'idR' where insertion_sequence like '%GTCCCTTAAGCGGAGCC%'"); +$sth->execute; +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set insertion_sequence = substring_index(insertion_sequence,'GTCCCTTAAGCGGAGCC',1) where type = 'idR';"); +print "3.1 - Identified RIght linker in remaining seqeunces and renamed to idR.\n"; + +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set type = 'idL' where insertion_sequence like '%TAGTCCCTTAAGCGGAG%'"); +$sth->execute; +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set insertion_sequence = substring_index(insertion_sequence,'TAGTCCCTTAAGCGGAG',1) where type = 'idL';"); +$sth->execute; +print "3.2 - Identified Left linker in remaining seqeunces and renamed to idL.\n"; + +# Part 3.3 Find and Remove GGATCC sequences +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set type = 'bam' where insertion_sequence like '_____GGATCC%'"); +$sth->execute; +print "3.3 - Identified seqeunce with GGATCC and renamed.\n"; + +# Part 3.4 Find and remove any remaining seqeunces that do not start with TA seqeunce +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set type = 'noTA' where insertion_sequence not like 'TA%'"); +$sth->execute; +print "3.4 - Identified seqeunce without TA and renamed to noTA\n"; + +# 3.5 Find and identify any sequences that are two short for meaningful mapping +$sth = $dbh->prepare("update illumina_without_IRDR_$proj set type = 'min' where (type = 'good' or type = 'idR' or type = 'idL') and char_length(insertion_sequence)<24"); +$sth->execute; +print "3.5 Identified short seqeunces and label them min\n"; + +#4.1 +$sth = $dbh->prepare("alter table illumina_without_IRDR_$proj add index (type)"); +$sth->execute; + +$sth = $dbh->prepare("alter table illumina_without_IRDR_$proj add index (insertion_sequence)"); +$sth->execute; + +#if ($quality) { + $sth = $dbh->prepare("alter table illumina_without_IRDR_$proj add index (insertion_quality)"); + $sth->execute; + print "indexed table illumina_without_IRDR\n"; +#} + +$sth = $dbh->prepare("alter table illumina_without_IRDR_$proj add index (library)"); +$sth->execute; +print "4.1 - indexed table illumina_without_IRDR\n"; + +#### +#4.2 Remove duplicate sequences maintaining count of all +#### +$sth = $dbh->prepare("create table illumina_nr_pre_map_$proj as select distinct count(type) as number, insertion_sequence, insertion_quality, library from illumina_without_IRDR_$proj where (type = 'good' or type = 'idR' or type = 'idL') group by library, insertion_sequence, insertion_quality"); +$sth->execute; + +print "4.2 - Created illumina_nr_pre_map table\n"; + +#4.3 +$sth = $dbh->prepare("create table illumina4dec_$proj (id INT unsigned not null auto_increment, primary key(ID), number varchar(20), library varchar(30),sequence varchar(100), quality varchar(100) )"); +$sth->execute; +print "4.3 - Created illumina4dec table\n"; + +#if ($quality) { + $sth = $dbh->prepare("insert into illumina4dec_$proj select NULL,number,library, insertion_sequence, insertion_quality from illumina_nr_pre_map_$proj"); +#} +#else { +# $sth = $dbh->prepare("insert into illumina4dec_$proj select NULL,number,library, insertion_sequence from illumina_nr_pre_map_$proj"); +#} +$sth->execute; + +print "4.4 - populated nr_id table\n"; + + +$sth = $dbh->prepare("create table illumina4dec2_$proj select * from illumina4dec_$proj"); +$sth->execute; +print "4.5 - Copied illumina4dec table to illumina4dec2 for later use\n"; + +#### +# Bowtie variable definitions +#### +if (length($bowtie_exe) == 0) { $bowtie_exe = "/project/ccbioinf/Projects/labs/largaespada/Illumina_data/bowtie-0.12.5/bowtie"; } +if (length($bowtie_idx) == 0) { $bowtie_idx = "mm9"; } +if (length($envDir) == 0) { $envDir = "."; } + +#### +#5 This section of the script runs the bowtie algorythm. +#### +&alignment(); +print "5.1c - FINISHED Bowtie iteration #1\n"; + +$sth = $dbh->prepare("drop table if exists bowtie_$proj "); +$sth->execute; +$sth = $dbh->prepare("drop table if exists bowtie_lib_$proj "); +$sth->execute; + +##### +# 6 reduce to NR set and load library and location mapping. +###### +$sth = $dbh->prepare("create table bowtie_$proj select substring_index(B.id,':',1) as id, substring_index(substring_index(B.id,':',-2),':',1) as library, substring_index(substring_index(B.id,':',-1),'-',1) as number,substring_index(B.id,'-',-1) as size, strand, chromo, start, mismatch from illumina_blastout_$proj B"); +$sth->execute; + +$sth = $dbh->prepare("alter table bowtie_$proj add pos varchar(20)"); +$sth->execute; +$sth = $dbh->prepare("alter table bowtie_$proj add stop varchar(20)"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set pos = size + start where strand = '-'"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set pos = start + 1 where strand = '+'"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set stop = start + size"); +$sth->execute; + +print "6.1 6.2 6.3 6.4 - created bowtie table and adjusted \n"; +### +#6.5 determine transposon orientation (is it in the A or B orientation?) +### + +$sth = $dbh->prepare("alter table bowtie_$proj add orient varchar(5) default 'U'"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set orient = '-' where library like '%-L' and strand = '+'"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set orient = '+' where library like '%-L' and strand = '-'"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set orient = '-' where library like '%-R' and strand = '-'"); +$sth->execute; + +$sth = $dbh->prepare("update bowtie_$proj set orient = '+' where library like '%-R' and strand = '+'"); +$sth->execute; + + + +print "6.5 - determined mapping orientation\n"; + +#6.6 +$sth = $dbh->prepare("select count(*) from temp_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print "6.6 - ".$row[0]." Number of unique seqeunces that mapped\n"; +} +#6.7 +$sth = $dbh->prepare("select count(distinct chromo, start) from temp_$proj order by chromo, start+0; "); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print "6.7 - ".$row[0]." Number of distinct genomic regions that were mapped to\n"; +$nr_count = $row[0]; +} + +#7.1 +$sth = $dbh->prepare("create table bowtie_lib_$proj select distinct library,chromo, start,stop, pos, sum(number) as count,strand, orient from bowtie_$proj group by library,chromo,start,stop,pos,strand order by chromo,start+0,orient"); +$sth->execute; + +print "7.1 - created bowtie_lib table\n"; + +$sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj"); +#$sth = $dbh->prepare("select chromo, start, start+1, concat(library,count),count,'+',start,start+1 from bowtie_lib_$proj"); +$sth->execute; +#7.2 +open OUT, "> results/raw_$proj.BED"; +print OUT "track type ='BED' name='raw$proj' description='all$proj' visibility=2 itemRgb='On'"; +while ((@row) = $sth->fetchrow_array) { + print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]";} + #print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t255,0,0";} +close OUT; +#7.3 +$sth = $dbh->prepare("drop table if exists convert_2_hex_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table convert_2_hex_$proj (orient varchar(5), hex varchar(20))"); +$sth->execute; +$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"A\", \"255,0,0\")"); +$sth->execute; +$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"B\", \"0,0,255\")"); +$sth->execute; +$sth = $dbh->prepare("insert into convert_2_hex_$proj VALUES(\"U\", \"0,0,0\")"); +$sth->execute; + +$sth = $dbh->prepare("select chromo, start, stop, concat(library,'-',count),count,strand,start,stop from bowtie_lib_$proj where count > 9"); +#select chromo, start, start+1, concat(library,count),count,'+',start,start+1, hex from bowtie_lib_$proj A, convert_2_hex B where A.orient = B.orient and count > 9"); +#$sth = $dbh->prepare("select chromo, start, start+1, concat(library,count),count,'+',start,start+1 from bowtie_lib_$proj where count > 9"); +$sth->execute; +open OUT, "> results/raw10_$proj.BED"; +print OUT "track type ='BED' name='raw10$proj' description='10$proj' visibility=2 itemRgb='On'"; +while ((@row) = $sth->fetchrow_array) { + print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t$row[8]";} + #print OUT "\n$row[0]\t$row[1]\t$row[2]\t$row[3]\t$row[4]\t$row[5]\t$row[6]\t$row[7]\t255,0,0";} +close OUT; + +#8.1 + +$sth = $dbh->prepare("drop table if exists illumina_hist_$proj"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists illumina_hist_raw_$proj"); +$sth->execute; + +$sth = $dbh->prepare("create table illumina_hist_raw_$proj select library, chromo,round(pos,-2) as start, count,orient from bowtie_lib_$proj;"); +$sth->execute; + +$sth = $dbh->prepare("update illumina_hist_raw_$proj set library = left(library,LENGTH(library)-2) where library like '%-L'"); +$sth->execute; +$sth = $dbh->prepare("update illumina_hist_raw_$proj set library = left(library,LENGTH(library)-2) where library like '%-R'"); +$sth->execute; + +$sth = $dbh->prepare("create table illumina_hist_$proj select distinct library, chromo,start, sum(count) as count,orient from illumina_hist_raw_$proj group by library,chromo,start,orient;"); +$sth->execute; + +$sth = $dbh->prepare("drop table if exists illumina_hist_raw_$proj"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists lib_count_$proj"); +$sth->execute; +#8.2 +$sth = $dbh->prepare("create table lib_count_$proj select distinct library, sum(count) as total from illumina_hist_$proj group by library;"); +$sth->execute; + +#8.3 the following was added to improve process. Rather then using the total mapped as the denominator in the nr ratio, the total mappable should be used. This will minimize the effect of the crossmapping problem by increasing the requirements for inclusion into the library nr lists sfor librarys wiht low percentage mappiung such as woud exist form mapping to the wrong species + +$sth = $dbh->prepare("drop table if exists lib_m_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table lib_m_$proj select distinct library, sum(number) as total from illumina4dec2_$proj group by library"); +$sth->execute; +$sth = $dbh->prepare("update lib_m_$proj set library = left(library,LENGTH(library)-2) where library like '%-L'"); +$sth->execute; +$sth = $dbh->prepare("update lib_m_$proj set library = left(library,LENGTH(library)-2) where library like '%-R'"); +$sth->execute; +$sth = $dbh->prepare("drop table if exists lib_mappable_$proj"); +$sth->execute; +$sth = $dbh->prepare("create table lib_mappable_$proj select library, sum(total) as total from lib_m_$proj group by library"); +$sth->execute; + + + +print "completed mapping!!!"; + +### +#9 Generate a report describing the mapping. +### + +open OUT, "> results/summary_$proj.txt"; +print OUT "Summary of project $proj\n\nA.Report of project based counts \n"; + +$sth = $dbh->prepare("select count(*) from illumina_raw_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Seqeunces\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_decoded_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Sequences that map to a barcode\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Sequences with a barcode that also have an IRDR\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'idR';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Ideal Right linker sequences\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'idL';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Ideal left linkersequences\n"; +} + + + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'good';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of good sequences\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'bam';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of Bamh1 sequence Artifact (removed)\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'noTA';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of sequences removed because of lack of TA sequence)\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_without_IRDR_$proj where type = 'min';"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of sequences removed because of sequence length < 24)\n"; +} + + + + +$sth = $dbh->prepare("select count(*) from illumina4dec2_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total number of unique seqeunces pryor to mapping\n"; +} + +$sth = $dbh->prepare("select sum(number) from bowtie_$proj;"); +$sth->execute; +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Total SUM of seqeunces that mapped\n"; +} + +$sth = $dbh->prepare("select count(*) from bowtie_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Number of unique sequences that mapped\n"; +} + +$sth = $dbh->prepare("select count(*) from bowtie_lib_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Number of distinct locations mapped\n"; +} + +$sth = $dbh->prepare("select count(*) from illumina_hist_$proj;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + print OUT $row[0]." Number of distinct regions mapped\n"; +} +close OUT; + +#report part B +open OUT, ">> results/summary_$proj.txt"; +print OUT"\n\nB. Library counts associated with project $proj\n"; + +%sequence=''; +%barcode_count=''; +%IRDR_count=''; +%IRDR_good=''; +%IRDR_unique=''; +%map_count=''; +%map_total=''; +%nr_count=''; +@library=''; + +$sth = $dbh->prepare("select * from barcode_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $sequence{$row[1]} = $row[0]; + push(@library,$row[1]); +} + +$sth = $dbh->prepare("select library, count(id) from illumina_decoded_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $barcode_count{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(id) from illumina_without_IRDR_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $IRDR_count{$row[0]} = $row[1]; +} + + + +$sth = $dbh->prepare("select library, sum(number) from illumina4dec2_$proj group by library;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $IRDR_good{$row[0]} = $row[1]; +} + + +$sth = $dbh->prepare("select library, count(number) from illumina4dec2_$proj group by library;"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $IRDR_unique{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, sum(number) from bowtie_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $map_count{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(id) from bowtie_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $map_total{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select library, count(chromo) from bowtie_lib_$proj group by library"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $map_nr{$row[0]} = $row[1]; +} + +open (my $lib_stats, "> results/lib_stats_$proj.txt"); +print OUT "Library\tBarcode Sequence\tBarcode\tIRDR\tMappable\tUnique mappable\tTotal map\tUnique map\tNR map\n"; +print $lib_stats "Library,Barcode Sequence,with Barcode,with Mutagen,Total Mappable,Total Mapped,Mappable,Mapped,NR Inserts\n"; +foreach $item (@library) { + print OUT "$item\t$sequence{$item}\t$barcode_count{$item}\t$IRDR_count{$item}\t$IRDR_good{$item}\t$IRDR_unique{$item}\t$map_count{$item}\t$map_total{$item}\t$map_nr{$item}\n"; + if (length($item) == 0) { next; } + print $lib_stats "$item,$sequence{$item}"; + &print_stat_val($lib_stats, \$barcode_count{$item}); + &print_stat_val($lib_stats, \$IRDR_count{$item}); + &print_stat_val($lib_stats, \$IRDR_good{$item}); + &print_stat_val($lib_stats, \$IRDR_unique{$item}); + &print_stat_val($lib_stats, \$map_count{$item}); + &print_stat_val($lib_stats, \$map_total{$item}); + &print_stat_val($lib_stats, \$map_nr{$item}); + print $lib_stats "\n"; +} +close $lib_stats; + +print OUT "\n\nC. Regions associated with project $proj\n"; + +%mappable=''; +%name=''; +%count01=''; +%count001=''; +%count0001=''; +%count0=''; +@library=''; + +$sth = $dbh->prepare("select * from lib_count_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $name{$row[0]} = $row[1]; + push(@library,$row[0]); +} + +$sth = $dbh->prepare("select * from lib_mappable_$proj"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $mappable{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > .01 group by A.library order by chromo,start+0"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $count01{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > .001 group by A.library order by chromo,start+0"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $count001{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > .0001 group by A.library order by chromo,start+0"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { + $count0001{$row[0]} = $row[1]; +} + +$sth = $dbh->prepare("select A.library, count(chromo) from illumina_hist_$proj A, lib_mappable_$proj B where A.library = B.library and count/total > 0 group by A.library order by chromo,start+0"); +$sth->execute; + +open my $region_stats, "> results/region_stats_$proj.txt"; +print OUT "Library\tTotal mappable\ttotal map\tLocations >0.01\tLocations >0.001\tLocations >0.0001\t All mapped Locations"; +print $region_stats "Library,Total mappable,total map,Locations >0.01,Locations >0.001,Locations >0.0001,All mapped Locations\n"; +while ((@row) = $sth->fetchrow_array) { + $count0{$row[0]} = $row[1]; +} + +foreach $item (@library) { + print OUT "$item\t$mappable{$item}\t$name{$item}\t$count01{$item}\t$count001{$item}\t$count0001{$item}\t$count0{$item}\n"; + if (length($item) == 0) { next; } + print $region_stats "$item"; + &print_stat_val($region_stats, \$mappable{$item}); + &print_stat_val($region_stats, \$name{$item}); + &print_stat_val($region_stats, \$count01{$item}); + &print_stat_val($region_stats, \$count001{$item}); + &print_stat_val($region_stats, \$count0001{$item}); + &print_stat_val($region_stats, \$count0{$item}); + print $region_stats "\n"; +} +close OUT; +close $region_stats; + +&set_project_status($proj, 1, 0); + +exit(0); + +sub add_default_quality { + print "Adding default quality values."; + open($input, "<", "data/seqs.tab") || die "Unable to open ${$in_fn_ref}: $!\n"; + open($output, ">", "data/seqs_w_qual.tab") || die "Unable to open ${$out_fn_ref}: $!\n"; + while(<$input>) { + chomp; + my @split = split("\t", $_); + if ($#split == 1) { + print $output join("\t", $split[0], "", $split[1]); + $split[1] =~ s/./I/g; + print $output sprintf("\t%s\n", $split[1]); + } + elsif ($#split == 2) { + print $output join("\t", $split[0], $split[1], $split[2]); + $split[2] =~ s/./I/g; + print $output sprintf("\t%s\n", $split[2]); + } + } + copy("data/seqs.tab", "data/original_seqs.tab") || die "Unable to move seqs.tab: $!\n"; + copy("data/seqs_w_qual.tab", "data/seqs.tab") || die "Unable to move seqs.tab: $!\n"; +} +sub alignment { + unless (-d "mapping") { + mkdir("mapping"); + } + my @seq_lengths = (-1, 33, 30, 28, 24); + my @bowtie_mismatches = (3, 3, 2, 1, 0); + + for (my $i = 0; $i <= $#seq_lengths; $i++) { + if($aligner eq "bwa") { + &prepare_fastq($seq_lengths[$i], "mapping/4map_$i.txt"); + &bwa($bowtie_mismatches[$i], "$envDir/mapping/4map_$i.txt", "$envDir/mapping/aln$i.txt", "$envDir/mapping/samse$i.txt", "$envDir/mapping/mapping$i.txt", $i != $#bowtie_mismatches); + } + elsif($aligner eq "bow_bwa") { + &prepare_fasta($seq_lengths[$i], "mapping/4map_$i.txt"); + &bowtie($bowtie_mismatches[$i], "$envDir/mapping/4map_$i.txt", "$envDir/mapping/mapping$i.txt", 1); + print "FINISHED Bowtie iteration #$i\n"; + &prepare_fastq($seq_lengths[$i], "mapping/4map_$i_part2.txt"); + &bwa($bowtie_mismatches[$i], "$envDir/mapping/4map_$i_part2.txt", "$envDir/mapping/aln$i.txt", "$envDir/mapping/samse$i.txt", "$envDir/mapping/mapping$i_part2.txt", $i != $#bowtie_mismatches); + } + else { + &prepare_fasta($seq_lengths[$i], "mapping/4map_$i.txt"); + &bowtie($bowtie_mismatches[$i], "$envDir/mapping/4map_$i.txt", "$envDir/mapping/mapping$i.txt", $i != $#bowtie_mismatches); + print "FINISHED Bowtie iteration #$i\n"; + } + } +} + +sub bowtie { + my ($mismatches, $input_file, $output_file, $tidy) = @_; + print "bowtie($mismatches, $input_file, $output_file, $tidy)\n"; + $sth = $dbh->prepare("create table if not exists illumina_blastout_$proj ( id varchar(50),strand varchar(20),chromo varchar(20),start varchar(20),mismatch varchar(30))"); + $sth->execute; + + my $cmd = "$bowtie_exe --quiet -a --best --strata -v $mismatches -m 1 --suppress 5,6,7 -f "; + #if ($quality) { $cmd = $cmd . "-q "; } + #else { $cmd = $cmd . "-f "; } + $cmd = $cmd . "$bowtie_idx $input_file $output_file |"; + print "bowtie cmd: $cmd\n"; + open($bowtie_out, $cmd); + close($bowtie_out); + + $sth = $dbh->prepare("load DATA local INFILE '$output_file' INTO TABLE illumina_blastout_$proj "); + $sth->execute; + + #Clean out mapped entries for the next round of fast(a|q) generation + if ($tidy) { + $sth = $dbh->prepare("drop table if exists temp_$proj "); + $sth->execute; + + $sth = $dbh->prepare("create table temp_$proj select substring_index(B.id,':',1) as id, substring_index(substring_index(B.id,'-',-2),'-',1) as number,substring_index(B.id,'-',-1) as size, strand, chromo, start, mismatch from illumina_blastout_$proj B; "); + $sth->execute; + + $sth = $dbh->prepare("delete illumina4dec_$proj from illumina4dec_$proj,temp_$proj where illumina4dec_$proj.id = temp_$proj.id "); + $sth->execute; + } +} + +sub bwa { + my ($mismatches, $input_file, $output_aln_file, $output_samse_file, $output_file, $tidy) = @_; + $sth = $dbh->prepare("create table if not exists illumina_blastout_$proj ( id varchar(50),strand varchar(20),chromo varchar(20),start varchar(20),mismatch varchar(30))"); + $sth->execute; + + my $cmd = "$bwa_exe aln -n $mismatches -M 1 $bwa_idx $input_file > $output_aln_file | "; + open ($bwa_out, $cmd); + while(<$bwa_out>) { print $_; } + close($bwa_out); + $cmd = "$bwa_exe samse $bwa_idx $output_aln_file $input_file > $output_samse_file | "; + open ($bwa_out, $cmd); + while(<$bwa_out>) { print $_; } + close($bwa_out); + + open ($sam, "<", $output_samse_file) || die "Unable to open samse output file, $output_samse_file: $!\n"; + open ($final_out, ">", $output_file) || die "Unable to open final output file, $output_file: $!\n"; + while(<$sam>) { + chomp; + if (/^@/) { next; } + my @sam_array = split("\t", $_); + if ($#sam_array < 11 || $sam_array[2] eq '*') { next; } + my $strand = '+'; + if ($sam_array[1] | 0b11110111111) { $strand = '-'; } + my @opts = split(" ", $sam_array[11]); + foreach (@opts) { + if (/NM:i:([0-9]*)/) { + if ($1 > $mismatches) { next; } + } + elsif (/X0:i:([0-9]*)/) { + if ($1 > 1) { next; } + } + } + #print "CHROM: $sam_array[2]"; + #$sam_array[2] =~ s/"SN:"//g; + #print "\t$sam_array[2]\n"; + print $final_out join("\t", $sam_array[0], $strand, $chrom_map_ref->{$sam_array[2]}, $sam_array[3]-1, $sam_array[4]) . "\n"; + } + close($final_out); + close($sam); + + $sth = $dbh->prepare("load DATA local INFILE '$output_file' INTO TABLE illumina_blastout_$proj "); + $sth->execute; + + #Clean out mapped entries for the next round of fast(a|q) generation + if ($tidy) { + $sth = $dbh->prepare("drop table if exists temp_$proj "); + $sth->execute; + + $sth = $dbh->prepare("create table temp_$proj select substring_index(B.id,':',1) as id, substring_index(substring_index(B.id,'-',-2),'-',1) as number,substring_index(B.id,'-',-1) as size, strand, chromo, start, mismatch from illumina_blastout_$proj B; "); + $sth->execute; + + $sth = $dbh->prepare("delete illumina4dec_$proj from illumina4dec_$proj,temp_$proj where illumina4dec_$proj.id = temp_$proj.id "); + $sth->execute; + } +} + +sub prepare_fasta { + my ($length, $mapping_file) = @_; + print "prepare_fasta($length, $mapping_file)\n"; + if ($length <= 0) { + $sth = $dbh->prepare("select concat(id,':',library,':',number,'-',char_length(sequence)),sequence from illumina4dec_$proj where length(sequence) > 33"); + } + else { + $sth = $dbh->prepare("select concat(id,':',library,':',number,'-','$length'),left(sequence,$length) from illumina4dec_$proj where length(sequence) > $length-1"); + } + $sth->execute; + + open (OUT, ">", $mapping_file) || die "Unable to open aligner input file, $mapping_file: $!\n"; + while ((@row) = $sth->fetchrow_array) { + print OUT ">$row[0]\n$row[1]\n"; + } + close OUT; +} + +sub prepare_fastq { + my ($length, $mapping_file) = @_; + if ($legnth <= 0) { + $sth = $dbh->prepare("select concat(id,':',library,':',number,'-',char_length(sequence)),sequence,quality from illumina4dec_$proj where length(sequence) > 33"); + } + else { + $sth = $dbh->prepare("select concat(id,':',library,':',number,'-','$length'),left(sequence,$length),left(quality,$length) from illumina4dec_$proj where length(sequence) > $length-1"); + } + $sth->execute; + + open (OUT, ">", $mapping_file) || die "Unable to open aligner input file, $mapping_file: $!\n"; + while ((@row) = $sth->fetchrow_array) { + print OUT sprintf("\@%s\n%s\n\+%s\n%s\n", $row[0], $row[1], $row[0], substr($row[2], 0, length($row[1]))); + } + close OUT; +} + +sub print_stat_val { + my ($fh_ptr, $val_ptr) = @_; + if (defined($val_ptr) && ${$val_ptr} > 0) { + print $fh_ptr ",${$val_ptr}"; + } else { + print $fh_ptr ",0"; + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/cis_finder.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,242 @@ +#This script takes a set of chromosomes and positions from a text file and generates defined CIS'es +#version 5.0 ALS +#Nov 15 2010 + +# Open the presorted NR chromosome file and load it into a hash. +require 'config.pl'; +$boxSize = $ARGV[0]; + +open OUT, "> CIS/cis$ARGV[0].txt"; +open SOURCE, "< CIS/nr.txt"; +while (defined($line = <SOURCE>)) { +$count++; +chomp $line; +@field= split(/\t/, $line); +$hash[$count]= $field[1]; +$chrom[$count]= $field[0]; +$lib[$count]= $field[2]; +$orient[$count]=$field[5]; +} + +#Count the number of nr positions within a box the size of which is defined below and add to a parallel hash. +foreach $n (1..$count) { +$cis_count = 0; +@lib_list = ''; +@pos_list = ''; +$lib_count = ''; +$orient_count = '0'; +$i =$n; +#print "$n\n"; +$j = $hash["$n"]+$boxSize; +#print "pos=>".$hash[$n]."\n"; +while (($hash["$n"] <= $hash["$i"]) and ($j > ($hash["$i"]+0)) and ($i <= $count)) { +push(@lib_list,$lib["$i"]); +push(@pos_list,$hash["$i"]); +if ($orient[$i] eq "+") { +$orient_count = $orient_count +1; +} + +$i=$i+1; +#print "$i\n"; +$cis_count=$cis_count+1; +#print "$cis_count\n"; + +} +$cis[$n]=$cis_count; +$strand[$n]=$orient_count; +#print "Cis_count=$cis_count\t"; +#print @lib_list; +#This section rather hackily counts the number of libraries represented in the CIS window. +%seen=(); +@uniq = (); +$libstring = ''; +foreach $item (@lib_list) { +unless ($seen{$item}) { +$seen{$item}= 1; +push(@uniq,$item) +} +} +#print "\n@uniq\n"; + +$lib_count = -1; +foreach $i (@uniq) { +$lib_count++; +$libstring = $libstring.$i.'::'; +} + +#print "Library_count=$lib_count"; + +$lib[$n]=$lib_count; +$lib_name[$n]=$libstring; +#print "$cis[$n]\t$lib[$n]"; + +#This section rather hackily counts the the number of regions represented in the CIS window. +%seen=(); +@uniq = (); +$posstring = ''; +foreach $item (@pos_list) { +unless ($seen{$item}) { +$seen{$item}= 1; +push(@uniq,$item) +} +} +#print "\n@uniq\n"; + +$pos_count = -1; +foreach $i (@uniq) { +$pos_count++; +$posstring = $posstring.$i.'::'; +} + +#print "Library_count=$lib_count"; + +$pos[$n]=$pos_count; +$pos_name[$n]=$posstring; +#print "\t$pos[$n]\n"; + + + +} + + +$cis[0] = 0; + +# select peaks and export them with complex logic scheme. +# update Sept22 seperate this into 4 cases. + +foreach $n (1..$count) { +$prev = $n-1; +$this = $n; +$next = $n+1; +#print "\t$ARGV[1]\n"; + + +if ($ARGV[1] eq library) { +#print "$ARGV[1]\t$cis[$this]\t$lib[$n]\n"; +$cis[$this]=$lib[$this]; +$cis[$next]=$lib[$next]; +$cis[$prev]=$lib[$prev]; +} +# outcome 1 no other cises are relevant i.e. nothing within + or - cis size. +if ((($hash[$this] - $hash[$prev] > $boxSize) or ($chrom[$this] ne $chrom[$prev])) and (($hash[$next]-$hash[$this] > $boxSize) or ($chrom[$next] ne $chrom[$this])) and ($cis[$this] > 1)){ +outputpart1(); +} + +# outcome 2 no other cis + cis size cis - cis exists and is smaller. +if (($hash[$this] - $hash[$prev] >0) and ($hash[$this] - $hash[$prev] <= $boxSize) and ($cis[$prev] < $cis[$this]) and ($hash[$next]-$hash[$this] > $boxSize) and ($cis[$this] > 1)){ +outputpart1(); +} + +# outcome 3 no other cis - cis size + cis exists and is smaller are relevant nothing within + or - cis size. +if ((($hash[$this] - $hash[$prev] > $boxSize) or ($chrom[$this] ne $chrom[$prev])) and ($hash[$next]-$hash[$this] >= 0) and ($hash[$next]-$hash[$this] <= $boxSize) and ($cis[$this] >= $cis[$next]) and ($cis[$this] > 1)){ +outputpart1(); +} + +# outcome 4 other cises on both sides. +if (($hash[$this] - $hash[$prev] >0) and ($hash[$this] - $hash[$prev] <= $boxSize) and ($hash[$next]-$hash[$this] > 0) and ($hash[$next]-$hash[$this] <= $boxSize) and ($cis[$prev] < $cis[$this]) and ($cis[$this] >= $cis[$next]) and $cis[$this] > 1 ) { +outputpart1(); +} +#print "$chrom[$n]\t$hash[$n]\t$cis[$n]\n"; +} +#hack to prevent permanent looping...observedon one occasion unsure why... +$iter = 0; +$count3 = 1; +$count2 = 0; +while (($count3 ne $count2) and ($iter < 100)){ +print "$iter"; +$iter++; +close OUT; +#print "$count3\t\t\t\t$count2\n\n"; +$count3 = $count2; +$count2 = 0; +%hash= (); +%chrom= (); +%cis=(); +%libraries=(); +%full_line=(); +#open OUT, "> cis2.txt"; +open SOURCE, "< CIS/cis$ARGV[0].txt"; +while (defined($line = <SOURCE>)) { +$count2++; +chomp $line; +$full_line[$count2]=$line; +@field= split(/\t/, $line); +$hash[$count2]= $field[1]; +$chrom[$count2]= $field[0]; +$cis[$count2]= $field[4]; +#$libraries[$count2]=$field[11]; +} +close SOURCE; +open OUT, "> CIS/cis$ARGV[0].txt"; +# select peaks and export them with complex logic scheme. +# update Sept22 seperate this into 4 cases. + +foreach $n (1..$count2) { +$prev = $n-1; +$this = $n; +$next = $n+1; + +# outcome 1 no other cises are relevant i.e. nothing within + or - cis size. +if ((($hash[$this] - $hash[$prev] > $boxSize) or ($chrom[$this] ne $chrom[$prev])) and (($hash[$this]-$hash[$next] < -$boxSize) or ($chrom[$next] ne $chrom[$this])) and ($cis[$this] > 1)){ +output(); +} + +# outcome 2 no other cis + cis size cis - cis exists and is smaller. +if (($hash[$this] - $hash[$prev] >0) and ($hash[$this] - $hash[$prev] <= $boxSize) and ($cis[$prev] < $cis[$this]) and ($hash[$next]-$hash[$this] > $boxSize) and ($cis[$this] > 1)){ +output(); +} + +# outcome 3 no other cis - cis size + cis exists and is smaller are relevant nothing within + or - cis size. +if ((($hash[$this] - $hash[$prev] > $boxSize) or ($chrom[$this] ne $chrom[$prev])) and ($hash[$next]-$hash[$this] >= 0) and ($hash[$next]-$hash[$this] <= $boxSize) and ($cis[$this] >= $cis[$next]) and ($cis[$this] > 1)){ +output(); +} + +# outcome 4 other cises on both sides. +if (($hash[$this] - $hash[$prev] >0) and ($hash[$this] - $hash[$prev] <= $boxSize) and ($hash[$next]-$hash[$this] >= 0) and ($hash[$next]-$hash[$this] <= $boxSize) and ($cis[$prev] < $cis[$this]) and ($cis[$this] >= $cis[$next]) and $cis[$this] > 1 ) { +output(); +} +#print "$chrom[$n]\t$hash[$n]\t$cis[$n]\n"; +} + +} +close OUT; + +#Subroutines +# provide data in the form of poisson('BoxSize','Total','count') +sub outputpart1 { +$pval = poissonBonf($boxSize,$count,$lib[$this]); +$pvalTotal = poissonBonf($boxSize,$count,$cis[$this]); +$pvalRegion = poissonBonf($boxSize,$count,$pos[$this]); +if ($pval < $CIS_total_pvalue) { +$end = $hash[$n]+$boxSize; +print OUT "$chrom[$n]\t$hash[$n]\t$end\t$chrom[$n]_$hash[$n]\t$lib[$this]\t$boxSize\t$pval\t$cis[$this]\t$pvalTotal\t$pos[$this]\t$pvalRegion\t$lib_name[$n]\t$strand[$this]\n"; +} +} + +sub output { +print OUT "$full_line[$n]\n"; +#if ($pval < 0.05) { +#$end = $hash[$n]+$boxSize; +#print OUT "$chrom[$n]\t$hash[$n]\t$end\t$chrom[$n]_$hash[$n]\t$cis[$this]\t$boxSize\t$pval\t$bonf\t$libraries[$n]\n"; +#} +} +sub poisson { +return ((($_[1]/(2393726033/$_[0]))**($_[2]))*(2.71828**-($_[1]/(2393726033/$_[0])))/(fac($_[2]))); +} + +sub poissonBonf { +return (((($_[1]/(2393726033/$_[0]))**($_[2]))*(2.71828**-($_[1]/(2393726033/$_[0])))/(fac($_[2])))*$_[1]); +} + +sub fac { + my ($n) = @_; + + if ($n < 2) { + return $n; + } + else { + return $n * fac($n-1); + } +} + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/cis_summary.txt Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,544 @@ + + +all_0.01library +number pos pvalue bonferroni gene_name library_name +151 chr5:28496400-28696400 0 0 Cnpy1, AC129184.1, En2, Prr8, ::M732-2NF::M988-4NF::F976-2NF::F991-3NF::M892-5NF::F849-6NF::F885-1NF::F957-3NF::M892-P::M920-5NF::F957spine::M1008-2NF::F548spine::F624-2NF::F976-5NF::M626-10NF::M878-1NF::F735-5NF::F991P::M1022-13NF::F957-1NF::M892-1NF::F877-1NF::F704-NF::M724-1NF::F737-2P::F969-7NF::F802-2NF::F884-3NF::F735-1NF::F1026-4NF::M704P::F1008-1P::F673-3NF::F947-1P::F849-7NF::F648-1NF::M878-4NF::F849-3NF::F957-2P::F760-3NF::F879-2P::F601-NF::M624-5NF::F695-4NF::F884-1NF::F729-1NF::F959-3NF::M724-4NF::F757spine::F983P::M952-4NF::F1026-1NF::F1027-8NF::F624-5NF::M624-1NF::F879-4NF::F947-3P::F959-5NF::F1026-3NF::M1013-2NF::F1027-6NF::F624-1NF::F879-2NF::M732-4NF::F969-1NF::F760-2NF::F976-3NF::F802-6NF::F1026-5NF::F624-3NF::F695-3NF::M892-7NF::F850-5NF::F884spine::F947-4NF::M851-3NF::F750-1P::F802-5NF::M950P::F1023spine::M1008-3NF::F1027-5NF::F849-8NF::F648-4NF::F957-11NF::F991-1NF::F841-2NF::M513-2P::M624-6NF::F884-2NF::F729-4NF::F968-3NF::m892spine::F760-6NF::F802-3NF::F1027-3NF::m565spine::M920-3NF::M988-3NF::F1027-9NF::m513::F850-4NF::F652-NF::M624-4NF::F879-6NF::F976-6NF::F1027-2NF::F841-5NF::F850-7NF::M626-7NF::M724-2NF::M732-5NF::F969-2NF::F976-4NF::F796-NF::F1027-7NF::F849-2NF::F849-4NF::F624-4NF::F850-2NF::F877-6NF::F879-1P::F959-4NF::F969-9NF::M920-4NF::M1013-1NF::F877-3NF::F879-1NF::M626-5NF::F947-5NF::F957-2NF::M892-2NF::M920-2NF::M513-3P::F695-2NF::F729-3NF::F729-5NF::F957-12NF::M892-6NF::M1008-1NF::F877-2NF::M624-7NF::F947-2NF::F947-3NF::F968-4NF::M892-9NF::F760-1NF::F1027-4NF::F841-6NF::M724-6NF:: +21 chr2:163468400-163480900 6.14391619026277e-63 1.11389200529464e-59 AL591488.2, 0610039K10Rik, Serinc3, ::M513-5P::F802-2NF::F994-7NF::F760-3NF::F850-4NF::F695-4NF::F850-7NF::F879-2P::M892-1NF::F959-4NF::F601-NF::F729-1NF::F849-7NF::M892-4NF::m748spine::F802-6NF::F849-4NF::F1026-3NF::F849-3NF::F849-5NF::F802-4NF:: +19 chr19:32851300-32901300 7.69188308777366e-45 1.39453840381336e-41 Pten, ::M680P::F959-2P::F704-1P::F812-2P::F812-1P::F715-1P::F806-1P::F806-2P::F806-4P::F806-3P::F879-3P::M1025-1NF::M620-2P::M741P::F1026P::F715-3P::M619-1P::F585P::F983P:: +9 chr2:98502800-98515300 1.66811378854424e-24 3.0242902986307e-21 AL837506.1, AL837506.2, ::F593spine::M628-1P::M732-3NF::F976-7NF::F624-6NF::F957spine::F729-4NF::M619-2P::F729-5NF:: +13 chr11:79155400-79355400 3.051593853827e-21 5.53253965698835e-18 Nf1, RP23-188A3.2, RP23-188A3.3, Omg, Evi2b, Evi2a, ::F879-1P::F673-1P::M1022-P::MYSTERY-2P::F983P::F991-5NF::F859P::F595P::M504P::F704-1P::M620-1P::F947-2P::M725P:: +6 chrX:7503900-7516400 9.90731762065713e-16 1.79619668462514e-12 Eras, Pcsk1n, Hdac6, ::M863P::F803P::F704-2P::F812-1P::M725P::F771-1P:: +6 chr10:57318100-57330600 9.90731762065713e-16 1.79619668462514e-12 No results within 2500 bp window ::F994-4NF::F994-1NF::F994-8NF::M910P::M552-NF::F994-3NF:: +5 chr3:158263500-158276000 6.27876115320903e-13 1.1383393970768e-09 No results within 2500 bp window ::F841-2NF::F947-5NF::F841-6NF::F648-1NF::M851-1NF:: +4 chr19:34737100-34749600 3.31597000053514e-10 6.01185361097022e-07 Slc16a12, ::F806-3P::F806-1P::F806-2P::F806-4P:: +4 chr11:4679000-4704000 5.25555897211829e-09 9.52832841645046e-06 Nf2, ::F976-3NF::m619spine::M619-2P::M513-4P:: +4 chr11:77388200-77438200 8.25117071228656e-08 0.000149593725013755 Taok1, ::M578P::F595P::M930-1P::M628-3P:: +3 chrX:8857800-8870300 1.40099701532099e-07 0.000254000758877696 Xk, 1700012L04Rik, ::F1027spine::m513::M950P:: +3 chr9:42788600-42801100 1.40099701532099e-07 0.000254000758877696 Arhgef12, ::F802-1NF::M651-2P::M651-3P:: +3 chr9:3025500-3038000 1.40099701532099e-07 0.000254000758877696 AC131780.5, AC131780.6, AC131780.12, AC131780.4, AC131780.2, AC131780.10, ::F630P::M513-4P::F596spine:: +3 chr7:35892300-35904800 1.40099701532099e-07 0.000254000758877696 Cebpa, ::F735-1NF::F735spine::F735-5NF:: +3 chr7:20345100-20357600 1.40099701532099e-07 0.000254000758877696 Bcam, AC149282.1, ::F806-4P::F806-2P::F806-1P:: +3 chr4:117257100-117269600 1.40099701532099e-07 0.000254000758877696 Eri3, ::M892-9NF::M725P::F812-1P:: +3 chr6:54872200-54884700 1.40099701532099e-07 0.000254000758877696 Nod1, ::F756-1P::F849spine::F756-2P:: +3 chr2:26322200-26334700 1.40099701532099e-07 0.000254000758877696 Notch1, ::M950P::F729-2NF::F729-3NF:: +3 chr2:62742700-62755200 1.40099701532099e-07 0.000254000758877696 Kcnh7, ::F806-1P::F806-2P::F806-4P:: +3 chr13:16745300-16757800 1.40099701532099e-07 0.000254000758877696 No results within 2500 bp window ::F969-4NF::F969-3NF::F969-1NF:: +3 chr10:41241300-41253800 1.40099701532099e-07 0.000254000758877696 Cd164, ::M620-2P::M620-1P::M628-3P:: +4 chr18:7874500-7974500 1.2711268946543e-06 0.00230455306000824 Wac, ::M851-2NF::F715-1P::M628-3P::M892-9NF:: +4 chr13:108554300-108654300 1.2711268946543e-06 0.00230455306000824 Zswim6, ::F806-2P::M704P::F750-1P::M930-1P:: +4 chrX:149494400-149594400 1.2711268946543e-06 0.00230455306000824 RP23-180D16.1, Foxr2, Rragb, RP23-415B4.3, ::F812-1P::M725P::F654-1P::F630P:: + +all_0.001library +number pos pvalue bonferroni gene_name library_name +156 chr2:163468400-163493400 0 0 AL591488.2, 0610039K10Rik, Serinc3, Pkig, ::F757spine???::M878-4NF::M892-4NF::M732-1NF::F849-6NF::M513-5P::m920spine::M624-4NF::M1008-2NF::F879-4NF::F1026-10NF::F991-1NF::M878-1NF::M952-2NF::M624-6NF::F976-7NF::F802-6NF::M988-P::F802-2NF::F959-1NF::M724-4NF::M732-6NF::F850-3NF::F957-2NF::F760-1NF::F968-4NF::m619spine::m918triqwere::F624-4NF::F802-3NF::M1013-5NF::F991-4NF::F601-NF::F969-9NF::F1027-4NF::F850-7NF::M626-4NF::F884-1NF::F1027-10NF::F850-1NF::F947-2NF::M624-1NF::F735-5NF::M952-1NF::M626-1NF::M851-1NF::F849-5NF::m1022spine::F729-4NF::F760-4NF::M920-1NF::M1013-4NF::F695-1NF::F1026-4NF::F593spine::F850-4NF::F968-3NF::M680P::F959-3NF::M988-8NF::M892-5NF::F849-2NF::F968-2NF::M892-P::M952-3NF::F877-4NF::M988-9NF::F885-2NF::F735-1NF::F735-2NF::M892-1NF::F735-4NF::F695-2NF::F652-NF::F624-1NF::F976-9NF::M952-4NF::F1026-3NF::M1022-13NF::F849-4NF::m748spine::F877-3NF::F841-4NF::M1013-2NF::m565spine::M892-11NF::m988spine::F968-1NF::F648-1NF::F760-3NF::M892-10NF::F849-7NF::F673spine::F877-6NF::F849-3NF::M920-4NF::F760-2NF::M920-5NF::F796-NF::F1027-5NF::F648-4NF::F994-7NF::M626-7NF::M892-3NF::M892-9NF::F729-1NF::F879-2NF::M624-5NF::F884P::F879-2P::F850-5NF::M1013-1NF::F771-5NF::M878-5NF::M724-1NF::M626-5NF::F959-1P::F1027-1NF::M892-2NF::F879-1NF::F595P::M626-11NF::F957-3NF::F841-2NF::F802-5NF::F959-4NF::F968-6NF::F757-1NF::F957-12NF::F757-3NF::M892-7NF::M724-5NF::F969-2NF::M920-3NF::F884-3NF::F802-4NF::M626-9NF::F957spine::M732-4NF::M1013-3NF::M732-5NF::M626-10NF::m1008spine::M732-2NF::F885-1NF::F959-5NF::F648spine::F876spine::F735spine::F841-1NF::M878-2NF::F695-4NF::F969-7NF::M878-3NF::M626-2NF::F750-1P:: +312 chr5:28412500-28612500 0 0 En2, Cnpy1, AC129184.1, ::M626-5NF::M988-1NF::F850-2NF::F879-1NF::M1008-1NF::F969-2NF::F968-1NF::F969-5NF::F947-4NF::F737-2P::M626-9NF::F802-5NF::M892-5NF::F648-2NF::F976-8NF::F704-NF::M892-11NF::M920-2NF::F802-3NF::F1026-4NF::M988-2NF::M626-10NF::F969-4NF::F884P::F850-6NF::M988-8NF::M624-7NF::M1013-2NF::M892-6NF::F648-3NF::F884-2NF::M878-1NF::F624-5NF::F649-3NF::F968-2NF::F957-3NF::m892spine::F729-3NF::M988-7NF::F624-1NF::F648-1NF::F879-5NF::m1022spine::F750-1P::M851-2NF::F548spine::F959-7NF::M920-3NF::F969-6NF::M952-2NF::M988-5NF::M920-5NF::M624-6NF::F849-6NF::F957spine::F976-16NF::M863P::F976-1NF::M930-2P::F991-4NF::M626-2NF::M732-2NF::M1013-1NF::F879-6NF::F1026-1NF::M851-3NF::F983-1NF::F959-5NF::M624-8NF::F850-1NF::F673spine::F760-5NF::F735-4NF::F976-2NF::F1027-1NF::F957-1NF::M1013-5NF::M624-4NF::F695-3NF::F1026-5NF::M892-P::F879-2P::F879-4NF::M892-10NF::F760-4NF::M478-P::M892-8NF::F991-3NF::F652-NF::F601-NF::F957-9NF::F957-10NF::F796-NF::F802-1NF::M1013-3NF::M892-1NF::F947-2NF::F991-1NF::M626-7NF::F959-2NF::F957-2NF::F976-4NF::M920-4NF::F1026-7NF::F737-NF::F729-4NF::M626-3NF::F959-4NF::M878-6NF::F885-2NF::F648-4NF::M478-NP::F648-5NF::F1023-NF::F1026-6NF::M988-4NF::F1026-8NF::M878-3NF::F959-3NF::m619spine::M952-3NF::F968-5NF::F976-11NF::F801spine::F757-1NF::F803P::M732-5NF::M920-1NF::F991-2NF::F959-9NF::F695-2NF::F976-3NF::F947-3NF::M1022-13NF::F760-2NF::F729-2NF::F1027-3NF::M892-4NF::F849-5NF::F850-7NF::M626-4NF::F877-5NF::F802-2NF::F959-8NF::F735-5NF::M892-9NF::F849-4NF::M988-6NF::F802-6NF::M724-1NF::M732-4NF::F957-11NF::F968-6NF::M628-2NF::F969-10NF::F624-4NF::M892-2NF::M651-2P::F877-1NF::F884-3NF::F1027-2NF::F957-2P::F841-1NF::F879-2NF::F841-2NF::M624-5NF::F877-3NF::F1026-10NF::F885-1NF::M724-2NF::F1026-2NF::F876-1P::F969-1NF::F729-1NF::F850-4NF::F968-3NF::F976-5NF::M704P::M878-5NF::F841-5NF::M952-4NF::F1027-10NF::M626-6NF::F877-6NF::M724-4NF::F849-2NF::F959-1P::F760-1NF::F1027-8NF::F802-4NF::M1008-4NF::m1008spine::F968-4NF::m918spine::F991P::M988-9NF::m918triqwere::m565spine::F1027-5NF::F959-10NF::F859P::M988-P::F735-2NF::F1027-7NF::F849-3NF::F850-3NF::M892-3NF::M952-1NF::M724-6NF::F695-4NF::F969-7NF::F976-6NF::F991-P::F760-3NF::F624-2NF::F1027spine::F885-3NF::F510P::F959-6NF::F884-1NF::F735-3NF::M624-1NF::M732-6NF::M1008-2NF::M988-3NF::M878-2NF::M626-1NF::F991-5NF::F850-5NF::F969-9NF::F849-7NF::F624-3NF::F735-1NF::F959-1NF::F947-1P::F806-1P::F735spine::M1008-3NF::F757spine::M724-5NF::m540spine::F983P::M892-7NF::M851-1NF::F947-5NF::F735-7NF::M626-11NF::m748spine::F1023spine::M930-1P::F596spine::MYSTERY-2P::F1026-3NF::F757spine???::F877-2NF::F879-3P::F1027-4NF::F1008-1P::F947-3P::F1008-2P::F877-4NF::F673-3NF::F771-1P::F771-2NF::m920spine::M878-4NF::F947-1NF::M732-3NF::F771-5NF::m988spine::F876spine::m1025spine::F757-3NF::F760P::F630P::F976-7NF::F957-12NF::M1013-4NF::F1027-6NF::m513::M1008-5NF::M1022-P::M513-3P::F841-6NF::M513-2P::F729-5NF::F876-2P::M624-2NF::F735-6NF::F884spine::F760-6NF::M725P::M950P::F969-8NF::F704-1P::F812-2P::M624-3NF::F849-8NF::F976-2P::F969-3NF::F841-4NF::F624-6NF::F648spine::F879-1P::F850-8NF::M651-3P::F1026-9NF::F695-1NF::M619-1P::F1027-9NF::M724-3NF::M626-8NF:: +152 chr2:98502500-98527500 0 0 AL837506.1, AL837506.2, ::M863P::F760-4NF::m988spine::F735-4NF::F1026-5NF::M626-8NF::M732-2NF::F850-6NF::M988-8NF::F983-1NF::F885-3NF::M624-3NF::F959-2NF::F947-3NF::M878-2NF::M626-2NF::M478-NP::F825-22P::F968-1NF::F729-3NF::F1026-10NF::F957-11NF::F756-1P::F991-3NF::M1008-4NF::F969-7NF::F976-16NF::M732-6NF::F969-5NF::F879-6NF::F1027-1NF::M988-6NF::F850-1NF::F991-2NF::F729-2NF::F968-4NF::M988-7NF::M724-1NF::M732-4NF::F735-3NF::F1026-4NF::M988-4NF::F841-2NF::M988-5NF::F1027-4NF::F648-2NF::F885-2NF::M724-3NF::M920-1NF::F1027-7NF::F959-9NF::F760-6NF::M988-3NF::M878-6NF::F1026-2NF::F1023-NF::M952-3NF::F959-1NF::F957-1NF::F991-5NF::F1026-9NF::F879-5NF::F968-5NF::F884-1NF::M626-6NF::F991-1NF::F648-5NF::F1026-6NF::F947-4NF::F1027-9NF::M626-3NF::M626-4NF::M988-2NF::M624-5NF::F976-11NF::F624-3NF::M988-1NF::M920-5NF::M624-6NF::F976-8NF::F957-12NF::M724-4NF::M624-1NF::M626-7NF::M920-3NF::F968-2NF::M626-1NF::F991-P::F729-4NF::M724-2NF::M732-5NF::F957-9NF::M732-3NF::F593spine::F1027-6NF::M628-1P::F877-2NF::M1025P::M952-4NF::F802-6NF::M892-9NF::M626-9NF::M952-1NF::F704-2P::F876-1P::F976-7NF::F624-5NF::M624-4NF::F884-2NF::F1027-2NF::F969-9NF::F968-6NF::M624-8NF::M1008-1NF::F959-8NF::F1027-5NF::F1027-8NF::F991-4NF::F841-4NF::F877-3NF::F729-5NF::F976-4NF::F624-6NF::F801spine::F760-5NF::F879-1NF::M988-9NF::M724-5NF::M892-2NF::F760-2NF::M620-1P::F1027-10NF::F969-1NF::M851-3NF::F850-2NF::F760-1NF::F957spine::M504P::M892-7NF::M892-11NF::F850-5NF::F877-4NF::F715-1P::M619-2P::M578P::F859P::F884P::F885-1NF::M628-2NF::M851P::F1026P::M952-2NF:: +55 chr3:158263500-158276000 3.10118021075076e-122 7.84598593319941e-118 No results within 2500 bp window ::M1013-3NF::F648-5NF::F1023-NF::F1026-8NF::F648-1NF::F969-2NF::F1027-5NF::M988-3NF::M988-6NF::F983-1NF::M1013-5NF::F959-2NF::M624-6NF::M988-7NF::F850-8NF::F885-2NF::M878-2NF::M952-3NF::F649-3NF::F760-2NF::F841-6NF::F850-1NF::F969-4NF::F879-4NF::F624-3NF::F885-3NF::F991-4NF::F737-NF::M952-1NF::M851-1NF::M626-7NF::F1026-5NF::M1008-5NF::F879-6NF::F885-1NF::F704-NF::F760-4NF::F991-P::F884-1NF::F969-6NF::M988-9NF::M988-1NF::F957-1NF::F735-7NF::F1027-8NF::F968-3NF::F976-8NF::F735-4NF::M624-1NF::M732-6NF::M892-8NF::F841-1NF::F947-5NF::F1027-2NF::F841-2NF:: +34 chrX:139917600-139930100 3.84560962520959e-69 9.72939235178027e-65 No results within 2500 bp window ::M1025P::M651-3P::M920-5NF::F802-6NF::F1027-7NF::F1027-8NF::F957-11NF::m1025spine::F991-2NF::F624-1NF::F959-4NF::M988-1NF::M988-3NF::M920-3NF::M988-8NF::F704-NF::M478-NP::M624-1NF::M988-6NF::F957-9NF::M724-1NF::F1027-9NF::F841-4NF::F959-5NF::M724-4NF::F1026-7NF::M878-5NF::M732-6NF::F976-3NF::M892-5NF::F760-1NF::M988-5NF::F715-2P::M952-2NF:: +31 chr13:31719100-31731600 5.98742046998136e-62 1.51481737890529e-57 Foxf2, RP23-322J11.2, ::m988spine::F968-4NF::F885-1NF::M624-4NF::F959-4NF::F735-5NF::M892-1NF::M1008-2NF::M624-6NF::F849-3NF::F757spine::F947-4NF::M626-5NF::F1026-4NF::F879-2NF::m918spine::F850-7NF::M732-3NF::F879-2P::M988-9NF::F849-2NF::M626-7NF::F729-4NF::F750-1P::F976-8NF::F760-1NF::M1013-1NF::F976-16NF::F850-5NF::F760-5NF::F695-2NF:: +40 chr11:79155400-79355400 1.49059987444013e-36 3.56804891944733e-32 Nf1, RP23-188A3.2, RP23-188A3.3, Omg, Evi2b, Evi2a, ::F879-1P::F991P::M988-P::F1026P::F849-5NF::F601-NF::M619-1P::F673-1P::F624-4NF::F704-2P::F1026-4NF::M1022-P::F760-3NF::MYSTERY-1P::MYSTERY-2P::F812-2P::F983P::F991-5NF::M930-1P::F859P::F825-22P::F595P::M628-2NF::M628-1P::F585P::M593P::M504P::M626-7NF::F1026-10NF::F704-1P::F812-1P::F510P::M578P::F994-7NF::M620-1P::M620-2P::F947-2P::F771-2NF::M725P::F879-3P:: +27 chr19:32839900-32889900 1.7986316681285e-36 4.55053812036511e-32 Pten, ::M732-3NF::F850-1NF::M1013-5NF::M680P::F959-2P::F704-1P::F704-NF::F812-2P::F812-3P::F812-1P::F715-1P::F806-2P::F806-1P::F806-3P::F806-4P::M570P::F879-3P::M1025-1NF::M620-2P::F649P::M741P::F1026P::M930-1P::F715-3P::M619-1P::F585P::M620-1P:: +15 chr10:57318100-57330600 4.36982913969745e-26 1.10556677234345e-21 No results within 2500 bp window ::M910-4NF::F994-1NF::M552-NF::F994-6NF::F994-5NF::F994-7NF::F994-3NF::F994-8NF::F994-4NF::M910-2NF::M513-1P::M732-1NF::F994-2NF::M910P::M910-1NF:: +24 chr11:3034900-3134900 2.11534789918874e-24 5.0635082662881e-20 RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Sfi1, Eif4enif1, Drg1, ::F959-9NF::F1027-10NF::F1027-9NF::F771-1P::F1027spine::M1013-2NF::F850-1NF::F673-2P::F969-4NF::F715-2P::M624-5NF::M878-1NF::F624-5NF::F796-NF::M624-7NF::M930-2P::F959-1NF::M504P::m920spine::M952-4NF::F969-1NF::F877-7NF::m540spine::F976-11NF:: +14 chr10:16578700-16591200 4.96134724337823e-24 1.25522085257469e-19 No results within 2500 bp window ::M920-1NF::F959-2NF::F976-16NF::F959-6NF::F1027-10NF::F841-1NF::F991-P::F695-2NF::F969-9NF::M1008-1NF::F957-3NF::F969-2NF::F957-12NF::F802-6NF:: +17 chr9:3004800-3054800 3.24112429532397e-20 8.20004446716964e-16 AC131780.1, AC131780.11, AC131780.3, AC131780.7, AC131780.2, AC131780.4, AC131780.6, AC131780.12, AC131780.10, AC131780.9, AC131780.8, AC131780.5, ::F757-1NF::M920-1NF::M988-P::m988spine::F760-5NF::M1025P::F771-1P::F630P::M513-4P::F596spine::F760-6NF::M680P::M892-8NF::F884-2NF::F648-3NF::M851-3NF::M952-3NF:: +19 chrX:39523100-39623100 8.18017249196248e-18 1.95808788940106e-13 Stag2, ::F947-2P::M878-1NF::M732-4NF::F983P::M578P::F885-1NF::M892-P::F884-3NF::F735-3NF::F771-1P::M892-7NF::M878-6NF::M626-10NF::M620-2P::M892-11NF::F1026-3NF::F968-1NF::F695-3NF::F630P:: +15 chrY:2850500-2900500 3.15669356761851e-17 7.98643472607482e-13 No results within 2500 bp window ::M626-7NF::M920-4NF::M732-5NF::M892-11NF::M930-2P::M878-5NF::M878-3NF::M624-5NF::m619spine::M620-1P::M1022-13NF::M920-1NF::F994-7NF::M513-4P::M651-2P:: +12 chr11:77384400-77409400 1.85669888879126e-16 4.69744818864189e-12 Taok1, ::M570P::F802-2NF::M578P::F850-7NF::M628-2NF::F760P::F976-7NF::F595P::M930-1P::F991-2NF::F825-22P::F879-1NF:: +10 chr4:96180000-96192500 3.91219576566095e-16 9.89785528712221e-12 Cyp2j6, ::F968-4NF::F760-5NF::M910-2NF::M910-1NF::F994-6NF::F994-5NF::F994-4NF::F994-3NF::M552-NF::F994-1NF:: +10 chr6:53243100-53255600 3.91219576566095e-16 9.89785528712221e-12 Creb5, ::F735-7NF::F735-1NF::M626-7NF::F735-3NF::F735-4NF::F735spine::M624-4NF::F735-2NF::F735-6NF::F735-5NF:: +10 chr9:123968200-123980700 3.91219576566095e-16 9.89785528712221e-12 No results within 2500 bp window ::F735-2NF::F735-5NF::F735-7NF::F735-6NF::M626-7NF::F735spine::F735-3NF::M624-4NF::F735-1NF::F735-4NF:: +21 chr16:4046900-4246900 1.58568469271995e-14 3.79565344896374e-10 AC132380.1, Crebbp, RP24-425F2.2, Gm5766, Trap1, ::F695-4NF::M851-1NF::MYSTERY-2P::F879-5NF::F983P::M878-6NF::F812-3P::M620-1P::F849-2NF::F849-3NF::M626-4NF::M930-1P::F849-4NF::M626-10NF::F879-2NF::M570P::F771-2NF::F884-1NF::F825-22P::F771-1P::M892-7NF:: +9 chr16:57523800-57536300 2.96117781832569e-14 7.49177988036399e-10 2610528E23Rik, Filip1l, ::F735-3NF::M624-4NF::F735-1NF::F735-7NF::F735-4NF::M626-7NF::F735-5NF::F735-6NF::F735-2NF:: +9 chr16:42526200-42538700 2.96117781832569e-14 7.49177988036399e-10 No results within 2500 bp window ::m619spine::F695-4NF::F624-5NF::F849-8NF::M626-1NF::F648-2NF::F802-4NF::M626-3NF::F1027-4NF:: +9 chr7:35892300-35904800 2.96117781832569e-14 7.49177988036399e-10 Cebpa, ::F735-4NF::F735-2NF::F735-6NF::M626-7NF::F735-7NF::F735-1NF::F735-5NF::F735-3NF::F735spine:: +9 chr9:21769300-21781800 2.96117781832569e-14 7.49177988036399e-10 Epor, Rgl3, ::F735-7NF::F735-3NF::F735-6NF::F735-4NF::F735-1NF::F735-2NF::F735-5NF::M626-7NF::F735spine:: +10 chrX:7491400-7516400 3.5102919247234e-13 8.88103856955021e-09 Pcsk1n, Eras, Hdac6, ::F802-6NF::M863P::F803P::F704-2P::F649-3NF::F812-1P::M725P::M562P::F595P::F771-1P:: +8 chr1:81528400-81540900 2.01720903995621e-12 5.10353887108921e-08 No results within 2500 bp window ::F994-1NF::F994-3NF::F994-8NF::M910P::F994-4NF::M910-2NF::M552-NF::F994-5NF:: + +all_0.0001library +number pos pvalue bonferroni gene_name library_name +351 chr5:28400700-28500700 0 0 En2, Insig1, ::F802-6NF::M624-4NF::M626-5NF::M624-7NF::F735-3NF::F510P::M1022-P::m540spine::M930-1P::F885-1NF::M892-11NF::M988-4NF::F877-1NF::F803P::F695-3NF::F969-9NF::m892spine::M878-5NF::F959-7NF::F849-2NF::F969-8NF::M626-6NF::F968-6NF::M620-2P::F624-4NF::M892-10NF::M478-NP::F729-3NF::F957-12NF::M724-2NF::M892-9NF::F771-5NF::m918spine::M930-2P::M626-3NF::m1025spine::M1013-3NF::F729-1NF::F849-5NF::F649-3NF::F801spine::F877-4NF::F1027-5NF::M1022-13NF::m619spine::F968-1NF::M624-1NF::F1008-2P::F648-1NF::M1013-2NF::M626-2NF::F991P::F969-6NF::F1026-2NF::F968-4NF::M851-3NF::M624-6NF::M478-P::F850-6NF::F1027-8NF::F969-7NF::F1026-10NF::F947-3NF::M628-2NF::M732-5NF::M624-3NF::F879-5NF::F968-3NF::F991-3NF::M1008-4NF::F648-5NF::F1023spine::M920-3NF::F756-1P::F850-4NF::M952-2NF::F969-5NF::M732-4NF::M952-3NF::M620-1P::F959-4NF::F624-3NF::M1008-1NF::M626-10NF::F841-1NF::F976-3NF::F1026-9NF::M626-9NF::F991-5NF::F884-1NF::F729-4NF::F991-2NF::F959-5NF::F957-9NF::F757-3NF::F983-2NF::F876spine::M1008-5NF::F959-8NF::F879-1NF::m565spine::F969-3NF::M724-1NF::F959-10NF::F735-1NF::F976-8NF::M619-1P::F957-11NF::F968-2NF::F1027-2NF::M988-7NF::M863P::F1027-4NF::F976-5NF::F976-16NF::M892-P::F841-2NF::F648-4NF::M624-2NF::F673spine::F760-5NF::F879-2P::M892-5NF::m513::F969-1NF::F850-7NF::F760-2NF::F959-6NF::F969-4NF::F947-4NF::M892-7NF::M988-1NF::M920-4NF::M988-6NF::M892-2NF::F850-2NF::F879-2NF::M626-7NF::F760-1NF::F876-2P::M624-8NF::F737-2P::F624-1NF::F957-2P::M952-4NF::M988-5NF::M624-5NF::F1027-10NF::F959-1NF::F624-2NF::F735-4NF::M988-2NF::F976-4NF::F959-2NF::F879-6NF::m1008spine::F879-4NF::M626-8NF::F695-1NF::M1013-1NF::F959-1P::M578P::F802-4NF::F1026-1NF::M988-P::M724-4NF::F849-4NF::M724-3NF::M732-3NF::F877-6NF::F841-5NF::M920-5NF::F695-4NF::M724-6NF::F947-2NF::F976-6NF::M851-2NF::F957-10NF::F969-10NF::F994-8NF::M1013-5NF::F735spine::F704-NF::F648-2NF::F976-2NF::M988-3NF::F1027-9NF::m715spine::F1026-7NF::F1026-6NF::M910-4NF::F947-1P::F735-7NF::M1008-2NF::F947-5NF::F885-3NF::F802-3NF::M892-8NF::F849-7NF::F976-7NF::F1023-NF::M920-2NF::F884-2NF::M952-1NF::M1025-1NF::M1013-4NF::F1027-1NF::F983-1NF::m918triqwere::F1027-3NF::F976-1P::F969-2NF::M704P::F991-1NF::F884-3NF::F750-2P::F750-1P::F876-1P::M651-2P::F885-2NF::F802-1NF::F1026-5NF::F757spine::F1026-4NF::F957spine::M626-1NF::F624-5NF::F652-NF::F976-1NF::M878-2NF::F760-3NF::F771-2NF::F802-5NF::F735-2NF::F849-3NF::F859P::F991-P::F1023-P::M988-8NF::F695-2NF::F991-4NF::F648-3NF::M732-2NF::F957-3NF::F994-1NF::F968-5NF::F796-NF::M878-3NF::F1026-8NF::M892-1NF::M570P::M892-3NF::F850-8NF::F1027-7NF::F802-2NF::m988spine::M851-1NF::M626-11NF::M732-6NF::F959-2P::M628-1P::F760-4NF::F849-8NF::M741P::F757spine???::M892-4NF::F959-3NF::F593spine::M988-9NF::F601-NF::F654-2P::F729-2NF::F1027spine::F757-1NF::F959-9NF::F849-6NF::F1027-6NF::M725P::F957-1NF::M878-6NF::M892-6NF::F850-3NF::m1022spine::M920-1NF::F884P::F825-22P::F957-2NF::F735-5NF::F841-4NF::F877-5NF::F850-1NF::F596spine::F704-2P::M626-4NF::F877-3NF::F737-NF::M878-1NF::F976-11NF::F735-6NF::F850-5NF::F548spine::F884spine::MYSTERY-2P::F704-1P::F947-3P::F1008-1P::F879-3P::F812-2P::F976-9NF::F806-3P::F806-1P::F947-2P::F812-4P::F983P::F994-6NF::F879-1P::M724-5NF::F673-3NF::F841-6NF::F825-21P::m920spine::F771-1P::M878-4NF::F1026-3NF::F760-6NF::M1008-3NF::F976-2P::F715-1P::F585P::F1026P::F947-1NF::F630P::M504P::F877-2NF::F760P::m748spine::M1008-6NF::F715-2P::F715-3P::F648spine::M625P::F812-1P::F624-6NF::M513-3P::F814-4NF::M680P::M950P::F729-5NF::M651-3P::M513-2P::F994-4NF:: +351 chr5:28496200-28546200 0 0 AC129184.1, En2, Cnpy1, ::F735-3NF::F510P::M1022-P::m540spine::M930-1P::F885-1NF::M892-11NF::M988-4NF::F877-1NF::F803P::F695-3NF::F969-9NF::m892spine::M878-5NF::F959-7NF::F849-2NF::F969-8NF::M626-6NF::F968-6NF::M620-2P::F624-4NF::M892-10NF::M478-NP::F729-3NF::F957-12NF::M724-2NF::M892-9NF::F771-5NF::m918spine::M930-2P::M626-3NF::m1025spine::M1013-3NF::F729-1NF::F849-5NF::F649-3NF::F801spine::F877-4NF::F1027-5NF::M1022-13NF::m619spine::F968-1NF::M624-1NF::F1008-2P::F648-1NF::M1013-2NF::M626-2NF::F991P::F969-6NF::F1026-2NF::F968-4NF::M851-3NF::M624-6NF::M478-P::F850-6NF::F1027-8NF::F969-7NF::F1026-10NF::F947-3NF::M628-2NF::M732-5NF::M624-3NF::F879-5NF::F968-3NF::F991-3NF::M1008-4NF::F648-5NF::F1023spine::M920-3NF::F756-1P::F850-4NF::M952-2NF::F969-5NF::M732-4NF::M624-4NF::M952-3NF::M620-1P::F959-4NF::F624-3NF::M1008-1NF::M626-10NF::F841-1NF::F976-3NF::F1026-9NF::M626-9NF::F991-5NF::F884-1NF::F729-4NF::F991-2NF::F959-5NF::F957-9NF::F757-3NF::F983-2NF::F876spine::M1008-5NF::F959-8NF::F879-1NF::m565spine::F969-3NF::M724-1NF::F959-10NF::F735-1NF::F976-8NF::M619-1P::F957-11NF::F968-2NF::F1027-2NF::M988-7NF::M863P::F1027-4NF::F976-5NF::F976-16NF::M892-P::F841-2NF::F648-4NF::M624-2NF::F673spine::F760-5NF::F879-2P::M892-5NF::m513::F969-1NF::F850-7NF::F760-2NF::F959-6NF::F969-4NF::F947-4NF::M892-7NF::M988-1NF::M920-4NF::M988-6NF::M892-2NF::F850-2NF::F879-2NF::M626-7NF::F760-1NF::F876-2P::M624-8NF::F737-2P::F624-1NF::F957-2P::M952-4NF::M988-5NF::M624-5NF::F1027-10NF::F959-1NF::F624-2NF::F735-4NF::F802-6NF::M988-2NF::F976-4NF::F959-2NF::F879-6NF::m1008spine::F879-4NF::M626-8NF::F695-1NF::M1013-1NF::F959-1P::M578P::F802-4NF::F1026-1NF::M988-P::M724-4NF::F849-4NF::M724-3NF::M732-3NF::F877-6NF::F841-5NF::M920-5NF::F695-4NF::M724-6NF::F947-2NF::F976-6NF::M851-2NF::F957-10NF::F969-10NF::F994-8NF::M1013-5NF::F735spine::F704-NF::F648-2NF::F976-2NF::M988-3NF::F1027-9NF::m715spine::F1026-7NF::F1026-6NF::M910-4NF::F947-1P::F735-7NF::M1008-2NF::F947-5NF::F885-3NF::F802-3NF::M892-8NF::F849-7NF::F976-7NF::F1023-NF::M920-2NF::F884-2NF::M952-1NF::M1025-1NF::M1013-4NF::F1027-1NF::F983-1NF::m918triqwere::F1027-3NF::F976-1P::F969-2NF::M704P::F991-1NF::F884-3NF::F750-2P::F750-1P::F876-1P::M651-2P::F885-2NF::F802-1NF::F1026-5NF::F757spine::F1026-4NF::F957spine::M626-1NF::F624-5NF::F652-NF::F976-1NF::M878-2NF::F760-3NF::F771-2NF::F802-5NF::F735-2NF::F849-3NF::F859P::F991-P::F1023-P::M988-8NF::F695-2NF::F991-4NF::F648-3NF::M732-2NF::F957-3NF::F994-1NF::F968-5NF::F796-NF::M626-5NF::M878-3NF::F1026-8NF::M892-1NF::M624-7NF::M570P::M892-3NF::F850-8NF::F1027-7NF::F802-2NF::m988spine::M851-1NF::M626-11NF::M732-6NF::F959-2P::M628-1P::F760-4NF::F849-8NF::M741P::F757spine???::M892-4NF::F959-3NF::F593spine::M988-9NF::F601-NF::F654-2P::F729-2NF::F1027spine::F757-1NF::F959-9NF::F849-6NF::F1027-6NF::M725P::F957-1NF::M878-6NF::M892-6NF::F850-3NF::m1022spine::M920-1NF::F884P::F825-22P::F957-2NF::F735-5NF::F841-4NF::F877-5NF::F850-1NF::F596spine::F704-2P::M626-4NF::F877-3NF::F737-NF::M878-1NF::F976-11NF::F735-6NF::F850-5NF::F548spine::F884spine::MYSTERY-2P::F704-1P::F947-3P::F1008-1P::F879-3P::F812-2P::F976-9NF::F806-3P::F806-1P::F947-2P::F812-4P::F983P::F994-6NF::F879-1P::M724-5NF::F673-3NF::F841-6NF::F825-21P::m920spine::F771-1P::M878-4NF::F1026-3NF::F760-6NF::M1008-3NF::F976-2P::F715-1P::F585P::F1026P::F947-1NF::F630P::M504P::F877-2NF::F760P::m748spine::M1008-6NF::F715-2P::F715-3P::F648spine::M625P::F812-1P::F624-6NF::M513-3P::F814-4NF::M680P::M950P::F729-5NF::M651-3P::M513-2P::F994-4NF:: +267 chr2:163431900-163481900 0 0 AL591488.2, Serinc3, 0610039K10Rik, Pkig, Ttpal, ::M892-3NF::F994-3NF::F968-4NF::M878-2NF::F1026-10NF::F1026P::F969-6NF::M626-8NF::M920-4NF::F652-NF::F957-3NF::F849-5NF::M513-5P::F850-4NF::F757spine::M724-1NF::M620-1P::m920spine::F947-2NF::F729-1NF::F757-3NF::F968-3NF::M1008-2NF::m619spine::m918spine::F802-6NF::F959-4NF::F849-4NF::M578P::F994-6NF::F884-3NF::F969-7NF::F802-3NF::F760-1NF::F802-5NF::M741P::F802-4NF::M626-4NF::F976-7NF::F729-2NF::F849-6NF::F760-3NF::F879-2NF::M920-3NF::M626-5NF::M626-3NF::F806-1P::F757spine???::m748spine::F947-1P::F849-3NF::F750-2P::M878-5NF::F849-2NF::m565spine::M626-2NF::m1022spine::M732-4NF::M892-P::F957-9NF::M878-4NF::M878-3NF::F957spine::F695-3NF::F735-5NF::F648-3NF::F969-2NF::F1026-5NF::M626-1NF::F802-2NF::F510P::M624-4NF::M624-5NF::F884P::M626-7NF::F695-2NF::M732-1NF::M930-2P::F760-5NF::F969-4NF::F648-4NF::F704-1P::F877-6NF::F735-4NF::M892-2NF::F959-1P::M724-6NF::F729-4NF::M892-5NF::F648-1NF::F630P::F849-7NF::F695-4NF::m988spine::F624-2NF::F1026-4NF::F991-1NF::M892-9NF::M624-6NF::M626-9NF::F850-2NF::F879-1P::F735spine::F876spine::M892-4NF::F1026-3NF::F850-7NF::F735-1NF::M892-11NF::F1008-2P::M878-1NF::M624-8NF::M892-6NF::M624-1NF::F884-1NF::m1025spine::M732-6NF::F879-4NF::M892-1NF::F796-NF::M1025P::M732-5NF::F1027-4NF::F841-4NF::F1023-NF::F648-5NF::F735-6NF::M878-6NF::M724-4NF::F957-11NF::M1013-1NF::F976-9NF::M732-2NF::M920-1NF::F1026-6NF::M952-2NF::F959-1NF::F877-2NF::M1013-2NF::F1023-P::M988-8NF::F994-2NF::F760-4NF::F969-1NF::F841-2NF::F947-1NF::F968-2NF::m513::F959-8NF::M1013-3NF::F601-NF::M1013-5NF::F850-5NF::M1008-5NF::F877-3NF::M988-9NF::M624-2NF::M892-7NF::M1022-13NF::F841-1NF::F991-2NF::F879-2P::F624-4NF::F976-8NF::M851-1NF::M724-5NF::F969-5NF::F1027-1NF::M988-6NF::F850-1NF::F760-2NF::F976-4NF::F801spine::F735-3NF::F812-4P::F947-4NF::M626-6NF::F756-2P::F994-7NF::F969-9NF::F884-2NF::F957-2NF::F957-10NF::F850-8NF::m918triqwere::M952-1NF::F737-NF::M724-2NF::F879-5NF::F879-1NF::F624-3NF::F735-7NF::F957-1NF::F885-2NF::F959-9NF::F991-5NF::F757-1NF::F968-6NF::M626-11NF::M1022-P::F1027-5NF::m540spine::F879-6NF::F595P::M988-2NF::M1008-4NF::M988-P::F593spine::F1027-10NF::M920-5NF::F969-3NF::F991-4NF::F969-10NF::F959-3NF::F957-12NF::F850-6NF::F976-11NF::F991-P::F1026-8NF::M1013-4NF::M620-2P::M724-3NF::M952-4NF::F959-5NF::M892-10NF::F1027-9NF::M851-3NF::F969-8NF::F1023spine::F877-4NF::F695-1NF::F976-16NF::F648spine::F649-3NF::F1026-7NF::M988-7NF::m1008spine::F771-2NF::F771-5NF::F673spine::M988-5NF::F737-2P::F947-3NF::M626-10NF::M570P::F624-5NF::F812-2P::F959-6NF::F750-1P::M725P::M920-2NF::M851-2NF::M680P::F885-3NF::F959-2NF::F983-1NF::F968-1NF::F850-3NF::M988-1NF::F624-1NF::M952-3NF::F885-1NF::M1008-1NF::F735-2NF::M988-4NF::F884spine::F877-1NF:: +259 chr2:98489000-98689000 0 0 AL837506.2, AL837506.1, ::F876-1P::F968-1NF::F991-P::F1026-5NF::M863P::M988-2NF::M724-3NF::M1008-1NF::F624-4NF::M952-4NF::M988-P::F1026-8NF::m988spine::F957-2NF::F760-4NF::M1013-4NF::F1026-9NF::M626-4NF::M724-1NF::F1027-7NF::F841-1NF::F1027-4NF::F969-5NF::F991-1NF::M878-2NF::M732-4NF::F1026-6NF::F983-1NF::M732-2NF::M988-6NF::F760-6NF::F884-3NF::F729-5NF::F991-2NF::F1027-3NF::F976-11NF::M724-2NF::M624-6NF::F1026-2NF::F729-4NF::F850-6NF::M626-6NF::M1008-4NF::F969-6NF::F735-3NF::F1026-7NF::M624-3NF::F879-6NF::M626-1NF::F850-3NF::F969-3NF::M988-3NF::F729-2NF::M920-3NF::F976-1NF::F957-12NF::M624-7NF::F802-4NF::F841-2NF::M624-5NF::M624-1NF::M626-11NF::M1008-5NF::M1025-1NF::F841-6NF::F968-2NF::F624-3NF::F976-8NF::F1023-P::F968-6NF::M988-8NF::F624-1NF::M626-3NF::M724-4NF::F1026-10NF::F959-1NF::F1027-9NF::F695-4NF::M626-7NF::F885-3NF::F695-2NF::F850-1NF::F969-8NF::M878-6NF::M626-8NF::F1023-NF::F968-5NF::M626-2NF::M920-2NF::F885-2NF::M952-3NF::F850-8NF::M892-3NF::M624-4NF::F729-3NF::F983-2NF::F1027-1NF::F1027-8NF::M878-5NF::M892-10NF::F648-4NF::M478-NP::F648-2NF::M1013-1NF::F968-4NF::F771-5NF::F756-1P::F879-4NF::M920-1NF::F957-10NF::F976-16NF::M624-2NF::F735-2NF::F649-3NF::M920-5NF::F877-4NF::F991-3NF::F991-4NF::F947-3NF::M988-4NF::M910-1NF::F969-7NF::F957-11NF::F959-2NF::F957-1NF::F947-2NF::F957-3NF::F735-6NF::F884-1NF::M952-1NF::F825-22P::M988-7NF::F695-3NF::F947-4NF::F648-5NF::M988-5NF::F991-5NF::F1026-4NF::F802-5NF::F959-9NF::F959-6NF::F969-2NF::F757-3NF::M920-4NF::M732-5NF::F959-8NF::F879-5NF::F760-2NF::M892-8NF::F757-1NF::F735-4NF::M732-6NF::F735-7NF::M988-1NF::F841-5NF::F593spine::F959-10NF::F959-5NF::F760-5NF::F1027-6NF::m619spine::F957-9NF::M952-2NF::M724-6NF::M851-1NF::F968-3NF::F850-7NF::F715-2P::F969-10NF::F850-2NF::F877-2NF::M732-3NF::M628-1P::M1025P::F1027-10NF::M1013-3NF::M878-3NF::F959-7NF::M892-6NF::F624-5NF::M626-9NF::F695-1NF::F969-1NF::M892-9NF::F969-4NF::F1026-1NF::F1026P::F1027-2NF::F802-6NF::M724-5NF::M1008-2NF::F877-5NF::F704-2P::M1022-13NF::F737-NF::F969-9NF::F1027-5NF::M624-8NF::F879-2NF::F877-3NF::F976-7NF::F884-2NF::M1013-5NF::F976-3NF::F796-NF::F648-3NF::m1022spine::F841-4NF::m715spine::F976-4NF::F624-6NF::F801spine::M478-P::M1013-2NF::M892-4NF::m513::M988-9NF::F976-6NF::M892-11NF::F879-1NF::F976-2P::F976-1P::M620-1P::M626-10NF::M892-2NF::M851-2NF::M628-2NF::F760-1NF::M892-5NF::M651-3P::m1025spine::M892-7NF::F850-5NF::M851-3NF::F959-4NF::F957spine::F652-NF::M504P::M578P::F947-1P::M626-5NF::F859P::M619-2P::F715-1P::F1008-2P::F884P::F959-2P::m565spine::F885-1NF::M878-1NF::M851P::M651-2P::F1026-3NF::M741P::F812-2P::M570P::F802-3NF::F704-NF::F879-1P:: +159 chrX:139917600-139930100 1.31739307940942e-288 2.34632977015134e-283 No results within 2500 bp window ::F947-3NF::F1023-P::F976-8NF::F969-5NF::F648-5NF::F1027-9NF::F695-4NF::M624-8NF::F1023-NF::M732-6NF::M1025-1NF::M988-8NF::F735-4NF::F968-6NF::M892-3NF::M626-3NF::F841-6NF::M988-6NF::M952-1NF::M626-4NF::M878-6NF::F1027-7NF::F969-8NF::M988-2NF::F841-4NF::M626-5NF::F983-1NF::F850-2NF::F715-2P::F877-3NF::F969-9NF::M878-5NF::F1027-5NF::F850-8NF::F976-11NF::F1026P::F983-2NF::F1026-1NF::F624-1NF::M988-9NF::M892-8NF::F704-NF::M1025P::F648-2NF::M892-10NF::F1027-2NF::M1008-2NF::F1026-8NF::M626-8NF::F991-2NF::M724-1NF::F1027-4NF::F957-11NF::M1013-3NF::F879-1NF::M988-5NF::F802-5NF::F959-6NF::M626-7NF::F735-7NF::F879-5NF::F1027-1NF::M724-3NF::F735-2NF::F760-3NF::F879-2NF::F959-4NF::F737-NF::F652-NF::F959-5NF::M1008-4NF::M624-2NF::F968-3NF::F1026-5NF::F757-3NF::F771-5NF::F969-2NF::F1027-8NF::F757-1NF::m619spine::F991-4NF::M878-2NF::M920-2NF::F969-10NF::M651-3P::F959-9NF::F968-1NF::F735-6NF::M920-3NF::M626-6NF::M626-1NF::F969-3NF::M626-9NF::F802-6NF::F885-3NF::M920-1NF::F957-9NF::M724-6NF::M724-4NF::F796-NF::M626-2NF::M988-7NF::F959-1NF::F969-6NF::M988-1NF::M624-6NF::M892-5NF::F959-8NF::F729-2NF::M626-11NF::F947-2NF::F991-5NF::F695-1NF::F825-22P::F760-1NF::F850-3NF::M1013-5NF::F735-3NF::F885-2NF::F760-2NF::M732-4NF::F957-2NF::F976-16NF::F879-4NF::M624-4NF::F877-4NF::F884-2NF::M724-5NF::F648-4NF::m1025spine::M724-2NF::M1013-4NF::F991-P::F968-5NF::M1013-1NF::F969-1NF::F1026-6NF::F1026-10NF::M1008-1NF::M988-4NF::M920-5NF::M988-3NF::m988spine::F976-3NF::M1008-5NF::M952-2NF::F850-6NF::F959-2NF::M624-1NF::M624-3NF::F841-1NF::F968-4NF::F991-1NF::M478-NP::F947-4NF::F1026-7NF::F1026-4NF::m565spine::M920-4NF:: +149 chr13:31719100-31731600 2.10453935100511e-266 3.74826876571415e-261 Foxf2, RP23-322J11.2, ::M1025P::M724-6NF::F648-1NF::m892spine::M624-5NF::F879-2P::F1026-8NF::F885-2NF::M892-P::M626-7NF::F968-3NF::F957-9NF::F737-2P::F510P::F959-7NF::M626-4NF::m918spine::F695-3NF::F841-5NF::M628-2NF::m513::F624-5NF::M724-1NF::F648-5NF::F968-6NF::F959-1P::M892-7NF::M988-9NF::m540spine::F969-5NF::F735-1NF::F876spine::F968-1NF::F947-5NF::F1027-8NF::F969-9NF::F715-2P::M626-5NF::M624-1NF::F750-1P::M732-3NF::M624-4NF::F849-8NF::M626-10NF::F757-3NF::F648-4NF::M1008-2NF::M1022-13NF::M920-5NF::F957-1NF::F760-4NF::m619spine::M1013-3NF::F760-3NF::F1026-5NF::F885-1NF::M626-11NF::F695-2NF::F849-3NF::M892-3NF::F849-2NF::F947-4NF::F796-NF::F1008-2P::F548spine::M920-4NF::F859P::F879-4NF::F760-5NF::M952-4NF::M892-5NF::M892-6NF::F729-4NF::F850-7NF::F991-5NF::F757spine::m1025spine::m918triqwere::F850-1NF::F735-5NF::F957-2NF::F959-4NF::F1026-4NF::F841-2NF::F947-2NF::M988-6NF::F850-3NF::M892-1NF::F849-7NF::F884-3NF::m748spine::M930-1P::F976-7NF::F596spine::F1023-NF::m988spine::F959-8NF::F957-3NF::F957-11NF::F957spine::M626-2NF::M624-6NF::M930-2P::F968-4NF::F969-2NF::F771-5NF::M724-4NF::F969-7NF::M878-1NF::F957-12NF::F704-1P::M988-5NF::F729-1NF::F879-2NF::M624-8NF::M892-10NF::M626-9NF::M892-2NF::F1026-10NF::M878-6NF::M878-3NF::F695-4NF::F976-11NF::F877-3NF::M878-5NF::F850-4NF::F991-1NF::M570P::F850-5NF::F959-2NF::F976-8NF::F624-3NF::F729-2NF::M732-6NF::F652-NF::F976-16NF::F959-5NF::F877-5NF::F876-2P::F757spine???::M892-8NF::F801spine::F1027-1NF::F1027-2NF::M1013-1NF::F877-4NF::M892-4NF::F760-1NF::F850-6NF:: +120 chr9:3024700-3037200 9.81289832968962e-204 1.74771644411104e-198 AC131780.5, AC131780.4, AC131780.6, AC131780.12, AC131780.10, AC131780.2, ::F771-1P::M952-3NF::F648-2NF::M988-5NF::M988-1NF::M513-4P::F1026-8NF::F1026-2NF::F957-12NF::F991-3NF::M892-9NF::M892-11NF::F771-2NF::M851-1NF::M878-6NF::F1027-8NF::M626-6NF::F652-NF::F841-6NF::F991-1NF::F968-6NF::M892-8NF::F947-2NF::F737-NF::M724-4NF::F735-3NF::F976-16NF::F991-2NF::F884-1NF::M626-1NF::F735-6NF::M988-2NF::F976-1NF::F947-4NF::F957-11NF::M988-6NF::F957-2NF::F969-7NF::M732-6NF::F884-2NF::F630P::M892-3NF::M878-5NF::M920-5NF::F959-1NF::F959-9NF::M920-1NF::F1026-10NF::M1008-1NF::F1027-1NF::F757-1NF::M651-2P::F704-2P::M624-5NF::F850-5NF::M626-4NF::F841-5NF::F648-5NF::F1027-5NF::M1013-3NF::M988-9NF::F1026-6NF::M988-3NF::M724-3NF::M626-2NF::M626-11NF::F735-2NF::F1027-2NF::M988-8NF::F735-4NF::F695-2NF::F968-1NF::F969-2NF::F969-8NF::F991-5NF::F1026-7NF::F757-3NF::M1013-1NF::F879-2NF::F959-8NF::F959-2NF::M624-2NF::F1026-9NF::F1027-4NF::F884-3NF::M851-2NF::F969-10NF::F1026-5NF::F760-6NF::F885-3NF::F596spine::F802-4NF::M892-2NF::M680P::F879-5NF::F624-1NF::F802-5NF::F850-3NF::M952-4NF::F968-4NF::F729-4NF::M952-1NF::F968-2NF::F983-1NF::M851-3NF::F648-3NF::F877-4NF::F1027-9NF::F825-22P::F695-1NF::F760-5NF::M724-6NF::F877-5NF::M878-2NF::F760-2NF::F879-6NF::M626-9NF::M624-3NF::F850-6NF::F850-2NF:: +99 chr3:158259800-158272300 3.22473017953216e-160 5.74337343895395e-155 No results within 2500 bp window ::M513-1P::F976-8NF::M878-5NF::M1013-5NF::F648-4NF::F957-2NF::F757-3NF::F1027-2NF::F796-NF::F968-6NF::F991-2NF::M1013-3NF::F737-NF::F879-4NF::M878-6NF::M952-1NF::M732-6NF::M851-1NF::F735-4NF::M626-2NF::F841-6NF::F850-1NF::F735-2NF::F757-1NF::F735-6NF::M988-6NF::F968-1NF::F885-2NF::F968-3NF::F884-1NF::M952-3NF::M892-8NF::F969-10NF::F983-1NF::M892-10NF::F885-1NF::M626-6NF::F648-1NF::F649-3NF::F735-7NF::F969-2NF::F983-2NF::F969-8NF::M624-4NF::F841-1NF::F877-4NF::F1027-5NF::F991-4NF::M988-1NF::M626-4NF::F957-1NF::F850-3NF::F695-3NF::F704-NF::M1013-4NF::M988-8NF::F885-3NF::F850-8NF::F1023-P::F969-4NF::M724-3NF::M988-9NF::M624-2NF::M626-7NF::F1026-10NF::M1008-4NF::F959-2NF::F1026-7NF::F695-4NF::F648-2NF::M988-3NF::M878-2NF::M988-2NF::M626-8NF::F841-2NF::F695-2NF::M624-6NF::F1026-8NF::F991-P::M1008-5NF::F947-4NF::F771-5NF::F1027-8NF::M988-7NF::F947-5NF::F969-6NF::F624-3NF::F1026-5NF::M1025-1NF::F760-4NF::F648-5NF::F760-2NF::F959-6NF::F969-3NF::F879-6NF::M1013-1NF::F1023-NF::M624-1NF::F825-22P:: +129 chr11:3000500-3100500 3.22260068428109e-109 7.71393925796365e-105 Pisd-ps1, Sfi1, RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Eif4enif1, Drg1, ::F876spine::F968-1NF::M988-1NF::F983-1NF::M892-11NF::M513-4P::m619spine::F1026P::F771-5NF::F757-1NF::M504P::F1027-1NF::M892-6NF::M626-4NF::F959-2P::M724-6NF::F1026-3NF::M732-4NF::F850-7NF::F959-9NF::F1026-10NF::M988-2NF::F735-4NF::M624-3NF::F976-11NF::M892-3NF::F1026-7NF::F1027-10NF::M952-4NF::F850-3NF::M680P::F959-6NF::F1027-9NF::F1023-P::F771-1P::F850-6NF::F968-6NF::F957-2NF::F757-3NF::F801spine::F991-4NF::M1013-3NF::M626-2NF::M626-6NF::M892-10NF::F715-2P::F959-1NF::F969-6NF::F850-2NF::F1027spine::M570P::F947-1NF::M1013-2NF::M624-8NF::F735-2NF::M988-3NF::F994-4NF::F969-8NF::M624-2NF::F850-1NF::F648-1NF::M626-7NF::F673-2P::M620-2P::F968-2NF::F715-3P::F991-P::M624-5NF::F969-4NF::F969-2NF::F1023-NF::M626-5NF::F957-3NF::m918triqwere::F969-3NF::M878-1NF::m565spine::F624-5NF::F802-6NF::M732-2NF::F959-2NF::F947-1P::F849-2NF::F969-10NF::F879-4NF::F796-NF::F735-6NF::M624-7NF::M988-8NF::M930-2P::M1008-4NF::F648-5NF::M625P::M878-2NF::M920-4NF::F760-1NF::F947-4NF::F991P::F649-3NF::M724-4NF::F812-2P::F879-5NF::M878-5NF::M628-1P::M626-3NF::F729-2NF::m920spine::F695-4NF::M892-P::F1027-2NF::F976-7NF::F976-6NF::F841-6NF::F1027-7NF::F885-3NF::F1026-1NF::F947-2NF::F1026-6NF::M988-5NF::F673-1P::F968-4NF::F969-1NF::M878-6NF::M892-4NF::F879-1NF::F877-4NF::F729-4NF::M513-2P::F877-7NF:: +58 chr10:57312100-57324600 2.50291714677627e-81 4.4577955550944e-76 No results within 2500 bp window ::M851P::m619spine::M513-1P::F994-4NF::m1025spine::F801spine::F947-1P::F757spine::MYSTERY-1P::M910-2NF::F750-1P::M910P::M1025P::F994-1NF::F994-2NF::M910-4NF::F994-3NF::F729-3NF::F1023spine::m1022spine::F849-2NF::M892-7NF::F673-2P::F663P::M552-NF::F1027-3NF::m748spine::F760P::m988spine::M478-P::F849-3NF::m715spine::m565spine::F976-1P::F654-2P::M732-1NF::F673spine::F548spine::F757spine???::F994-6NF::F976-2P::m920spine::m918spine::F994-5NF::F673-3NF::F593spine::m1008spine::M910-1NF::F1027spine::F994-8NF::m696spine::F596spine::F648spine::F959-2P::F957spine::m513::F994-7NF::m892spine:: +57 chr6:103588400-103600900 1.56086457393642e-79 2.77996224076372e-74 Chl1, ::F757-3NF::F983-1NF::F735-3NF::MYSTERY-1P::F957-1NF::F1026-8NF::F879-6NF::M878-5NF::F1023-P::M724-2NF::M626-10NF::F969-2NF::M1013-1NF::M626-2NF::F802-4NF::M628-2NF::F624-1NF::M892-2NF::F850-8NF::M724-6NF::F695-1NF::F841-1NF::F715-2P::F771-5NF::F969-10NF::F756-1P::F947-3NF::M952-2NF::M952-3NF::M626-8NF::M988-8NF::F969-5NF::m619spine::F968-4NF::M988-9NF::F695-2NF::F991-1NF::M920-1NF::F877-4NF::M1008-4NF::F879-5NF::M626-6NF::F969-3NF::F877-3NF::M624-2NF::M1013-4NF::M892-8NF::F959-6NF::F735-7NF::F1027-4NF::F959-8NF::M624-8NF::F1026-10NF::F1008-2P::M732-6NF::M626-3NF::F757-1NF:: +50 chr3:48818900-48831400 3.45516858135588e-67 6.15379345013807e-62 No results within 2500 bp window ::F735-5NF::M504P::m920spine::F1027-5NF::F695-1NF::F796-NF::m1025spine::M626-7NF::F1027-3NF::F968-4NF::F729-3NF::F1026-6NF::F1026-4NF::M1013-3NF::F968-5NF::F802-2NF::F1026-8NF::F849-5NF::F760-5NF::F841-5NF::F624-4NF::F1008-2P::F850-7NF::MYSTERY-2P::M624-1NF::F735spine::M892-P::F704-2P::M878-1NF::F649P::M878-2NF::M619-2P::F841-6NF::F850-6NF::F1027-9NF::F663P::F876spine::F959-3P::m918triqwere::F976-2NF::M626-3NF::F771-5NF::M1025P::M952-4NF::M878-4NF::M920-4NF::F802-5NF::M851-1NF::F548spine::F849-2NF:: +70 chr19:32843800-32893800 1.76103985141396e-62 4.21540109232959e-58 Pten, ::F1026-6NF::F850-1NF::M1013-5NF::M892-6NF::M910P::M680P::F959-2P::F1026-7NF::F704-1P::F750-2P::F760-4NF::F704-NF::M724-4NF::F850-2NF::F849-5NF::F1026-10NF::F879-1P::M920-4NF::F771-5NF::M626-5NF::F1026-9NF::F715-3P::F812-3P::F812-1P::F812-2P::m513::F885-3NF::M1013-4NF::F959-9NF::F715-1P::F806-1P::F806-4P::F806-2P::F806-3P::M570P::F802-4NF::F879-3P::F876-1P::M626-2NF::F624-1NF::M1025-1NF::F885-2NF::F850-3NF::M620-1P::M620-2P::F991-2NF::F649P::F947-1P::M741P::F1026P::F1027-5NF::M626-8NF::M625P::M930-1P::M626-6NF::F757spine::F1023-NF::F715-2P::M619-1P::F729-6NF::F585P::M724-3NF::M724-6NF::F959-2NF::M988-5NF::M952-2NF::F825-22P::M513-4P::F983P::F959-4NF:: +46 chr9:3727700-3740200 2.55233366221244e-60 4.54580834574684e-55 Gucy1a2, ::F825-21P::F806-3P::F959-7NF::M1022-13NF::M892-3NF::F695-1NF::M732-6NF::F624-4NF::F760-4NF::F849-7NF::F757-3NF::M851-3NF::F849-5NF::F968-2NF::F1026-10NF::F735-1NF::F1026-2NF::F968-4NF::M1008-2NF::F850-6NF::F1026-4NF::F652-NF::M619-2P::F802-4NF::F1026-6NF::F802-3NF::M892-11NF::F771-2NF::M892-8NF::M878-3NF::F876spine::F879-2NF::F1026-7NF::M626-9NF::F1026-5NF::M892-4NF::m1025spine::M920-4NF::F976-7NF::M724-3NF::F877-5NF::M892-1NF::F704-1P::M625P::M1013-3NF::F1027-9NF:: +40 chr16:42526200-42538700 2.65954052976076e-50 4.7367480651251e-45 No results within 2500 bp window ::m513::F715-2P::F947-1P::F976-1NF::F757-1NF::M504P::F1026P::F760-2NF::M1013-5NF::M626-3NF::F850-3NF::M988-6NF::F849-8NF::F771-2NF::F850-6NF::F976-11NF::F1027-4NF::F802-4NF::M892-10NF::M952-4NF::F968-2NF::M741P::F648-2NF::M920-1NF::F760-6NF::F771-1P::F947-3NF::F879-4NF::F735-2NF::F969-5NF::M724-3NF::F976-9NF::M626-1NF::F695-4NF::m619spine::F825-21P::F760-5NF::F624-5NF::M620-1P::M626-6NF:: +46 chrY:2853800-2878800 7.08596817613513e-47 1.69616820232147e-42 No results within 2500 bp window ::F976-16NF::M988-1NF::M626-4NF::M892-3NF::m619spine::M624-7NF::M988-9NF::M626-8NF::M920-4NF::M892-8NF::M570P::M878-3NF::M724-6NF::M626-3NF::M920-1NF::M1022-13NF::M680P::M732-5NF::M920-5NF::M1022-P::M624-3NF::M1008-1NF::M952-1NF::M724-2NF::M988-7NF::M892-4NF::M892-7NF::M878-2NF::M1008-4NF::M732-4NF::M892-10NF::M892-11NF::M626-10NF::M624-6NF::M930-2P::M851-3NF::M878-5NF::M620-2P::M1013-4NF::M1013-1NF::M920-2NF::M626-6NF::M624-5NF::M988-3NF::M988-2NF::M620-1P:: +72 chrX:39517400-39617400 5.45511977405383e-45 1.30579202031526e-40 Stag2, ::M920-4NF::F630P::F968-2NF::F947-3NF::M1013-3NF::F729-4NF::F947-2P::F756-1P::M624-3NF::M624-8NF::M620-1P::F841-2NF::M878-1NF::F969-2NF::M920-2NF::m918triqwere::M920-5NF::M952-1NF::M892-7NF::M626-3NF::F850-6NF::F969-7NF::M732-4NF::M651-2P::F983P::F976-16NF::F673-2P::M578P::F757-1NF::F959-9NF::M892-5NF::F884-2NF::F760-3NF::F624-1NF::F735-3NF::F885-1NF::M892-P::F884-3NF::F771-1P::F959-2NF::M626-6NF::F1027-5NF::F879-3P::M851-3NF::F760-1NF::F884-1NF::F879-5NF::F1026-8NF::F885-3NF::M624-4NF::M878-6NF::F959-1P::M892-8NF::F884P::M626-10NF::M626-4NF::M930-1P::M620-2P::M892-11NF::F812-3P::F812-2P::F877-4NF::F959-5NF::F825-22P::F1023-NF::F959-1NF::F959-10NF::M988-3NF::M741P::F1026-3NF::F968-1NF::F695-3NF:: +36 chr10:16573800-16586300 7.796138733775e-44 1.38852349304026e-38 No results within 2500 bp window ::F735-2NF::F976-16NF::F1027-10NF::F959-2NF::M988-6NF::M1008-5NF::M988-5NF::F735-4NF::F957-12NF::F735-7NF::F695-2NF::F969-2NF::F885-3NF::F959-9NF::M724-2NF::F879-4NF::M878-6NF::F648-4NF::M1008-1NF::F1026-8NF::M892-10NF::M988-7NF::F841-1NF::F1026-5NF::M920-1NF::F652-NF::F959-6NF::M624-2NF::F969-9NF::F991-4NF::F802-6NF::F1023-NF::F991-P::F957-3NF::M892-6NF::F983-2NF:: +33 chr9:3000000-3012500 4.15146414198221e-39 7.39392369543599e-34 AC131780.8, AC131780.9, AC131780.5, AC131780.1, ::M878-5NF::F630P::F983-1NF::F1027-5NF::F884P::F968-4NF::M624-6NF::M952-2NF::F729-2NF::F760-4NF::F801spine::M892-10NF::M878-2NF::F1027-4NF::F877-4NF::M724-6NF::F652-NF::M1008-4NF::F757-1NF::F959-3NF::F735-3NF::M988-P::F1026-1NF::m988spine::F976-8NF::M892-8NF::M920-1NF::F991-1NF::F757-3NF::F885-3NF::M626-2NF::F969-7NF::F879-4NF:: +85 chr11:79133700-79333700 5.76756487304358e-36 1.38058200366044e-31 RP23-188A3.2, RP23-188A3.3, Omg, Evi2b, Nf1, ::M1008-4NF::F879-1P::F947-4NF::M626-7NF::M626-4NF::m565spine::F850-6NF::F991P::F704-2P::F859P::M892-10NF::F630P::F968-4NF::M988-P::M920-5NF::F1026P::F849-5NF::F1023-P::M1008-2NF::M892-7NF::M732-4NF::F601-NF::F879-5NF::F850-7NF::F750-1P::M619-1P::F673-1P::F624-4NF::F510P::M628-2NF::M1022-P::F1026-9NF::F1026-4NF::F1026-7NF::F1026-6NF::F760-3NF::MYSTERY-2P::MYSTERY-1P::M578P::F812-2P::F983P::M892-3NF::M628-1P::F991-5NF::M930-1P::m1022spine::F825-22P::F825-21P::M626-1NF::M724-6NF::F729-6NF::F968-1NF::F648-5NF::F1023-NF::F595P::F585P::F876spine::F976-8NF::M593P::M741P::M624-6NF::M1013-4NF::M504P::F1026-10NF::F1008-2P::F841-5NF::F704-1P::M619-2P::M725P::F812-1P::M952-2NF::M626-2NF::F994-7NF::F1027-1NF::M620-1P::M620-2P::M626-5NF::M626-6NF::M624-1NF::F947-2P::F969-10NF::F771-2NF::m619spine::F771-1P::M1013-1NF:: +31 chr6:69880000-69892500 5.06811805519111e-36 9.02652098101757e-31 AC154006.7, ::M513-5P::M552-NF::F1023spine::F884spine::F959-2P::F994-3NF::m513::F849-2NF::m696spine::F729-3NF::F994-1NF::F994-2NF::F673-2P::m988spine::F1027spine::F994-8NF::F994-6NF::F673spine::F760P::M910P::M910-4NF::F1027-3NF::F673-3NF::M513-1P::F957-2P::F801spine::F947-1P::M910-2NF::F994-4NF::F957spine::F879-1NF:: +58 chr17:10393300-10493300 8.91742282955869e-32 2.13456350271146e-27 Qk, ::F957-12NF::F841-1NF::M626-8NF::M892-2NF::F969-3NF::F729-2NF::F991-1NF::F877-2NF::F850-4NF::F1026P::M628-2NF::M620-2P::M920-3NF::F757-3NF::F806-4P::M988-8NF::F624-4NF::F849-5NF::F879-2NF::F760-5NF::m918triqwere::F624-1NF::F648-2NF::M878-5NF::F729-3NF::M892-7NF::M626-1NF::F959-8NF::M920-1NF::F1026-7NF::F850-6NF::F976-1NF::M626-6NF::F757spine???::F695-2NF::M920-2NF::F812-3P::F1026-10NF::F969-7NF::F715-2P::M988-3NF::F510P::M892-3NF::M1013-2NF::F957-10NF::F735-2NF::M624-7NF::F850-3NF::F735-6NF::M952-3NF::F760-6NF::F704-NF::F968-2NF::F849-6NF::F983-1NF::M578P::M1013-1NF::F648-4NF:: +57 chr11:104200400-104300400 6.95133346872739e-31 1.66394069240928e-26 1700081L11Rik, AL593843.1, ::F760-2NF::F976-2P::F760-4NF::M1013-2NF::M741P::M892-11NF::F959-7NF::F673-1P::M724-2NF::F968-6NF::F850-4NF::F796-NF::F649-3NF::M704P::F1027-2NF::F760-6NF::F648-1NF::F1026-6NF::F959-2P::F879-2NF::F991-2NF::F885-2NF::F695-1NF::M513-2P::M892-10NF::F968-1NF::F947-1P::F968-2NF::F760-5NF::F1026-1NF::F648-2NF::F994-6NF::M626-6NF::F812-3P::F735-4NF::F735-1NF::M1013-3NF::F976-4NF::F729-2NF::M892-5NF::F812-2P::F879-5NF::M1022-13NF::F969-8NF::M626-10NF::F976-8NF::F841-1NF::M624-5NF::F959-1NF::F735-3NF::M1013-5NF::F1008-2P::F771-1P::F969-9NF::M624-7NF::F947-2NF::F850-6NF:: +28 chr1:147289800-147302300 1.69902566466017e-31 3.02603266978636e-26 No results within 2500 bp window ::M920-5NF::F1027-4NF::F1023-P::F859P::F959-2P::F601-NF::m748spine::M626-4NF::F991-1NF::F735-6NF::F850-5NF::F959-4NF::F624-4NF::F1027-6NF::F648-4NF::F648-3NF::F695-2NF::M920-4NF::F649P::m918triqwere::F877-4NF::M626-3NF::F648spine::F735-5NF::F673-2P::M499P::F969-2NF::F957-2NF:: +42 chr11:77372500-77422500 1.58692877240533e-29 3.79863140250665e-25 Taok1, ::F802-3NF::M570P::M628-1P::F802-2NF::M624-7NF::M578P::F673-2P::M513-2P::F750-1P::F850-7NF::F1026-7NF::M892-P::M628-2NF::F976-6NF::F760P::F976-7NF::F595P::M930-1P::M619-1P::M878-6NF::F991-2NF::M624-8NF::F648-2NF::F825-21P::F825-22P::M920-1NF::F879-1NF::F1008-2P::F812-2P::F1026-8NF::F735-3NF::F991-5NF::F704-1P::M624-2NF::F877-4NF::MYSTERY-2P::F695-4NF::F812-3P::M892-8NF::M628-3P::F649P::F850-8NF:: + +all_0library +number pos pvalue bonferroni gene_name library_name +172 chr1:147091300-147291300 0 0 SNORA17, ::F648-2NF::M1025-1NF::M988-7NF::F825-21P::F957-12NF::F760-2NF::F1026-1NF::F968-6NF::F735-6NF::F885-2NF::F757-3NF::M1013-4NF::F969-6NF::M952-2NF::F624-5NF::M626-5NF::F802-3NF::M732-4NF::F850-8NF::M513-4P::M628-2NF::M626-3NF::F879-2P::M626-2NF::F750-2P::F879-1NF::F735-4NF::M626-11NF::F1023-NF::F969-2NF::M724-1NF::F1027-9NF::M1022-13NF::F735-7NF::F947-1P::F991-5NF::F648-5NF::F976-8NF::F630P::F771-5NF::F876spine::F750-1P::F1008-1P::F879-6NF::F879-5NF::F735-3NF::F876-1P::M624-3NF::F957-2NF::F735-2NF::F969-10NF::F695-2NF::F947-1NF::F959-5NF::F649P::F957-11NF::F760-4NF::F991-P::F1008-2P::F1023-P::F969-9NF::F976-9NF::F969-3NF::F884P::M570P::F969-8NF::M988-6NF::F796-NF::m748spine::F959-2NF::F735-5NF::M724-6NF::F1027-7NF::F1027-2NF::M626-1NF::M626-4NF::F735-1NF::F1026-8NF::M851-2NF::F1027-6NF::M878-2NF::M988-5NF::F812-3P::F959-1NF::M878-5NF::F729-2NF::M878-4NF::M626-10NF::F877-3NF::M988-1NF::M1025P::M1008-1NF::M952-4NF::F957-1NF::M920-5NF::F850-7NF::M1022-P::M920-4NF::M920-1NF::F879-2NF::F729-4NF::F877-4NF::F947-2NF::M624-7NF::F729-1NF::F729-6NF::F957-10NF::M1008-5NF::F601-NF::M892-10NF::F802-6NF::M892-P::F757spine::F968-1NF::F1027-4NF::M619-2P::F884-3NF::F969-1NF::F695-3NF::F983-2NF::m918triqwere::M724-3NF::M619-1P::M851P::F991-2NF::F969-5NF::F715-1P::F757-1NF::M625P::F704-1P::F884-2NF::F624-3NF::F756-1P::m565spine::M988-2NF::F648spine::F859P::M624-6NF::F947-3NF::M892-2NF::F1026P::M651-2P::M628-1P::F715-2P::F624-1NF::F959-2P::M1013-5NF::F648-3NF::M624-1NF::F947-2P::F976-16NF::F850-5NF::F1026-10NF::F885-3NF::F976-11NF::F879-4NF::F959-1P::M851-3NF::F673-2P::M732-6NF::F1026-6NF::F624-4NF::M499P::M920-2NF::F947-4NF::F648-4NF::F991-1NF::F968-2NF::M724-2NF::F1026-7NF::F806-1P::F959-4NF:: +192 chr6:103500400-103600400 0 0 Chl1, U7, ::F750-2P::M988-6NF::F648-5NF::M952-3NF::F673-2P::F756-1P::M626-10NF::M624-4NF::M1008-5NF::F976-11NF::F695-2NF::F760-1NF::F648-4NF::F969-10NF::F959-2NF::F695-4NF::F1026-10NF::M988-7NF::F735-3NF::F729-4NF::F885-2NF::F969-8NF::M892-10NF::M624-3NF::F648-2NF::M1013-1NF::M988-1NF::F947-3NF::M892-1NF::F695-3NF::F959-8NF::F877-3NF::F841-1NF::F879-5NF::M878-6NF::F957-10NF::F801spine::F947-2P::F771-1P::M619-2P::F624-3NF::F879-2NF::F802-6NF::F510P::F750-1P::M620-2P::M952-1NF::F760-4NF::M732-4NF::M988-5NF::F968-2NF::M892-3NF::F806-1P::M626-11NF::F969-5NF::M624-6NF::F959-10NF::F624-1NF::M892-11NF::F968-6NF::M626-4NF::F735-7NF::M851-3NF::F1023-NF::F757-3NF::F983-1NF::M892-7NF::F841-4NF::MYSTERY-1P::F957-1NF::m619spine::M626-2NF::F959-1NF::F1027-10NF::M624-8NF::M920-1NF::F850-8NF::F969-2NF::M626-3NF::F957-9NF::F877-5NF::F947-4NF::F968-5NF::F969-6NF::F737-NF::M952-2NF::F841-5NF::F649-3NF::F1027-2NF::F1027-7NF::F695-1NF::F1026-7NF::F735-6NF::F991-2NF::F1027-5NF::F771-5NF::M988-3NF::F877-4NF::M892-P::F885-1NF::F825-22P::F1027-6NF::F976-8NF::F715-3P::M724-5NF::F1026-5NF::M1022-13NF::M624-5NF::F729-6NF::F976-16NF::F1026-6NF::F1023-P::F1026-8NF::F959-7NF::M724-2NF::F976-1NF::M988-4NF::F1027-8NF::F1027-1NF::M920-3NF::F976-6NF::F969-3NF::M988-2NF::F879-6NF::M724-6NF::F735-4NF::F1026-1NF::F760-2NF::F1026-2NF::F991-5NF::M892-8NF::M878-5NF::M626-1NF::F760-6NF::F879-1NF::F735-2NF::M920-2NF::M1013-4NF::F968-1NF::M988-P::M952-4NF::M724-1NF::M851-2NF::M878-2NF::F1026-4NF::M1008-4NF::F991-4NF::F1026P::F630P::F885-3NF::M624-2NF::F991-1NF::M626-9NF::F802-4NF::M626-6NF::F757-1NF::M628-1P::F969-1NF::F968-4NF::F957-11NF::F1008-2P::m513::F983-2NF::M892-2NF::F959-4NF::F959-6NF::F959-9NF::F879-4NF::M732-6NF::F796-NF::F947-2NF::F760-3NF::F884-2NF::F850-6NF::M620-1P::F969-4NF::M624-7NF::F976-1P::M626-8NF::F729-2NF::M988-8NF::F1027-9NF::M920-5NF::F968-3NF::M988-9NF::M1025-1NF::F715-2P::M1025P::M628-2NF::F1027-4NF::F593spine::M851P:: +181 chr6:103558500-103608500 0 0 Chl1, ::F802-6NF::F510P::F750-1P::M620-2P::M952-1NF::F760-4NF::F969-8NF::M732-4NF::M988-5NF::F968-2NF::M892-3NF::F806-1P::M626-11NF::F735-3NF::F969-5NF::M624-6NF::F695-2NF::M1013-1NF::F959-10NF::M892-10NF::F624-1NF::M892-11NF::M988-1NF::F968-6NF::M626-4NF::F735-7NF::M851-3NF::F1023-NF::F757-3NF::F983-1NF::M892-7NF::F841-4NF::MYSTERY-1P::F957-1NF::m619spine::M626-2NF::F959-1NF::F1027-10NF::M624-8NF::M920-1NF::M878-6NF::F850-8NF::F969-2NF::F841-1NF::M626-3NF::F957-9NF::F879-5NF::F877-5NF::F947-4NF::F968-5NF::F969-6NF::M988-7NF::F737-NF::M952-2NF::F841-5NF::F649-3NF::F1027-2NF::F1027-7NF::F695-1NF::F1026-7NF::F735-6NF::F991-2NF::F1027-5NF::F771-5NF::M988-3NF::F877-4NF::M892-P::F959-8NF::F885-1NF::F825-22P::F1027-6NF::F976-8NF::F715-3P::M724-5NF::F1026-5NF::M1022-13NF::M624-5NF::M988-6NF::F729-6NF::F976-16NF::F1026-6NF::F801spine::F648-5NF::F1023-P::F1026-8NF::F959-7NF::M724-2NF::F976-1NF::M988-4NF::F1027-8NF::F1027-1NF::M920-3NF::F976-6NF::F969-3NF::M988-2NF::F879-6NF::M724-6NF::F1026-10NF::F735-4NF::F1026-1NF::F760-2NF::F1026-2NF::F991-5NF::M892-8NF::M878-5NF::M626-1NF::F760-6NF::F877-3NF::F879-1NF::F735-2NF::M920-2NF::M1013-4NF::F968-1NF::M988-P::F959-2NF::M952-4NF::M724-1NF::M851-2NF::F947-3NF::M878-2NF::F1026-4NF::M1008-4NF::M952-3NF::F991-4NF::F1026P::F630P::F885-3NF::M624-2NF::F991-1NF::M626-9NF::F885-2NF::F695-3NF::F802-4NF::M626-6NF::F757-1NF::M624-4NF::M628-1P::F756-1P::F648-2NF::M626-10NF::F969-1NF::F968-4NF::M1008-5NF::F957-11NF::F1008-2P::m513::F983-2NF::M892-2NF::F959-4NF::F959-6NF::F959-9NF::F879-4NF::M732-6NF::F796-NF::F947-2NF::F695-4NF::F760-3NF::F884-2NF::F850-6NF::M620-1P::F969-4NF::F969-10NF::M624-7NF::F976-1P::M626-8NF::F729-2NF::M988-8NF::F1027-9NF::M920-5NF::F968-3NF::F729-4NF::M988-9NF::M1025-1NF::F715-2P::M1025P::M628-2NF::F1027-4NF::F593spine::M851P::F850-3NF::F771-2NF:: +174 chr6:69781600-69881600 0 0 AC155333.1, AC155333.3, ::F959-8NF::F885-3NF::M892-8NF::F947-2NF::F760-2NF::MYSTERY-1P::M920-4NF::M626-3NF::M988-6NF::F1026-8NF::M626-8NF::M626-2NF::F850-3NF::M624-8NF::M680P::F947-3NF::F760-5NF::F735-4NF::F1027-3NF::F735-2NF::F735-6NF::F1023-P::M1013-4NF::M619-2P::M651-3P::M988-5NF::F649-3NF::F959-4NF::F879-5NF::F969-9NF::m696spine::F729-5NF::F859P::F654-2P::F654-1P::F959-2NF::m1025spine::M910-4NF::F877-3NF::F630P::M910P::F735-3NF::F983-2NF::F548spine::F806-1P::M552-NF::F976-1P::F756-1P::F771-1P::F750-2P::F1027spine::F735spine::F991-5NF::M851P::F737-1P::F771-2NF::F879-1NF::F825-21P::F850-2NF::F947-2P::F760P::F959-9NF::F969-6NF::F1027-1NF::F735-7NF::m988spine::F968-1NF::F959-3P::F1023spine::F695-4NF::M578P::M624-5NF::F969-10NF::M741P::M892-9NF::F969-3NF::F806-3P::F806-2P::F879-1P::F884spine::M920-2NF::F947-1P::m748spine::F957-10NF::F596spine::F957-11NF::M625P::m513::M920-1NF::F884P::m918triqwere::M988-2NF::m565spine::F976-11NF::F801spine::M910-2NF::M513-5P::M504P::F849-2NF::m892spine::m540spine::M478-NP::F652-NF::F704-2P::F959-2P::M1022-13NF::F957-2P::F673-2P::M513-1P::F876spine::F593spine::F757spine???::F991-2NF::M478-P::F704-1P::F585P::m1022spine::F673spine::F757spine::M628-1P::F850-6NF::M513-4P::F673-3NF::F947-3P::M1025P::F715-3P::F825-22P::m619spine::F850-1NF::F812-1P::F715-2P::F695-3NF::M626-6NF::F757-1NF::M624-4NF::F959-1NF::F729-3NF::m920spine::F663P::F1008-2P::F812-2P::F994-1NF::M1013-1NF::M988-P::F994-2NF::F695-1NF::M513-2P::F648spine::F991P::F849-4NF::M930-2P::F994-8NF::m715spine::M620-1P::M732-1NF::F968-6NF::F959-1P::F957spine::F994-4NF::m918spine::M892-10NF::F649P::F994-7NF::m1008spine::M628-3P::M892-7NF::F994-6NF::F673-1P::F994-3NF::M628-2NF::F1027-7NF::F957-9NF::F969-1NF::F756-2P:: +273 chr10:57303500-57328500 0 0 No results within 2500 bp window 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+371 chr5:28496200-28508700 0 0 En2, 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+201 chr11:3048600-3098600 0 0 RP23-191E3.2, RP23-191E3.18, Fau-ps2, Sfi1, Drg1, 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::M988-1NF::F735-6NF::M952-1NF::M878-2NF::F704-1P::M1013-1NF::F959-9NF::M988-5NF::M741P::F969-4NF::F1026-2NF::M878-6NF::F947-1P::M626-9NF::F1027-3NF::F947-4NF::M988-3NF::F991-P::M724-4NF::F825-21P::M920-1NF::F757spine???::F624-1NF::M624-4NF::M626-2NF::F548spine::F957-12NF::M851P::F771-5NF::M851-1NF::F652-NF::M988-2NF::F959-6NF::F649-3NF::M892-7NF::M626-6NF::F760-4NF::F959-10NF::M732-5NF::F976-9NF::M988-8NF::F695-4NF::M952-3NF::M892-8NF::F879-5NF::F1026-8NF::M851-3NF::F968-2NF::F1023-NF::F969-10NF::F715-1P::F771-1P::F1026-4NF::F884-2NF::M851-2NF::F876-1P::F1023-P::F1026-10NF::F976-16NF::m748spine::F957-9NF::F976-8NF::F624-3NF::F1026-7NF::M624-1NF::F849-2NF::F1026-1NF::F947-3NF::F983-1NF::F729-3NF::M626-1NF::F959-8NF::F750-1P::F850-3NF::F802-4NF::F876spine::F991-1NF::F947-1NF::F884-3NF::F885-2NF::F850-1NF::M620-2P::M878-5NF::F969-5NF::M892-P::F976-5NF::F771-2NF::M988-7NF::F648-4NF::M732-4NF::F806-3P::F969-1NF::MYSTERY-2P::M724-3NF::F796-NF::M1008-2NF::F735-2NF::F991P::M624-8NF::F968-6NF::F841-6NF::M878-4NF::F879-1NF::F991-3NF::F957-3NF::M626-3NF::M1008-4NF::F957-2NF::M878-1NF::F957-10NF::M952-4NF::M892-9NF::F1027-1NF::M626-11NF::F1027-4NF::F850-7NF::F757spine::F969-3NF::F760-2NF::F704-2P::M920-2NF::F957-11NF::m1025spine::m619spine::M892-10NF::F1026-5NF::m565spine::M619-2P::F991-5NF::F885-3NF::F850-8NF::F879-2NF::F735spine::F959-2NF::F983P::M988-6NF::F968-4NF::M892-4NF::m920spine::F976-2P::m540spine::F957-1NF::M628-1P::M626-7NF::F802-2NF::F959-3P::F1026P::M1013-4NF::M1013-3NF::F841-5NF::M732-6NF::F976-2NF::F1008-2P::M625P::F663P::F812-2P::F850-2NF::F1027-10NF::M892-5NF::F991-2NF::m892spine::F735-1NF::F648-3NF::F695-1NF::M624-2NF::M624-3NF::M988-P::F877-4NF::M624-7NF::F695-3NF::M626-10NF::F649P::F968-1NF::F648-5NF::M624-6NF::F1027-5NF::M892-3NF::M626-4NF::F585P::M504P::F735-7NF::F715-2P::F841-4NF::F1026-6NF::M724-5NF::F976-11NF::F673-1P::F510P::F850-6NF::M1025-1NF::F850-4NF::F812-3P::F757-3NF::F806-1P::F991-4NF::M680P::F947-2NF::F735-5NF::M570P::F959-3NF::F969-9NF::m715spine::F624-4NF::M1008-1NF::F735-4NF::F760-5NF::M920-5NF::F879-4NF::M1025P::F1027-9NF::m513::F593spine::F825-22P::F959-2P::M892-2NF::F841-2NF::F849-5NF::M628-2NF::M513-4P::F737-NF::M651-3P::F735-3NF::F757-1NF::M1022-P::M619-1P::m918triqwere::F802-5NF::F695-2NF::M1008-5NF::F750-2P::F968-5NF::F760-1NF::M920-4NF:: +233 chr3:48818900-48831400 0 0 No results within 2500 bp window ::F959-9NF::M988-5NF::M741P::F969-4NF::F1026-2NF::M878-6NF::F947-1P::M626-9NF::F1027-3NF::F947-4NF::M988-3NF::F991-P::M724-4NF::F825-21P::M920-1NF::F757spine???::F624-1NF::M624-4NF::M626-2NF::F548spine::F957-12NF::M851P::F771-5NF::M851-1NF::F652-NF::M988-2NF::F959-6NF::F649-3NF::M892-7NF::M626-6NF::F760-4NF::F959-10NF::M732-5NF::F976-9NF::M988-8NF::F695-4NF::M952-3NF::M892-8NF::F879-5NF::F1026-8NF::M851-3NF::F968-2NF::F1023-NF::F969-10NF::F715-1P::F771-1P::M878-2NF::F1026-4NF::F884-2NF::M851-2NF::F876-1P::F1023-P::F1026-10NF::F976-16NF::m748spine::F957-9NF::F976-8NF::F624-3NF::F1026-7NF::M624-1NF::F849-2NF::F1026-1NF::F947-3NF::F983-1NF::F729-3NF::M626-1NF::F959-8NF::F750-1P::F850-3NF::F802-4NF::F876spine::F991-1NF::F947-1NF::F884-3NF::F885-2NF::F850-1NF::M620-2P::M878-5NF::F969-5NF::M892-P::F976-5NF::F771-2NF::M988-7NF::F648-4NF::M732-4NF::F806-3P::F969-1NF::MYSTERY-2P::M724-3NF::F796-NF::M1008-2NF::F735-2NF::F991P::M624-8NF::F968-6NF::F841-6NF::M878-4NF::F879-1NF::F991-3NF::F957-3NF::M626-3NF::M1008-4NF::F957-2NF::M878-1NF::F957-10NF::M952-4NF::M892-9NF::F1027-1NF::M626-11NF::F1027-4NF::F850-7NF::F757spine::F969-3NF::F760-2NF::F704-2P::M920-2NF::F957-11NF::F735-6NF::m1025spine::m619spine::M892-10NF::F1026-5NF::m565spine::M619-2P::F991-5NF::F885-3NF::F850-8NF::F879-2NF::F735spine::F959-2NF::F983P::M988-6NF::F968-4NF::M892-4NF::M988-1NF::m920spine::F976-2P::M952-1NF::m540spine::F957-1NF::M628-1P::M626-7NF::F802-2NF::F959-3P::F1026P::M1013-4NF::M1013-3NF::F841-5NF::M732-6NF::F976-2NF::F1008-2P::M625P::F663P::F812-2P::F850-2NF::F1027-10NF::M892-5NF::F991-2NF::m892spine::F735-1NF::F648-3NF::F695-1NF::M624-2NF::F704-1P::M624-3NF::M988-P::F877-4NF::M624-7NF::F695-3NF::M626-10NF::F649P::F968-1NF::F648-5NF::M624-6NF::F1027-5NF::M892-3NF::M626-4NF::F585P::M504P::F735-7NF::F715-2P::F841-4NF::F1026-6NF::M724-5NF::F976-11NF::F673-1P::F510P::F850-6NF::M1025-1NF::F850-4NF::F812-3P::F757-3NF::F806-1P::F991-4NF::M680P::F947-2NF::F735-5NF::M570P::F959-3NF::F969-9NF::m715spine::F624-4NF::M1008-1NF::F735-4NF::F760-5NF::M920-5NF::M1013-1NF::F879-4NF::M1025P::F1027-9NF::m513::F593spine::F825-22P::F959-2P::M892-2NF::F841-2NF::F849-5NF::M628-2NF::M513-4P::F737-NF::M651-3P::F735-3NF::F757-1NF::M1022-P::M619-1P::m918triqwere::F802-5NF::F695-2NF::M1008-5NF::F750-2P::F968-5NF::F760-1NF::M920-4NF:: +233 chr3:48796900-48821900 0 0 No results within 2500 bp window ::F704-1P::M1013-1NF::F959-9NF::M988-5NF::M741P::F969-4NF::F1026-2NF::M878-6NF::F947-1P::M626-9NF::F1027-3NF::F947-4NF::M988-3NF::F991-P::M724-4NF::F825-21P::M920-1NF::F757spine???::F624-1NF::M624-4NF::M626-2NF::F548spine::F957-12NF::M851P::F771-5NF::M851-1NF::F652-NF::M988-2NF::F959-6NF::F649-3NF::M892-7NF::M626-6NF::F760-4NF::F959-10NF::M732-5NF::F976-9NF::M988-8NF::F695-4NF::M952-3NF::M892-8NF::F879-5NF::F1026-8NF::M851-3NF::F968-2NF::F1023-NF::F969-10NF::F715-1P::F771-1P::M878-2NF::F1026-4NF::F884-2NF::M851-2NF::F876-1P::F1023-P::F1026-10NF::F976-16NF::m748spine::F957-9NF::F976-8NF::F624-3NF::F1026-7NF::M624-1NF::F849-2NF::F1026-1NF::F947-3NF::F983-1NF::F729-3NF::M626-1NF::F959-8NF::F750-1P::F850-3NF::F802-4NF::F876spine::F991-1NF::F947-1NF::F884-3NF::F885-2NF::F850-1NF::M620-2P::M878-5NF::F969-5NF::M892-P::F976-5NF::F771-2NF::M988-7NF::F648-4NF::M732-4NF::F806-3P::F969-1NF::MYSTERY-2P::M724-3NF::F796-NF::M1008-2NF::F735-2NF::F991P::M624-8NF::F968-6NF::F841-6NF::M878-4NF::F879-1NF::F991-3NF::F957-3NF::M626-3NF::M1008-4NF::F957-2NF::M878-1NF::F957-10NF::M952-4NF::M892-9NF::F1027-1NF::M626-11NF::F1027-4NF::F850-7NF::F757spine::F969-3NF::F760-2NF::F704-2P::M920-2NF::F957-11NF::F735-6NF::m1025spine::m619spine::M892-10NF::F1026-5NF::m565spine::M619-2P::F991-5NF::F885-3NF::F850-8NF::F879-2NF::F735spine::F959-2NF::F983P::M988-6NF::F968-4NF::M892-4NF::M988-1NF::m920spine::F976-2P::M952-1NF::m540spine::F957-1NF::M628-1P::M626-7NF::F802-2NF::F959-3P::F1026P::M1013-4NF::M1013-3NF::F841-5NF::M732-6NF::F976-2NF::F1008-2P::M625P::F663P::F812-2P::F850-2NF::F1027-10NF::M892-5NF::F991-2NF::m892spine::F735-1NF::F648-3NF::F695-1NF::M624-2NF::M624-3NF::M988-P::F877-4NF::M624-7NF::F695-3NF::M626-10NF::F649P::F968-1NF::F648-5NF::M624-6NF::F1027-5NF::M892-3NF::M626-4NF::F585P::M504P::F735-7NF::F715-2P::F841-4NF::F1026-6NF::M724-5NF::F976-11NF::F673-1P::F510P::F850-6NF::M1025-1NF::F850-4NF::F812-3P::F757-3NF::F806-1P::F991-4NF::M680P::F947-2NF::F735-5NF::M570P::F959-3NF::F969-9NF::m715spine::F624-4NF::M1008-1NF::F735-4NF::F760-5NF::M920-5NF::F879-4NF::M1025P::F1027-9NF::m513::F593spine::F825-22P::F959-2P::M892-2NF::F841-2NF::F849-5NF::M628-2NF::M513-4P::F737-NF::M651-3P::F735-3NF::F757-1NF::M1022-P::M619-1P::m918triqwere::F802-5NF::F695-2NF::M1008-5NF::F750-2P::F968-5NF::F760-1NF::M920-4NF:: +321 chr2:163445400-163470400 0 0 AL591488.2, 0610039K10Rik, Serinc3, Ttpal, ::F959-2NF::F968-4NF::F1023-NF::F1027-8NF::F969-3NF::M878-2NF::F947-4NF::F969-8NF::F802-4NF::F850-8NF::F1026-10NF::F884-3NF::M732-6NF::F969-6NF::F1026P::M626-11NF::F735-4NF::F1023-P::M626-10NF::F648-2NF::M988-1NF::M626-8NF::F879-5NF::M624-3NF::F624-1NF::F879-1NF::F850-3NF::F957-12NF::F735-6NF::M950P::F649-3NF::M988-5NF::F849-4NF::F648-4NF::M892-3NF::F1008-2P::F812-3P::M930-2P::F884P::F825-21P::F877-5NF::F957-3NF::M626-7NF::F876spine::F1026-4NF::m619spine::F877-1NF::F957-11NF::M570P::F648-1NF::M624-5NF::F959-6NF::F849-7NF::F983-1NF::M952-4NF::F947-1P::F1027-5NF::F849-6NF::M920-5NF::M578P::F983P::M892-4NF::F849-8NF::m920spine::M626-5NF::F695-3NF::M920-4NF::M513-2P::F806-1P::M892-1NF::F1026-3NF::F957-2NF::F991-5NF::F976-1NF::M920-1NF::F771-5NF::M878-3NF::F976-11NF::m1025spine::F729-1NF::F959-5NF::F729-4NF::M1008-2NF::m918triqwere::F648-3NF::M513-5P::M624-8NF::M851-2NF::F959-10NF::F959-1NF::F991-3NF::F959-3NF::F877-6NF::F1027-7NF::F849-5NF::F695-2NF::M1008-5NF::M988-8NF::F729-5NF::F1027-1NF::F802-3NF::M626-3NF::M626-4NF::M620-1P::F624-2NF::F879-1P::F850-2NF::M878-4NF::m988spine::F624-4NF::F969-1NF::F976-16NF::F957-10NF::M626-9NF::F976-8NF::F947-2NF::F735-1NF::F947-3NF::M724-5NF::m1022spine::M624-6NF::M724-4NF::F760-2NF::F760-3NF::F850-6NF::M892-9NF::F976-3NF::F969-2NF::F957-9NF::F624-5NF::M920-3NF::F877-3NF::F991-4NF::F630P::m565spine::F510P::F802-6NF::M892-8NF::F968-3NF::M626-2NF::F715-1P::F1026-8NF::m540spine::F735-3NF::M988-3NF::F879-2NF::F729-2NF::M1013-1NF::F814-4NF::M988-4NF::F802-2NF::F976-4NF::F884-1NF::F756-1P::F976-5NF::M628-3P::F877-4NF::F1026-2NF::F652-NF::F850-7NF::M878-1NF::M892-P::F969-4NF::F735-2NF::F1026-1NF::M892-10NF::F1027-9NF::M513-4P::F959-8NF::F735-7NF::F877-2NF::F812-2P::F737-NF::M1013-4NF::M878-6NF::F757spine???::F771-2NF::F850-5NF::M892-6NF::F757spine::M892-2NF::M988-7NF::M892-7NF::F850-4NF::M1013-2NF::F729-3NF::F885-2NF::F825-22P::F704-NF::F802-5NF::F695-4NF::F991-1NF::M1022-13NF::F959-7NF::F884-2NF::F760-1NF::F879-4NF::F757-3NF::F968-2NF::M952-2NF::M724-6NF::F994-6NF::F969-7NF::M878-5NF::F957-1NF::F968-1NF::M626-6NF::M988-9NF::F735spine::F976-2NF::M1008-1NF::F976-9NF::F841-5NF::F1027-4NF::F750-2P::F1026-5NF::F969-9NF::M1013-3NF::F1027-2NF::F885-3NF::F841-4NF::M724-1NF::F1026-9NF::F596spine::M732-5NF::F750-1P::M741P::M624-4NF::m748spine::F760-4NF::M988-2NF::F648-5NF::F849-2NF::F947-1NF::M988-6NF::F976-6NF::F849-3NF::M732-1NF::F957spine::F879-6NF::M952-3NF::F991P::M892-11NF::M724-2NF::m513::F969-10NF::F976-7NF::M1008-4NF::F959-4NF::M851-3NF::F968-6NF::F704-1P::F1027-10NF::F959-9NF::F841-2NF::M624-7NF::F760-5NF::M732-2NF::M651-2P::F796-NF::F991-2NF::M952-1NF::M988-P::M732-4NF::F850-1NF::m918spine::F735-5NF::M1025P::F959-1P::F624-3NF::m892spine::F1026-6NF::F969-5NF::M892-5NF::M851-1NF::M624-2NF::M626-1NF::M624-1NF::F801spine::F841-1NF::M628-2NF::F1026-7NF::F737-2P::F1023spine::F695-1NF::F729-6NF::F991-P::F812-4P::M704P::F757-1NF::M920-2NF::F760P::F812-1P::M1025-1NF::F1027-3NF::m1008spine::F715-3P::F885-1NF::F595P::F593spine::F585P::M1013-5NF::F601-NF::F879-2P::M478-NP::F994-2NF::F976-2P::M725P::F849-1NF::F673spine::F803P::F649P::F802-1NF::F756-2P::F648spine::M1022-P::M724-3NF::M680P::M620-2P::F994-7NF::F884spine:: +308 chr2:98497700-98510200 0 0 AL837506.2, AL837506.1, ::F968-1NF::F876-2P::F1026-5NF::M988-1NF::F771-1P::F991-P::F969-8NF::F648-5NF::F801spine::M988-2NF::F802-2NF::M624-2NF::F757-1NF::F735-4NF::M626-6NF::M1025-1NF::M988-8NF::F704-2P::M892-10NF::F876spine::F760-4NF::M952-4NF::M624-3NF::F1027-8NF::M1008-4NF::F1026-8NF::F991-4NF::M988-9NF::F983-2NF::F968-3NF::F585P::M988-P::M724-4NF::M570P::F796-NF::F957-2NF::F648-2NF::F1026-9NF::M878-5NF::F760-6NF::M863P::M626-2NF::F969-3NF::F957-11NF::F1023-P::F1026-10NF::F624-4NF::m988spine::M892-11NF::M1013-5NF::M626-4NF::M1013-4NF::M1008-1NF::M988-6NF::F1026-7NF::F879-5NF::F859P::M626-8NF::M732-6NF::F652-NF::F1026-6NF::F850-5NF::M988-7NF::F959-9NF::F983-1NF::F959-8NF::F729-2NF::F884-3NF::M724-3NF::M892-2NF::F757spine???::F969-2NF::F1026-4NF::M920-5NF::M988-3NF::M626-10NF::F630P::F735-7NF::F959-4NF::m565spine::F976-16NF::F624-3NF::M878-2NF::M988-5NF::F884-2NF::M1013-1NF::F1027-7NF::M1008-5NF::F812-4P::M851P::F976-11NF::F850-6NF::M1025P::F1027-9NF::M513-4P::M624-6NF::F991-2NF::F1026P::M626-7NF::F812-2P::F959-1NF::F885-3NF::F991-1NF::F596spine::F756-2P::M878-6NF::m748spine::M920-2NF::M732-5NF::M851-2NF::F850-3NF::F841-1NF::M724-1NF::F968-2NF::F850-4NF::F969-10NF::F969-5NF::M732-4NF::M626-11NF::F1027-4NF::F968-6NF::F969-6NF::M619-2P::F959-6NF::F969-7NF::F735spine::M910-1NF::M724-6NF::M892-8NF::F991-5NF::F976-8NF::F729-4NF::F695-2NF::F735-2NF::F1027-5NF::F825-22P::F877-5NF::F729-3NF::F968-4NF::F877-4NF::F877-3NF::F729-5NF::F957-9NF::M1013-3NF::M988-4NF::F885-2NF::F649-3NF::M624-1NF::F885-1NF::F1023-NF::F957-3NF::M892-9NF::M478-NP::M878-3NF::F715-3P::m1022spine::F735-3NF::F802-4NF::F947-4NF::M624-4NF::F879-6NF::F850-1NF::F648-4NF::F841-5NF::M724-2NF::F771-5NF::M624-8NF::F624-1NF::F969-4NF::F1026-2NF::F947-2NF::M732-2NF::M628-2NF::F884-1NF::F648-1NF::F1027-3NF::M624-7NF::M624-5NF::F957-12NF::F1027-1NF::F841-6NF::F991-3NF::M952-3NF::F695-3NF::F802-5NF::M920-3NF::F756-1P::F841-2NF::F957-10NF::M892-4NF::F695-4NF::M626-1NF::M626-3NF::F947-3NF::F729-6NF::F750-1P::F735-6NF::F968-5NF::F695-1NF::F957-1NF::F850-8NF::M851-3NF::F879-4NF::M952-1NF::F760-2NF::F1027-10NF::F959-2NF::M724-5NF::F704-1P::M892-3NF::M920-1NF::M920-4NF::F976-1NF::F757-3NF::F729-1NF::M851-1NF::F1026-3NF::F877-2NF::F593spine::F959-7NF::F1027-6NF::M628-1P::M1022-13NF::M626-9NF::M593P::F1027-2NF::M1013-2NF::F959-5NF::F715-2P::M952-2NF::F704-NF::F850-2NF::M704P::M892-6NF::M732-3NF::F959-10NF::F760-5NF::F1026-1NF::F850-7NF::m619spine::F624-5NF::m540spine::M892-7NF::F802-6NF::M1008-2NF::F969-1NF::M620-1P::F737-NF::F969-9NF::F737-2P::F976-4NF::F812-1P::F879-2NF::F947-5NF::F976-7NF::m892spine::M725P::F735-1NF::F876-1P::F879-1NF::F648-3NF::F976-9NF::F976-3NF::F976-1P::F841-4NF::m715spine::F624-6NF::F735-5NF::M651-3P::F760-3NF::M478-P::F812-3P::M892-P::m513::F884spine::F976-2P::F976-6NF::F760-1NF::M1022-P::M892-5NF::m1025spine::F947-2P::F957spine::F959-3NF::M504P::M578P::F715-1P::F884P::M651-2P::F959-1P::F1008-2P::M626-5NF::F947-1P::F877-1NF::F806-1P::F959-2P::F947-1NF::M741P::F771-2NF::M878-1NF::F849-2NF::m918triqwere::F825-21P::F976-2NF::F802-3NF::M619-1P::F849-5NF::F879-2P:: +309 chr2:98484100-98509100 0 0 AL837506.2, AL837506.1, ::M620-2P::F876-1P::F968-1NF::F729-4NF::F876-2P::F1026-5NF::M988-1NF::F771-1P::F991-P::F969-8NF::F648-5NF::F801spine::M988-2NF::F802-2NF::M624-2NF::F757-1NF::F735-4NF::M626-6NF::M1025-1NF::M988-8NF::F704-2P::M892-10NF::F876spine::F760-4NF::M952-4NF::M624-3NF::F1027-8NF::M1008-4NF::F1026-8NF::F991-4NF::M988-9NF::F983-2NF::F968-3NF::F585P::M988-P::M724-4NF::M570P::F796-NF::F957-2NF::F648-2NF::F1026-9NF::M878-5NF::F760-6NF::M863P::M626-2NF::F969-3NF::F957-11NF::F1023-P::F1026-10NF::F624-4NF::m988spine::M892-11NF::M1013-5NF::M626-4NF::M1013-4NF::M1008-1NF::M988-6NF::F1026-7NF::F879-5NF::F859P::M626-8NF::M732-6NF::F652-NF::F1026-6NF::F850-5NF::M988-7NF::F959-9NF::F983-1NF::F959-8NF::F729-2NF::F884-3NF::M724-3NF::M892-2NF::F757spine???::F969-2NF::F1026-4NF::M920-5NF::M988-3NF::M626-10NF::F630P::F735-7NF::F959-4NF::m565spine::F976-16NF::F624-3NF::M878-2NF::M988-5NF::F884-2NF::M1013-1NF::F1027-7NF::M1008-5NF::F812-4P::M851P::F976-11NF::F850-6NF::M1025P::F1027-9NF::M513-4P::M624-6NF::F991-2NF::F1026P::M626-7NF::F812-2P::F959-1NF::F885-3NF::F991-1NF::F596spine::F756-2P::M878-6NF::m748spine::M920-2NF::M732-5NF::M851-2NF::F850-3NF::F841-1NF::M724-1NF::F968-2NF::F850-4NF::F969-10NF::F969-5NF::M732-4NF::M626-11NF::F1027-4NF::F968-6NF::F969-6NF::M619-2P::F959-6NF::F969-7NF::F735spine::M910-1NF::M724-6NF::M892-8NF::F991-5NF::F976-8NF::F695-2NF::F735-2NF::F1027-5NF::F825-22P::F877-5NF::F729-3NF::F968-4NF::F877-4NF::F877-3NF::F729-5NF::F957-9NF::M1013-3NF::M988-4NF::F885-2NF::F649-3NF::M624-1NF::F885-1NF::F1023-NF::F957-3NF::M892-9NF::M478-NP::M878-3NF::F715-3P::m1022spine::F735-3NF::F802-4NF::F947-4NF::M624-4NF::F879-6NF::F850-1NF::F648-4NF::F841-5NF::M724-2NF::F771-5NF::M624-8NF::F624-1NF::F969-4NF::F1026-2NF::F947-2NF::M732-2NF::M628-2NF::F884-1NF::F648-1NF::F1027-3NF::M624-7NF::M624-5NF::F957-12NF::F1027-1NF::F841-6NF::F991-3NF::M952-3NF::F695-3NF::F802-5NF::M920-3NF::F756-1P::F841-2NF::F957-10NF::M892-4NF::F695-4NF::M626-1NF::M626-3NF::F947-3NF::F729-6NF::F750-1P::F735-6NF::F968-5NF::F695-1NF::F957-1NF::F850-8NF::M851-3NF::F879-4NF::M952-1NF::F760-2NF::F1027-10NF::F959-2NF::M724-5NF::F704-1P::M892-3NF::M920-1NF::M920-4NF::F976-1NF::F757-3NF::F729-1NF::M851-1NF::F1026-3NF::F877-2NF::F593spine::F959-7NF::F1027-6NF::M628-1P::M1022-13NF::M626-9NF::M593P::F1027-2NF::M1013-2NF::F959-5NF::F715-2P::M952-2NF::F704-NF::F850-2NF::M704P::M892-6NF::M732-3NF::F959-10NF::F760-5NF::F1026-1NF::F850-7NF::m619spine::F624-5NF::m540spine::M892-7NF::F802-6NF::M1008-2NF::F969-1NF::M620-1P::F737-NF::F969-9NF::F737-2P::F976-4NF::F812-1P::F879-2NF::F947-5NF::F976-7NF::m892spine::M725P::F735-1NF::F879-1NF::F648-3NF::F976-9NF::F976-3NF::F976-1P::F841-4NF::m715spine::F624-6NF::F735-5NF::M651-3P::F760-3NF::M478-P::F812-3P::M892-P::m513::F884spine::F976-2P::F976-6NF::F760-1NF::M1022-P::M892-5NF::m1025spine::F947-2P::F957spine::F959-3NF::M504P::M578P::F715-1P::F884P::M651-2P::F959-1P::F1008-2P::M626-5NF::F947-1P::F877-1NF::F806-1P::F959-2P::F947-1NF::M741P::F771-2NF::M878-1NF::F849-2NF::m918triqwere::F825-21P::F976-2NF::F802-3NF::M619-1P::F849-5NF::F879-2P:: +173 chr19:32819300-32919300 0 0 Pten, ::M952-2NF::F1027-2NF::M1008-1NF::M988-2NF::M626-6NF::F812-2P::F812-1P::F760-2NF::F715-1P::M624-5NF::F802-4NF::F968-6NF::F735-4NF::F760-6NF::F750-1P::F715-2P::F850-3NF::F1027-10NF::F969-10NF::M732-3NF::F812-3P::F825-22P::F885-3NF::F976-16NF::F959-5NF::F947-4NF::M1008-4NF::F735-3NF::M680P::F1026-6NF::F957-11NF::F1026-9NF::F850-1NF::F947-2NF::F976-11NF::F959-1NF::F969-8NF::M626-11NF::M626-9NF::M892-10NF::F624-1NF::F735-2NF::M1013-5NF::M892-6NF::M910P::M620-1P::M624-2NF::F756-1P::M725P::F959-1P::F1026-7NF::F959-2P::F1023-NF::F704-1P::M628-1P::F648-2NF::M1013-4NF::F879-5NF::F750-2P::F968-1NF::F760-4NF::M878-5NF::M732-5NF::F704-NF::F735-6NF::M724-4NF::F959-6NF::F879-1P::M892-P::M988-1NF::F1027-5NF::F969-6NF::F991-1NF::F976-9NF::M892-7NF::M626-1NF::F850-2NF::M1008-5NF::F849-5NF::M988-P::F1026-10NF::F947-3NF::M920-4NF::M624-7NF::F624-3NF::F771-5NF::M626-4NF::F959-10NF::M626-5NF::F969-4NF::M892-3NF::F715-3P::F884-2NF::M704P::F771-2NF::F876-2P::m513::F959-9NF::F876-1P::F652-NF::M499P::F806-1P::F673-2P::F630P::F879-3P::M741P::F806-3P::F771-2P::F991P::F649P::F806-2P::F654-3P::F825-21P::F983P::F663P::F1008-1P::M578P::F806-4P::M570P::M724-6NF::M628-2NF::F648-5NF::M626-2NF::m918triqwere::F624-4NF::M624-3NF::M1022-P::M952-1NF::M1025-1NF::F885-2NF::F1026P::F510P::M620-2P::F991-2NF::M619-2P::M651-2P::F947-1P::M930-2P::M626-8NF::F884-1NF::M625P::M930-1P::F757spine::M988-6NF::M878-2NF::M851P::F673-1P::M504P::M628-3P::M593P::M619-1P::F729-6NF::F585P::F756-2P::F757-1NF::F957-1P::M724-3NF::F959-2NF::M988-5NF::M626-10NF::F983-2NF::M513-4P::F760P::F959-4NF::F1026-1NF::M624-6NF::M732-6NF::F1008-2P::M1013-2NF::F850-8NF::M624-1NF::M988-8NF::M952-3NF:: +172 chr5:22761900-22961900 0 0 BC050254, Lhfpl3, Mll5, ::F957-11NF::M988-2NF::M724-2NF::F959-2NF::M732-6NF::F771-1P::M628-2NF::F1023-NF::M988-8NF::F877-4NF::F957-2NF::F885-3NF::M851P::F1027-8NF::M878-1NF::F735-7NF::M504P::F757spine::F959-1NF::F850-1NF::F969-6NF::F771-2NF::F968-5NF::M910-2NF::M624-3NF::M478-P::F806-2P::M910-1NF::F648spine::F771-5NF::F756-2P::F624-3NF::F735-3NF::M732-1NF::F757spine???::F976-3NF::F735-4NF::F991-P::F648-5NF::M626-10NF::M626-1NF::F994-7NF::F1027-2NF::F968-6NF::m1022spine::F801spine::F994-1NF::F959-2P::m540spine::F959-1P::F825-21P::F957spine::F994-3NF::F849-1NF::F879-1NF::M892-4NF::m565spine::F885-2NF::M988-5NF::M626-8NF::F969-3NF::M892-3NF::F994-4NF::F648-1NF::F968-1NF::F704-1P::M892-11NF::F976-1P::F876-1P::M892-8NF::F695-2NF::m696spine::F750-2P::F994-8NF::F802-4NF::m748spine::F735-2NF::F695-3NF::M626-6NF::M552-NF::F991-5NF::F994-6NF::F947-2P::M920-3NF::M625P::M620-1P::F969-1NF::F825-22P::F673-3NF::F652-NF::m1025spine::M626-4NF::F704-2P::M1013-1NF::F957-9NF::F806-1P::F593spine::M626-5NF::F760-6NF::M513-1P::M741P::M724-6NF::F1027-3NF::F994-5NF::M988-7NF::F959-9NF::m619spine::F624-1NF::F729-4NF::m918triqwere::M578P::m918spine::F601-NF::F548spine::F673-1P::F947-1P::M892-10NF::M910P::F737-2P::F947-2NF::M732-4NF::F976-16NF::M624-8NF::M910-4NF::M878-5NF::F947-4NF::F585P::F715-2P::F624-4NF::F879-6NF::m988spine::m715spine::M892-6NF::F596spine::M620-2P::M1013-3NF::F969-8NF::M878-2NF::F969-10NF::F756-1P::F1026-8NF::M920-1NF::F850-5NF::M851-2NF::F648-4NF::F812-2P::F959-6NF::F879-5NF::F735-6NF::F959-8NF::M988-6NF::F850-8NF::M624-7NF::M952-4NF::M952-2NF::F1027-1NF::F957-10NF::M1008-2NF::M624-2NF::F968-4NF::F812-3P::F959-10NF::M892-2NF::M724-3NF::F1027-10NF::M952-1NF::M988-4NF::M851-1NF::M626-11NF::M570P::F737-NF::F850-6NF:: +180 chr1:81434400-81534400 0 0 No results within 2500 bp window ::M1025-1NF::M892-7NF::M626-1NF::F959-9NF::F976-1P::F735spine::F885-2NF::F737-NF::M732-1NF::F994-7NF::F648-3NF::F695-3NF::M988-6NF::F877-4NF::F991-2NF::M952-1NF::M988-7NF::M988-3NF::F825-21P::F976-11NF::F757-1NF::F957-2NF::F976-8NF::F884-2NF::M724-2NF::M624-2NF::F968-3NF::F1026-7NF::F969-8NF::F879-1NF::F771-2NF::F812-1P::F750-1P::F850-1NF::F859P::F806-4P::F806-3P::M624-6NF::m1025spine::m920spine::F994-6NF::F994-1NF::M624-7NF::F994-3NF::F983-2NF::F994-4NF::m715spine::F994-5NF::F994-8NF::F991-5NF::F991P::F968-5NF::F850-3NF::M626-2NF::F947-3P::F959-1P::M626-8NF::F983-1NF::F825-22P::F1026-5NF::F760-5NF::M851P::F884P::F673spine::M624-8NF::M952-2NF::MYSTERY-1P::F884spine::F735-3NF::F757-3NF::m892spine::M626-6NF::M513-5P::m540spine::M741P::M1013-2NF::M724-6NF::F630P::F673-3NF::M513-3P::F652-NF::m988spine::F695-2NF::F976-4NF::m748spine::F1027spine::F876spine::F648-5NF::F1027-3NF::F876-1P::M513-1P::m619spine::F802-4NF::M513-2P::F673-2P::M593P::F849-2NF::F947-1P::M478-P::F947-3NF::F593spine::F850-6NF::F704-1P::F959-5NF::F750-2P::F715-1P::M1013-3NF::F957-11NF::F806-1P::m696spine::M620-2P::M499P::F1023-NF::M892-10NF::F510P::F548spine::F735-2NF::M552-NF::M565P::m565spine::F969-4NF::m513::F976-2NF::M892-8NF::F648-2NF::F983P::F802-3NF::F959-2P::F1027-5NF::F715-3P::F760P::F648spine::F654-2P::F756-1P::F1008-2P::F771-1P::F757spine::F850-7NF::M892-3NF::m918spine::M628-2NF::F760-4NF::F760-6NF::F654-1P::m1022spine::F596spine::F737-2P::F801spine::M1013-1NF::M910P::F1023spine::F1027-2NF::F969-3NF::F649-3NF::F957spine::F959-10NF::F968-1NF::F735-4NF::M1025P::F673-1P::M910-4NF::M988-5NF::m1008spine::m918triqwere::M878-2NF::M910-2NF::F729-4NF::M732-5NF::F1027-9NF::F879-1P::F715-2P::F796-NF::F1027-4NF::M628-3P::F957-9NF::F1026-10NF::M892-1NF::F757spine???::M625P::F969-6NF:: +172 chrX:39512200-39712200 0 0 RP23-418E2.1, Stag2, 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+248 chr13:31683500-31733500 0 0 RP23-467M8.2, Foxf2, RP23-322J11.2, ::F803P::F957-2NF::M724-3NF::F757spine???::F756-1P::M626-1NF::F968-2NF::F879-1NF::M1008-1NF::M952-3NF::F648-5NF::M626-2NF::F624-3NF::F884-1NF::F841-4NF::F850-1NF::M624-8NF::F1027-7NF::F879-2NF::F812-2P::M732-6NF::F801spine::F849-2NF::F849-3NF::m513::M626-7NF::M892-7NF::m540spine::F968-1NF::M626-11NF::M626-10NF::F760-3NF::F715-2P::F1026-10NF::F737-NF::M628-2NF::F841-6NF::M920-4NF::F957-10NF::F1023-NF::m988spine::F976-16NF::F735-3NF::F1026-7NF::F969-2NF::M920-5NF::F760-4NF::F879-5NF::F850-7NF::m565spine::F1027-4NF::F1023-P::F548spine::F802-3NF::F991-5NF::m748spine::F947-5NF::F879-6NF::M892-3NF::M732-3NF::M892-6NF::F757spine::F750-1P::F976-11NF::F947-3NF::M1008-2NF::F968-6NF::F947-4NF::F1026-6NF::F991-4NF::F968-4NF::F957-11NF::F812-3P::F841-5NF::F695-3NF::M624-6NF::F969-1NF::M892-4NF::M732-4NF::M624-1NF::M741P::M851-1NF::F879-2P::M851-2NF::F1008-2P::M724-6NF::M892-5NF::F624-5NF::F976-8NF::F976-1P::M626-8NF::F957-1NF::M892-2NF::F884-2NF::F947-2NF::M1013-3NF::F976-7NF::F850-6NF::F1026-9NF::F969-3NF::F957-3NF::m619spine::F850-2NF::F796-NF::F957-12NF::F969-10NF::M988-6NF::M952-4NF::F968-3NF::F976-6NF::M725P::M1008-5NF::F760-2NF::m1025spine::F1027-8NF::F991P::M1025P::M892-P::F959-1P::M878-3NF::M988-2NF::F729-1NF::F959-5NF::M724-5NF::F735-6NF::F877-4NF::F947-1NF::F1027-2NF::F850-3NF::M1013-5NF::m918triqwere::M952-2NF::M878-2NF::F969-5NF::M892-1NF::F969-9NF::F737-2P::M624-7NF::M626-4NF::M988-7NF::F596spine::F959-6NF::F959-2P::F959-7NF::M724-4NF::F959-1NF::F959-2NF::F969-7NF::M988-1NF::F850-8NF::M1022-13NF::M1008-4NF::F652-NF::M1022-P::F879-4NF::F991-1NF::F849-7NF::F771-5NF::F729-4NF::F876spine::F849-8NF::F959-3NF::M724-1NF::F959-8NF::F802-6NF::M624-4NF::M988-9NF::M704P::F959-4NF::M724-2NF::F760-5NF::F510P::F648-4NF::M878-1NF::F877-1NF::F735-5NF::M624-5NF::F695-2NF::F812-1P::F1026-4NF::F969-8NF::F1027-10NF::F802-5NF::F969-4NF::F771-2NF::F991-P::F648-1NF::F885-3NF::M988-5NF::M624-2NF::M920-1NF::F884-3NF::F1026-5NF::F841-2NF::M878-6NF::M626-5NF::F735-4NF::F757-3NF::M930-2P::F877-3NF::m892spine::M930-1P::F624-4NF::M851-3NF::F704-1P::F735-2NF::m918spine::F1026-8NF::F991-2NF::F735-1NF::F885-1NF::M920-2NF::F885-2NF::F957spine::F957-9NF::F859P::M1013-2NF::F850-4NF::F802-4NF::F760-1NF::F959-9NF::F729-2NF::F695-4NF::M626-9NF::F1026-1NF::M1013-1NF::F983-2NF::F802-2NF::M920-3NF::F1026-3NF::F750-2P::M878-5NF::F624-1NF::F976-9NF::F877-5NF::F812-4P::M988-4NF::M570P::F850-5NF::F969-6NF::M624-3NF::M892-8NF::M892-10NF::F876-2P::M952-1NF::M626-3NF::F1027-1NF::F1027-5NF:: +182 chr9:3640700-3740700 0 0 Gucy1a2, ::m619spine::F760-1NF::F1027-2NF::M952-2NF::M1013-1NF::M732-3NF::F968-2NF::F976-6NF::M988-5NF::F968-6NF::F884P::M892-10NF::F1026-6NF::F947-1NF::M513-2P::F879-1NF::F704-1P::F959-8NF::F877-1NF::F877-4NF::m918triqwere::F947-4NF::F648-4NF::F648-3NF::M626-1NF::M651-2P::F959-4NF::M988-1NF::F879-2NF::F968-5NF::F947-3NF::F959-9NF::F1026-4NF::M892-8NF::F969-3NF::F737-NF::M920-2NF::M624-3NF::F825-21P::F806-3P::F959-7NF::M988-8NF::M626-8NF::M1022-13NF::F959-3NF::F957-9NF::M626-11NF::M624-6NF::F957-10NF::F969-8NF::M620-2P::F704-2P::F735-4NF::M732-6NF::F969-10NF::F760-4NF::F991P::F757spine::F695-1NF::F624-4NF::F850-6NF::M1022-P::F969-1NF::F735-3NF::F885-2NF::F991-5NF::F957-2NF::M626-2NF::F1026-8NF::F735-7NF::F850-3NF::F585P::F812-2P::M651-3P::F969-9NF::F959-2NF::F976-11NF::M570P::F884-2NF::M851-3NF::M851-2NF::M892-3NF::M892-2NF::F624-1NF::M952-3NF::F757-3NF::F849-7NF::F841-4NF::F648spine::F991-2NF::M1008-2NF::F760-5NF::F1023-NF::M988-7NF::F968-1NF::F735-2NF::F849-5NF::M626-3NF::F850-1NF::F879-5NF::M732-4NF::M619-1P::M1013-3NF::F959-1NF::F735-5NF::F957-11NF::F969-5NF::M988-9NF::F825-22P::F1008-2P::F771-2NF::F624-3NF::M741P::M724-6NF::F1026-10NF::F850-8NF::M626-9NF::F812-3P::F976-7NF::F801spine::F976-1P::m1025spine::F885-1NF::F1026-5NF::M625P::m540spine::M619-2P::F757-1NF::M724-3NF::F1026P::F649-3NF::M988-2NF::M624-2NF::M892-4NF::F802-4NF::F947-2NF::F1027-9NF::M724-2NF::M624-7NF::M1008-5NF::F735-6NF::F1027-10NF::M920-4NF::F983-2NF::F715-3P::M626-5NF::M892-11NF::F1027-7NF::M628-2NF::M892-1NF::F850-2NF::F695-3NF::F1023-P::F877-5NF::M626-7NF::F876spine::F876-1P::F735-1NF::M626-6NF::M626-4NF::F1026-7NF::M1013-2NF::M1008-4NF::M878-3NF::F983-1NF::M878-6NF::F959-10NF::F959-6NF::F968-4NF::F796-NF::M1008-1NF::F1026-2NF::F884-3NF::F802-3NF::F959-3P::F652-NF::F959-5NF::F760-6NF::M920-1NF::M504P::M620-1P::F859P:: +192 chrX:139839800-139939800 0 0 SNORA17, 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+173 chr9:3694500-3744500 0 0 Gucy1a2, 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+188 chrX:139899600-139949600 0 0 No results within 2500 bp window ::F801spine::M892-10NF::M892-5NF::M1025P::M624-6NF::F695-2NF::F695-1NF::F879-5NF::F1026-1NF::F1027-1NF::M920-5NF::M626-11NF::M626-6NF::F757-3NF::F704-NF::F735-6NF::F969-6NF::F976-4NF::M626-7NF::M988-3NF::M920-1NF::F969-5NF::F735-3NF::M920-3NF::M988-7NF::F969-2NF::F947-3NF::M626-5NF::F729-2NF::M724-6NF::F968-6NF::F968-1NF::F959-2NF::F991-4NF::F850-6NF::M626-1NF::M988-P::M724-4NF::F991-1NF::F957-2NF::M892-7NF::F1026-5NF::M892-3NF::F1023-P::F760-3NF::F959-8NF::F841-6NF::F968-5NF::M651-3P::F850-8NF::M988-9NF::M1008-5NF::F802-4NF::m1025spine::M624-3NF::F947-5NF::F968-4NF::F885-3NF::F959-1NF::F648-2NF::M920-2NF::F983-2NF::F879-4NF::F957-9NF::M988-2NF::M626-4NF::F624-1NF::F879-2NF::M624-2NF::M626-3NF::F1027-5NF::M626-2NF::F879-1NF::M988-8NF::F983-1NF::M878-2NF::M624-7NF::F850-3NF::M1025-1NF::M724-2NF::M724-5NF::F1026-8NF::F1027-2NF::M988-6NF::F877-3NF::F841-1NF::M1013-5NF::F884-2NF::F884-1NF::F695-4NF::F1026-4NF::M1008-1NF::F969-3NF::F976-16NF::F802-6NF::F757-1NF::M988-1NF::M878-3NF::F947-4NF::F1027-8NF::M624-8NF::F959-4NF::F802-5NF::M851-3NF::F771-5NF::F959-5NF::F760-6NF::M1013-4NF::F771-1P::M478-NP::M892-8NF::F976-3NF::M1008-2NF::F760-2NF::M1008-4NF::F735-7NF::M626-8NF::F969-8NF::F648-4NF::M920-4NF::F976-11NF::F735-4NF::M952-1NF::M732-4NF::F959-10NF::m918triqwere::F737-NF::M878-5NF::M626-9NF::M624-1NF::M732-6NF::F648-5NF::F704-2P::F652-NF::F1026P::M851-2NF::F825-22P::F968-3NF::F959-9NF::F649-3NF::F1023-NF::F735-1NF::M952-2NF::M988-5NF::M988-4NF::m619spine::M892-1NF::F750-1P::M1013-3NF::m988spine::F976-8NF::F969-10NF::F877-4NF::F796-NF::F1026-10NF::F1026-7NF::F760-1NF::F850-2NF::M724-3NF::F959-6NF::F991-P::F1027-4NF::F991-5NF::F1026-6NF::M624-4NF::F991-2NF::M1008-3NF::F885-2NF::F957-11NF::M952-3NF::M1013-1NF::F715-2P::F735-2NF::F841-4NF::F969-1NF::F947-2NF::F1027-9NF::F624-3NF::F1026-9NF::F969-9NF::M878-6NF::M892-11NF::M724-1NF::F1027-7NF::F957-1NF::m565spine::F812-3P::F879-1P:: +205 chr9:3000000-3025000 0 0 AC131780.8, AC131780.9, AC131780.1, AC131780.11, AC131780.3, AC131780.7, AC131780.2, AC131780.5, AC131780.4, ::F850-2NF::F957-9NF::M878-5NF::M1025P::F947-3NF::M1008-5NF::F876spine::F947-5NF::F1026-7NF::F959-8NF::M988-3NF::F879-2NF::F884-1NF::F991-5NF::M1013-4NF::M651-2P::F1027-4NF::M626-4NF::M878-6NF::F630P::F1027-7NF::F1026P::F1027-5NF::F957-2NF::F968-4NF::M626-11NF::M1008-1NF::F695-4NF::F695-2NF::M624-6NF::M626-6NF::F735-2NF::M624-3NF::M513-2P::F983-1NF::M988-1NF::F884P::F879-4NF::F879-5NF::F877-1NF::F735-4NF::M952-2NF::M724-5NF::M988-6NF::F1026-6NF::F968-3NF::F957-12NF::F884-2NF::M724-6NF::M920-2NF::M952-3NF::F983-2NF::F673-3NF::F1023-P::M1025-1NF::F1027-2NF::F885-3NF::F624-3NF::M988-7NF::F969-3NF::F959-1NF::F1026-1NF::F969-4NF::F760-4NF::F729-2NF::F735-7NF::M624-2NF::F624-1NF::M619-2P::F976-8NF::M724-2NF::F801spine::M732-4NF::F959-9NF::F850-8NF::F968-1NF::F969-6NF::M878-2NF::M892-10NF::M626-2NF::F968-2NF::F991-4NF::F585P::F802-6NF::M1008-4NF::m748spine::F877-4NF::F652-NF::M513-4P::F969-8NF::F825-22P::F1026-9NF::F729-5NF::F969-5NF::M624-4NF::F1027-1NF::F737-2P::F648-2NF::F959-2NF::M1013-5NF::F968-6NF::F884-3NF::M651-3P::F841-1NF::M920-3NF::F850-5NF::M628-2NF::m513::F757-1NF::M741P::M624-7NF::F735-6NF::M952-1NF::F802-3NF::F991-P::M593P::F957-10NF::F735-3NF::F1023-NF::M988-P::F991-1NF::F841-2NF::m988spine::M892-8NF::M920-4NF::F959-3NF::F947-4NF::M920-1NF::F757-3NF::F648-3NF::M851-3NF::M988-4NF::F968-5NF::F673-2P::M878-3NF::F969-7NF::M952-4NF::F976-1NF::F877-5NF::M988-5NF::F991-3NF::F947-1NF::F648-5NF::F1027-8NF::M1013-1NF::F1026-5NF::F879-1NF::F969-10NF::F1027-3NF::M988-2NF::M920-5NF::F1027-6NF::M892-3NF::F704-2P::F976-1P::M624-5NF::M1013-2NF::M892-4NF::F760-5NF::F991-2NF::F849-2NF::M732-3NF::F969-9NF::M1013-3NF::M892-9NF::F969-2NF::F624-5NF::F957-1NF::F976-2NF::F1026-10NF::F695-1NF::M724-3NF::F771-5NF::F885-2NF::M732-5NF::M626-8NF::F737-NF::F877-3NF::F825-21P::M892-7NF::F757spine::F976-3NF::M626-3NF::F850-7NF::M620-1P::F1027-9NF::M732-2NF::F1026-8NF::M892-P::F879-6NF::M626-7NF::F735-1NF::F1026-3NF::M892-11NF::F959-2P::M851P::F760-3NF::M732-6NF::M988-8NF::M619-1P::F850-6NF::F976-11NF::M988-9NF::M624-8NF::F771-1P:: +228 chr9:3017600-3030100 0 0 AC131780.5, AC131780.7, AC131780.2, AC131780.4, AC131780.6, AC131780.3, AC131780.11, AC131780.12, ::M513-4P::F760-5NF::M732-3NF::F969-9NF::M626-2NF::F850-8NF::M1013-3NF::M892-9NF::F969-2NF::F624-5NF::F1023-P::F976-8NF::F969-6NF::F957-1NF::M624-6NF::F968-1NF::F884-2NF::F983-2NF::M624-3NF::M878-2NF::F976-2NF::F737-2P::m988spine::M988-1NF::F1026-10NF::F991-2NF::F1026-6NF::F1027-2NF::F969-8NF::F695-1NF::M724-3NF::F771-5NF::M626-11NF::F735-4NF::F983-1NF::F1027-1NF::M892-4NF::F877-5NF::F885-2NF::M732-5NF::F876spine::F959-1NF::M626-8NF::F648-5NF::M624-2NF::M1013-2NF::F957-2NF::M878-5NF::M724-6NF::F737-NF::M892-8NF::M988-2NF::F877-3NF::M1008-5NF::F825-21P::M892-7NF::F757spine::M878-6NF::F704-2P::F976-3NF::F991-4NF::M626-3NF::F879-2NF::F1026P::M593P::F850-7NF::M892-10NF::F1023-NF::F879-1NF::F947-3NF::M620-1P::F1026-5NF::F879-5NF::F1026-9NF::M988-P::F968-3NF::F1027-9NF::M732-2NF::F1026-7NF::F1026-8NF::M892-P::F879-6NF::M851-3NF::M626-7NF::F735-1NF::F1026-3NF::F1027-5NF::M892-11NF::F991-1NF::F959-9NF::F884P::F969-5NF::F968-2NF::F957-10NF::F959-2P::M1008-1NF::M851P::F760-3NF::M732-6NF::M988-8NF::M651-2P::M952-3NF::M619-2P::F968-6NF::M988-7NF::M1025P::M619-1P::F969-10NF::F850-6NF::M624-7NF::M626-4NF::F976-11NF::F947-4NF::M988-9NF::M624-8NF::F695-4NF::F771-1P::M892-3NF::F947-1NF::M952-4NF::M1013-4NF::M626-1NF::F652-NF::F760-4NF::F1008-2P::M988-5NF::F735-7NF::F648-4NF::F630P::F1026-1NF::F959-6NF::M988-3NF::F850-2NF::M952-2NF::F959-10NF::F969-7NF::M988-4NF::F735-6NF::F991-5NF::F715-1P::F648-2NF::F1027-8NF::F959-8NF::M624-5NF::F695-3NF::M988-6NF::F968-4NF::F991-3NF::F841-4NF::M1013-1NF::M1025-1NF::F841-5NF::F1027-4NF::F760-6NF::F850-5NF::F771-2NF::m748spine::F695-2NF::M625P::F976-16NF::F673-1P::F976-1NF::F976-4NF::F969-3NF::F1026-4NF::M1008-4NF::F959-4NF::F801spine::F959-2NF::F585P::F729-2NF::M851-2NF::F885-3NF::F729-5NF::F802-3NF::F841-6NF::M952-1NF::F649-3NF::F959-1P::F983P::M724-4NF::F879-4NF::F1026-2NF::F884-1NF::F735-3NF::F957-11NF::F624-1NF::F757-1NF::F624-4NF::F959-3NF::F947-2NF::F991-P::F802-4NF::F959-7NF::F735-2NF::F957-12NF::M626-6NF::F841-1NF::F877-4NF::F596spine::M851-1NF::M724-2NF::F859P::F757-3NF::F704-NF::M920-1NF::M920-5NF::M628-2NF::F624-3NF::F850-3NF::M920-2NF::F729-4NF::F756-1P::M863P::F884-3NF::M724-5NF::m565spine::M680P::M1013-5NF::M892-2NF::F1027-10NF::F802-5NF::F729-3NF::m715spine::F1027-6NF::F812-2P::M1022-13NF::F957-9NF:: + +PNST_0.01library +number pos pvalue bonferroni gene_name library_name +15 chr5:28496400-28508900 4.00885791731127e-47 3.98079591189009e-44 En2, ::F737-2P::M704P::M892-P::F991P::F947-1P::F1008-1P::F957-2P::F879-2P::M513-2P::F983P::F879-1P::M513-3P::F947-3P::F750-1P::M950P:: +18 chr19:32851300-32901300 7.72427180376557e-47 7.67020190113921e-44 Pten, ::M680P::F959-2P::F704-1P::F812-1P::F812-2P::F715-1P::F806-2P::F806-4P::F806-3P::F806-1P::F879-3P::M620-2P::M741P::F1026P::F715-3P::M619-1P::F585P::F983P:: +12 chr11:79155400-79355400 2.04403633899031e-22 2.02972808461738e-19 Nf1, RP23-188A3.2, RP23-188A3.3, Omg, Evi2b, Evi2a, ::F879-1P::F673-1P::M1022-P::MYSTERY-2P::F983P::F859P::F595P::M504P::F704-1P::M620-1P::F947-2P::M725P:: +6 chrX:7503900-7516400 2.68611382613301e-17 2.66731102935008e-14 Eras, Pcsk1n, Hdac6, ::M863P::F803P::F704-2P::M725P::F812-1P::F771-1P:: +4 chr19:34737100-34749600 2.99692607240415e-11 2.97594758989732e-08 Slc16a12, ::F806-1P::F806-2P::F806-4P::F806-3P:: +4 chr11:77388200-77438200 7.55370444776235e-09 7.50082851662802e-06 Taok1, ::M578P::F595P::M930-1P::M628-3P:: +3 chr7:20345100-20357600 2.31180502186997e-08 2.29562238671688e-05 Bcam, AC149282.1, ::F806-2P::F806-1P::F806-4P:: +3 chr2:62742700-62755200 2.31180502186997e-08 2.29562238671688e-05 Kcnh7, ::F806-4P::F806-1P::F806-2P:: +3 chr10:41241300-41253800 2.31180502186997e-08 2.29562238671688e-05 Cd164, ::M620-2P::M620-1P::M628-3P:: +4 chr13:108554300-108654300 1.18378262568165e-07 0.000117549614730188 Zswim6, ::F806-2P::F750-1P::M704P::M930-1P:: +4 chrX:149494400-149594400 1.18378262568165e-07 0.000117549614730188 RP23-180D16.1, Foxr2, Rragb, RP23-415B4.3, ::F812-1P::M725P::F654-1P::F630P:: +3 chr2:169937100-169987100 1.45671693713568e-06 0.00144651991857573 Zfp217, ::F654-3P::F510P::F957-1P:: +4 chr16:10989000-11189000 1.81708785425847e-06 0.00180436823927866 U1, AC164093.1, Gm10832, AC164093.4, Gm9861, Snn, Txndc11, Zc3h7a, mmu-mir-689-2, mmu-mir-2134-4, U1, RP23-230D17.2, RP23-230D17.3, AC087541.3, Litaf, ::F947-2P::F803P::F756-2P::F756-1P:: +3 chr12:26656900-26756900 1.14145067009356e-05 0.0113346051540291 No results within 2500 bp window ::F812-4P::F947-2P::F947-3P:: +3 chr16:4125600-4225600 1.14145067009356e-05 0.0113346051540291 Crebbp, ::M620-1P::M570P::F771-1P:: +3 chr8:93476600-93576600 1.14145067009356e-05 0.0113346051540291 Chd9, ::M620-1P::M930-1P::F876-2P:: +2 chrX:58136800-58149300 1.33748105476019e-05 0.0132811868737687 Sox3, RP23-174O19.2, ::F947-2P::F947-3P:: +2 chr9:45905000-45917500 1.33748105476019e-05 0.0132811868737687 Sik3, ::F812-3P::F812-2P:: +2 chr9:42795700-42808200 1.33748105476019e-05 0.0132811868737687 Arhgef12, ::M651-2P::M651-3P:: +2 chr9:3025500-3038000 1.33748105476019e-05 0.0132811868737687 AC131780.5, AC131780.6, AC131780.12, AC131780.4, AC131780.2, AC131780.10, ::M513-4P::F630P:: +2 chr8:70225600-70238100 1.33748105476019e-05 0.0132811868737687 Psd3, ::M651-2P::M651-3P:: +2 chr8:89350300-89362800 1.33748105476019e-05 0.0132811868737687 N4bp1, ::F715-2P::F715-3P:: +2 chr8:110104200-110116700 1.33748105476019e-05 0.0132811868737687 Psmd7, ::M725P::F812-1P:: +2 chr8:129605700-129618200 1.33748105476019e-05 0.0132811868737687 Pard3, ::F649P::M680P:: +2 chr7:142904600-142917100 1.33748105476019e-05 0.0132811868737687 Mki67, ::F825-21P::F825-22P:: + +PNST_0.001library +number pos pvalue bonferroni gene_name library_name +43 chr5:28496400-28508900 4.53600182335816e-118 2.73974510130833e-114 En2, ::M988-P::F876-1P::M651-2P::M704P::M863P::F859P::M892-P::F750-1P::F884P::F737-2P::F803P::F991P::F957-2P::F991-P::F959-1P::M930-2P::F510P::M478-P::F879-2P::F983P::MYSTERY-2P::F947-3P::F947-1P::F771-1P::M930-1P::F1008-1P::F1008-2P::F760P::F630P::F806-1P::F879-3P::M513-2P::M651-3P::F704-1P::F976-2P::F812-2P::M1022-P::M950P::F876-2P::F879-1P::M725P::M619-1P::M513-3P:: +23 chr19:32851300-32901300 7.14761498559367e-44 4.31715945129858e-40 Pten, ::M680P::F959-2P::F704-1P::F812-2P::F812-3P::F812-1P::F715-1P::F806-2P::F806-1P::F806-3P::F806-4P::M570P::F879-3P::M620-2P::F649P::M741P::F1026P::M930-1P::F715-3P::M619-1P::F585P::M620-1P::F983P:: +17 chr2:98502500-98515000 8.24263657110723e-41 4.97855248894876e-37 AL837506.1, AL837506.2, ::M863P::F756-1P::F991-P::F825-22P::M1025P::M628-1P::F704-2P::F876-1P::M620-1P::M504P::M619-2P::F715-1P::M578P::F859P::F884P::M851P::F1026P:: +29 chr11:79155400-79355400 1.66370279882812e-40 1.00487649049218e-36 Nf1, RP23-188A3.2, RP23-188A3.3, Omg, Evi2b, Evi2a, ::F879-1P::F991P::M988-P::F1026P::M619-1P::F673-1P::F704-2P::M1022-P::MYSTERY-1P::MYSTERY-2P::F812-2P::F983P::M930-1P::F859P::F825-22P::F595P::M628-1P::F585P::M593P::M504P::F704-1P::F812-1P::F510P::M578P::M620-1P::M620-2P::F947-2P::M725P::F879-3P:: +9 chr2:163468400-163480900 8.24881502373913e-20 4.98228427433844e-16 AL591488.2, 0610039K10Rik, Serinc3, ::M513-5P::F884P::F750-1P::F879-2P::M988-P::M892-P::F959-1P::F595P::M680P:: +8 chrX:7503900-7516400 2.35375668044414e-17 1.42166903498826e-13 Eras, Pcsk1n, Hdac6, ::M863P::F803P::F704-2P::F812-1P::M725P::F595P::M562P::F771-1P:: +6 chr9:3005600-3030600 8.21649450920571e-11 4.96276268356025e-07 AC131780.5, AC131780.1, AC131780.11, AC131780.3, AC131780.7, AC131780.2, AC131780.4, AC131780.9, AC131780.6, AC131780.12, ::M988-P::M1025P::F771-1P::M513-4P::F630P::M680P:: +6 chr11:77384400-77409400 8.21649450920571e-11 4.96276268356025e-07 Taok1, ::M570P::M578P::F760P::F595P::M930-1P::F825-22P:: +6 chrX:149538600-149563600 8.21649450920571e-11 4.96276268356025e-07 RP23-180D16.1, Foxr2, ::F585P::F737-1P::F654-1P::F812-2P::F812-3P::F630P:: +9 chrX:39423200-39623200 3.53184559390387e-09 2.13323473871793e-05 RP23-295D9.1, Stag2, Xiap, ::F649P::M1022-P::F947-2P::F983P::M578P::M892-P::F771-1P::M620-2P::F630P:: +4 chr14:21347400-21359900 3.99558903678281e-08 0.000241333577821682 Ppp3cb, ::F630P::F756-1P::F756-2P::MYSTERY-2P:: +4 chr19:34737100-34749600 3.99558903678281e-08 0.000241333577821682 Slc16a12, ::F806-3P::F806-1P::F806-4P::F806-2P:: +8 chr16:4086300-4286300 6.29871164602452e-08 0.000380442183419881 RP24-425F2.2, Gm5766, Adcy9, Crebbp, ::MYSTERY-2P::F983P::F812-3P::M620-1P::M930-1P::M570P::F825-22P::F771-1P:: +5 chr11:3041800-3091800 2.34795264622858e-07 0.00141816339832206 Sfi1, RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Drg1, ::F771-1P::F673-2P::F715-2P::M930-2P::M504P:: +5 chrX:148444700-148494700 2.34795264622858e-07 0.00141816339832206 RP23-419G22.5, Smc1a, Ribc1, ::F673-2P::F806-4P::F750-1P::F750-2P::M504P:: +6 chr8:13605500-13705500 2.78521443490678e-07 0.00168226951868369 Rasa3, ::F649P::M741P::M930-2P::F1026P::M570P::F991-P:: +4 chr4:5049600-5074600 6.19445090857895e-07 0.00374144834878168 No results within 2500 bp window ::M628-3P::F959-1P::M651-2P::M651-3P:: +4 chr17:95231400-95256400 6.19445090857895e-07 0.00374144834878168 AC144860.1, ::F884P::F715-3P::F715-2P::M570P:: +4 chr17:27222800-27247800 6.19445090857895e-07 0.00374144834878168 Itpr3, RP23-328O21.2, ::F715-3P::F715-2P::F825-21P::F825-22P:: +4 chr13:3563200-3588200 6.19445090857895e-07 0.00374144834878168 Gdi2, BC016423, ::F715-1P::F715-3P::F715-2P::M499P:: +3 chr11:4686600-4699100 5.06720291100207e-06 0.0306059055824525 Nf2, ::F1023-P::M619-2P::M513-4P:: +3 chr10:41241300-41253800 5.06720291100207e-06 0.0306059055824525 Cd164, ::M620-2P::M620-1P::M628-3P:: +3 chr13:63982000-63994500 5.06720291100207e-06 0.0306059055824525 0610007P08Rik, ::MYSTERY-1P::M651-2P::M504P:: +3 chr13:85371700-85384200 5.06720291100207e-06 0.0306059055824525 Rasa1, ::F859P::F806-1P::M741P:: +3 chr13:99570200-99582700 5.06720291100207e-06 0.0306059055824525 Fcho2, ::M620-1P::M620-2P::M504P:: + +PNST_0.0001library +number pos pvalue bonferroni gene_name library_name +70 chr5:28496400-28508900 2.3446453844029e-154 7.73193708414544e-150 En2, ::F947-1P::M930-2P::F825-22P::F957-2P::M741P::F1008-2P::F750-2P::M892-P::M651-2P::M704P::F756-1P::M1022-P::F737-2P::M478-P::F750-1P::F803P::M725P::M570P::M988-P::F884P::F959-2P::M620-2P::M619-1P::F976-1P::F876-1P::M930-1P::F1023-P::M628-1P::F991P::F879-2P::M863P::F510P::M620-1P::F704-2P::F654-2P::F859P::F991-P::M578P::F876-2P::F959-1P::F1026P::MYSTERY-2P::F812-4P::F630P::F704-1P::F715-1P::F715-2P::F715-3P::F976-2P::F879-3P::F1008-1P::F771-1P::F825-21P::F947-3P::F983P::F947-2P::F760P::M504P::F806-1P::F812-2P::F879-1P::F585P::F806-3P::M513-3P::M680P::M651-3P::M625P::M513-2P::F812-1P::M950P:: +33 chr2:163461900-163474400 5.97128896252413e-63 1.96915196117158e-58 AL591488.2, 0610039K10Rik, Serinc3, ::F1026P::F959-1P::M513-5P::M578P::F750-2P::M741P::M620-1P::M1025P::F630P::F884P::F704-1P::F806-1P::F947-1P::M930-2P::F1008-2P::F879-1P::F510P::M892-P::F812-4P::M988-P::M570P::M725P::F1023-P::F812-2P::F595P::F991-P::F756-2P::F879-2P::M1022-P::F750-1P::M620-2P::F737-2P::M680P:: +31 chr2:98502400-98514900 2.12636873361625e-58 7.01212617284631e-54 AL837506.1, AL837506.2, ::F991-P::M863P::M988-P::F825-22P::F756-1P::F1023-P::F715-2P::M1025P::M628-1P::F704-2P::F1026P::F876-1P::M478-P::F976-2P::F976-1P::M620-1P::M651-3P::M504P::M619-2P::F947-1P::F1008-2P::F859P::F715-1P::M578P::F959-2P::F884P::M851P::M741P::F812-2P::M651-2P::M570P:: +29 chr19:32871500-32896500 3.0137704910582e-45 9.93851094836264e-41 Pten, ::M680P::F715-1P::F806-1P::F806-2P::F806-3P::F806-4P::M570P::F812-2P::F879-3P::F876-1P::F812-1P::M620-2P::M910P::M620-1P::F649P::M741P::F947-1P::F1026P::M625P::M930-1P::F715-2P::F715-3P::F704-1P::M619-1P::F585P::F825-22P::M513-4P::F983P::F1008-2P:: +37 chr11:79155400-79355400 8.92948023907374e-29 2.13744968482708e-24 Nf1, RP23-188A3.2, RP23-188A3.3, Omg, Evi2b, Evi2a, ::F879-1P::F991P::F704-2P::F859P::F630P::M988-P::F1026P::F1023-P::F750-1P::M619-1P::F673-1P::F510P::M1022-P::MYSTERY-1P::MYSTERY-2P::M578P::F812-2P::F983P::M628-1P::M930-1P::F825-22P::F825-21P::F595P::F585P::M593P::M741P::M504P::F1008-2P::F704-1P::M619-2P::M725P::F812-1P::M620-2P::M620-1P::F947-2P::F771-1P::F879-3P:: +15 chr10:57312100-57324600 2.235698868924e-24 7.37266416005069e-20 No results within 2500 bp window ::M851P::M478-P::F976-1P::F663P::F959-2P::F673-2P::F760P::M1025P::F654-2P::MYSTERY-1P::F976-2P::M910P::F750-1P::F947-1P::M513-1P:: +15 chr13:31719100-31731600 2.235698868924e-24 7.37266416005069e-20 Foxf2, RP23-322J11.2, ::F750-1P::F737-2P::F1008-2P::F879-2P::F859P::M892-P::M1025P::M930-2P::F959-1P::F510P::F704-1P::M930-1P::F715-2P::F876-2P::M570P:: +15 chr11:77393300-77418300 6.16702126963544e-20 2.03369860408768e-15 Taok1, ::F760P::M570P::F595P::M930-1P::M619-1P::M578P::F825-21P::F825-22P::F1008-2P::F812-2P::F704-1P::MYSTERY-2P::F812-3P::M628-3P::F649P:: +22 chr11:3001900-3101900 2.58189436121068e-19 6.18028053243001e-15 Pisd-ps1, Sfi1, RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Eif4enif1, Drg1, ::M513-4P::F1026P::M504P::F959-2P::M680P::F1023-P::F771-1P::F715-2P::M570P::M620-2P::F673-2P::F991-P::F715-3P::F947-1P::M625P::M930-2P::F991P::F812-2P::M628-1P::M892-P::F673-1P::M513-2P:: +19 chrX:39518000-39618000 9.12431639523089e-16 2.18408761552642e-11 Stag2, ::F630P::F947-2P::F756-1P::M620-1P::M651-2P::F983P::M578P::F673-2P::M892-P::F771-1P::F879-3P::F959-1P::F884P::M930-1P::M620-2P::F812-2P::F812-3P::F825-22P::M741P:: +10 chr3:48818900-48831400 5.32005735018332e-15 1.75439531236995e-10 No results within 2500 bp window ::F704-2P::M892-P::M504P::MYSTERY-2P::F1008-2P::M1025P::F663P::F959-3P::M619-2P::F649P:: +9 chrX:7503900-7516400 3.08936768685734e-13 1.01878078209494e-08 Eras, Pcsk1n, Hdac6, ::F803P::M863P::F704-1P::F704-2P::F812-1P::M725P::M562P::F595P::F771-1P:: +13 chr16:4105200-4155200 6.33805017913282e-13 2.09009880757263e-08 Crebbp, ::F983P::M892-P::F812-2P::F812-3P::M620-2P::M620-1P::M619-2P::M628-1P::F510P::F737-2P::M930-1P::F585P::F771-1P:: +8 chr16:42526200-42538700 1.61460166098443e-11 5.32447189742837e-07 No results within 2500 bp window ::F1026P::F715-2P::F771-1P::M620-1P::F825-21P::M504P::F947-1P::M741P:: +8 chr6:69880000-69892500 1.61460166098443e-11 5.32447189742837e-07 AC154006.7, ::F673-2P::M910P::F959-2P::M513-5P::M513-1P::F957-2P::F947-1P::F760P:: +8 chr9:3023500-3036000 1.61460166098443e-11 5.32447189742837e-07 AC131780.5, AC131780.2, AC131780.4, AC131780.6, AC131780.12, AC131780.10, AC131780.7, ::M1025P::F771-1P::M651-2P::F630P::M513-4P::F704-2P::M680P::F825-22P:: +9 chr19:32834100-32859100 1.33153248097534e-10 4.39099466251236e-06 Pten, ::F812-2P::F812-1P::F715-1P::F825-22P::M910P::M680P::F959-2P::F704-1P::F750-2P:: +9 chrX:139917600-139942600 1.33153248097534e-10 4.39099466251236e-06 No results within 2500 bp window ::F1023-P::M1025P::F1026P::F825-22P::F991-P::F715-2P::M651-3P::F812-3P::F879-1P:: +11 chr16:94871600-94921600 2.08385194853857e-10 6.87191857069563e-06 Dyrk1a, ::F947-2P::M725P::F750-1P::F812-2P::F812-1P::M628-1P::F585P::F595P::M620-2P::F510P::M504P:: +11 chrY:2856100-2906100 2.08385194853857e-10 6.87191857069563e-06 No results within 2500 bp window ::M570P::M680P::M1022-P::M930-2P::M620-2P::M620-1P::M1025P::M625P::M513-4P::F750-1P::M651-2P:: +18 chr1:133221000-133421000 8.31868715567611e-10 1.99124414445419e-05 Srgap2, AC109299.1, ::M680P::F585P::F715-3P::F879-1P::F649P::F673-2P::F825-21P::F884P::M504P::M892-P::F812-3P::F630P::M741P::M628-1P::F510P::M651-3P::M625P::F947-2P:: +7 chr1:96856200-96868700 7.50081868710625e-10 2.47354497844703e-05 No results within 2500 bp window ::M910P::F673-2P::F947-1P::F760P::M513-1P::F947-4P::F959-2P:: +7 chr1:81528400-81540900 7.50081868710625e-10 2.47354497844703e-05 No results within 2500 bp window ::F947-1P::F959-2P::F947-3P::M910P::M513-5P::F760P::M513-1P:: +7 chr13:108598000-108610500 7.50081868710625e-10 2.47354497844703e-05 Zswim6, ::M704P::F812-2P::F750-1P::M725P::F812-1P::F750-2P::F704-1P:: +8 chrX:149538600-149563600 3.47950579755122e-09 0.000114743662685847 RP23-180D16.1, Foxr2, ::F585P::F737-1P::F771-1P::F654-1P::F812-1P::F812-2P::F812-3P::F630P:: + +PNST_0library +number pos pvalue bonferroni gene_name library_name +86 chr5:28496400-28508900 4.25302001577773e-153 4.55009346387981e-148 En2, ::F983P::M593P::F510P::F957-2P::F859P::M863P::F812-4P::F879-1P::F947-3P::M620-1P::M619-1P::M628-3P::M504P::M620-2P::F876-2P::F654-1P::F750-2P::F771-1P::M1025P::M1022-P::M562P::M892-P::F654-2P::F947-4P::F663P::F976-2P::F976-1P::F737-2P::M651-3P::F1008-1P::M628-1P::F715-2P::F750-1P::F884P::M741P::F947-1P::M930-1P::M570P::M565P::M725P::M513-2P::F959-1P::M988-P::M930-2P::F825-22P::M478-P::F1008-2P::F812-1P::F991-P::F1026P::F959-2P::F879-2P::F756-1P::F803P::F1023-P::F947-2P::F771-2P::F704-2P::M704P::F704-1P::F991P::F876-1P::F715-3P::F715-1P::M651-2P::F806-4P::F812-3P::M578P::F812-2P::F1027P::M680P::F649P::F806-3P::F585P::F825-21P::MYSTERY-2P::M851P::F806-1P::F654-3P::F760P::F879-3P::F630P::M950P::F806-2P::M625P::M513-3P:: +64 chr10:57312100-57324600 2.96548502872028e-106 3.17262415797639e-101 No results within 2500 bp window ::M851P::F825-22P::M863P::F704-2P::F673-2P::F976-2P::F976-1P::M578P::M513-1P::F959-2P::F991-P::F750-2P::M625P::F673-1P::F654-1P::M988-P::M513-4P::F715-3P::F630P::F947-2P::F947-1P::F595P::M620-2P::F510P::F756-1P::F760P::F715-1P::M478-P::F876-1P::F585P::M513-2P::F663P::M619-2P::F750-1P::F806-3P::F654-2P::F959-1P::F756-2P::M680P::F991P::F825-21P::F812-2P::M704P::F806-2P::F884P::M1025P::F771-1P::F812-1P::M620-1P::MYSTERY-1P::F1008-2P::M910P::F806-4P::F859P::F806-1P::M741P::M504P::F704-1P::F715-2P::F737-2P::M725P::M628-3P::M651-2P::M930-2P:: +57 chr6:69880000-69892500 5.46587646824584e-92 5.84766793955281e-87 AC154006.7, ::F1008-2P::MYSTERY-1P::F715-2P::M478-P::F806-3P::M988-P::F737-1P::M504P::M1025P::F756-2P::M513-2P::F806-1P::M851P::F756-1P::F673-1P::F959-3P::M910P::F663P::F879-1P::F654-2P::F760P::M578P::F991P::M628-3P::F585P::F654-1P::F959-2P::F704-2P::F704-1P::M680P::F947-3P::F806-2P::F947-1P::M930-2P::F649P::M741P::F959-1P::F947-2P::F976-1P::M625P::M628-1P::M513-5P::M620-1P::F630P::F771-1P::F715-3P::F812-2P::F884P::F859P::F825-22P::F812-1P::M513-1P::F750-2P::F957-2P::F673-2P::M513-4P::F825-21P:: +55 chr2:98500900-98513400 5.58992232024846e-88 5.98037839431781e-83 AL837506.2, AL837506.1, ::F876-2P::F771-1P::F991-P::F1023-P::M570P::F704-2P::M988-P::F585P::F859P::M863P::F630P::M1025P::F812-4P::M513-4P::F812-2P::M851P::M619-2P::F756-2P::F1026P::F715-3P::F756-1P::F750-1P::F825-22P::F704-1P::M628-1P::M593P::F715-2P::M704P::M620-1P::F812-1P::M725P::F876-1P::F737-2P::F976-1P::M651-3P::M892-P::F812-3P::M478-P::F976-2P::M1022-P::F947-2P::M504P::F947-1P::M578P::F715-1P::F959-1P::F1008-2P::M651-2P::F884P::F806-1P::M741P::F959-2P::M619-1P::F825-21P::F879-2P:: +53 chr2:163461900-163474400 5.31918750862811e-84 5.69073275610578e-79 AL591488.2, 0610039K10Rik, Serinc3, ::F1026P::F1023-P::M950P::M513-2P::F884P::M620-1P::F806-1P::F812-3P::M930-2P::F756-1P::F983P::F947-1P::F959-1P::F750-2P::M741P::F704-1P::F991P::M651-2P::F812-2P::F510P::M988-P::F750-1P::M892-P::F825-22P::M513-5P::F825-21P::F1008-2P::M570P::M513-4P::M1025P::F879-1P::M578P::F715-1P::F630P::M628-3P::F737-2P::F715-3P::M680P::F585P::F991-P::F756-2P::F879-2P::M620-2P::F595P::F760P::M725P::M1022-P::F976-2P::F649P::F812-1P::F803P::M704P::F812-4P:: +50 chr1:81528400-81540900 4.28764979814801e-78 4.58714213654865e-73 No results within 2500 bp window ::F715-1P::F959-2P::M513-1P::F983P::F884P::MYSTERY-1P::F737-2P::M1025P::F673-2P::F760P::M625P::F947-1P::F976-1P::M620-2P::M593P::F654-2P::M478-P::F704-1P::M513-2P::F876-1P::M851P::F1008-2P::M499P::F879-1P::F750-2P::F806-4P::F715-3P::M513-5P::F654-1P::M910P::F756-1P::F959-1P::M628-3P::F859P::M565P::F825-21P::F510P::F673-1P::F630P::F771-1P::F812-1P::F947-3P::F991P::M513-3P::F825-22P::F806-3P::M741P::F750-1P::F806-1P::F715-2P:: +57 chr19:32863000-32888000 4.50547612273955e-75 1.07847581950017e-70 Pten, ::M988-P::F879-1P::F715-3P::F812-3P::F812-2P::F876-2P::F750-1P::F812-1P::M704P::F704-1P::M680P::F715-1P::M499P::F876-1P::F806-1P::M578P::F649P::F630P::F654-3P::F806-4P::F825-21P::F663P::F806-2P::M741P::F806-3P::F879-3P::F673-2P::F1008-1P::F771-2P::F756-1P::F983P::F991P::M570P::M725P::M1022-P::F1026P::M910P::F510P::M620-2P::M620-1P::M651-2P::M619-2P::F947-1P::M930-2P::M625P::M930-1P::F825-22P::F715-2P::M851P::F673-1P::M504P::M593P::M628-3P::M619-1P::F756-2P::F585P::F957-1P:: +46 chr3:48818900-48831400 2.43271168891992e-70 2.60263660039098e-65 No results within 2500 bp window ::M513-4P::M504P::F663P::M625P::MYSTERY-2P::F704-2P::M741P::M1022-P::F771-1P::F991P::F976-2P::F1026P::M892-P::M619-2P::F806-1P::M619-1P::M680P::M1025P::F812-3P::F750-1P::F959-2P::M628-1P::F812-2P::M620-2P::F1023-P::F649P::M651-3P::F750-2P::F947-1P::M988-P::F959-3P::F1008-2P::F510P::F585P::F715-2P::F825-21P::F983P::F991-P::F806-3P::M851P::F715-1P::F704-1P::F825-22P::F876-1P::M570P::F673-1P:: +45 chr1:96848800-96861300 2.00304180081579e-68 2.14295427060277e-63 No results within 2500 bp window ::F812-3P::F879-1P::F859P::M910P::F630P::F947-1P::F756-1P::F654-2P::M478-P::M1025P::F750-1P::M651-3P::M680P::F756-2P::F806-1P::F884P::F812-1P::F673-2P::F806-2P::M513-1P::M863P::F959-1P::M620-1P::F947-4P::F876-1P::F715-2P::M513-2P::F654-1P::F715-3P::MYSTERY-1P::F750-2P::F760P::F1008-2P::F585P::M625P::F879-3P::F959-2P::F673-1P::M513-4P::M741P::F825-22P::F976-1P::F663P::F649P::F825-21P:: +40 chr9:17524300-17536800 5.39590755267571e-59 5.77281169523011e-54 No results within 2500 bp window ::F959-3P::F715-2P::F884P::F991P::F806-2P::M513-4P::M513-5P::F1008-2P::F750-2P::F715-3P::MYSTERY-1P::F959-2P::F959-1P::M504P::F630P::F806-4P::M620-2P::M625P::M910P::F947-3P::F859P::F760P::F649P::F876-1P::F654-1P::F663P::M741P::F825-21P::F806-3P::M1025P::F756-1P::M513-1P::F947-1P::M578P::M930-2P::F957-2P::F585P::F812-1P::F654-2P::F737-1P:: +39 chr3:31845000-31857500 3.86336757653911e-57 4.13322380176037e-52 Kcnmb2, ::F812-2P::M513-4P::M851P::MYSTERY-2P::M570P::M504P::F649P::F663P::F825-22P::M619-2P::F585P::M680P::F959-3P::F1023-P::F750-1P::M625P::F771-1P::F1026P::F825-21P::M628-1P::F715-1P::M620-2P::F704-2P::F884P::F806-3P::M725P::F991-P::F704-1P::F750-2P::F715-2P::F991P::F806-1P::F673-1P::M1025P::F983P::M741P::M892-P::F1008-2P::F976-2P:: +36 chr9:3024700-3037200 1.21490012091653e-51 1.29976089436255e-46 AC131780.5, AC131780.4, AC131780.6, AC131780.12, AC131780.10, AC131780.2, ::F771-1P::M988-P::F991-P::F1026P::M863P::F756-1P::M651-2P::F585P::F704-2P::F983P::F959-1P::F673-1P::M851P::F859P::F630P::M593P::F737-2P::M620-1P::M625P::M513-4P::F1008-2P::F715-1P::M680P::M619-1P::M1025P::F1023-P::F884P::F812-2P::F825-22P::F825-21P::M619-2P::M628-1P::F750-2P::F715-2P::M651-3P::F715-3P:: +34 chr4:96179500-96192000 4.9044938958802e-48 5.24707279450743e-43 Cyp2j6, ::F715-1P::F959-2P::F806-3P::MYSTERY-1P::F715-3P::F825-22P::F756-2P::F760P::F812-2P::F976-1P::M625P::F825-21P::F704-1P::M513-1P::F756-1P::F806-4P::M570P::M863P::F715-2P::F976-2P::M478-P::M620-1P::F806-1P::M680P::F704-2P::F673-2P::F654-2P::M504P::F859P::M513-4P::F991P::F630P::F947-1P::F1008-2P:: +34 chr1:109142400-109154900 4.9044938958802e-48 5.24707279450743e-43 AC157660.1, ::M1022-P::F654-2P::F760P::M988-P::F715-2P::F976-1P::F750-2P::F673-2P::F991P::F812-2P::F959-2P::M513-3P::F957-2P::MYSTERY-1P::M628-3P::F715-3P::F947-1P::F812-1P::F806-3P::F859P::F756-2P::F947-3P::M851P::M625P::F630P::F704-1P::M513-1P::M741P::M680P::M1025P::M620-1P::F756-1P::F654-1P::F673-1P:: +33 chr9:53003600-53016100 2.98479600233134e-46 3.19328400309418e-41 Ddx10, ::M513-5P::F959-2P::F976-1P::F649P::F859P::M565P::F806-3P::M625P::F825-21P::M1025P::F959-1P::F630P::F771-1P::MYSTERY-1P::M620-1P::M619-1P::M513-2P::F825-22P::F947-3P::F806-4P::F806-1P::F947-1P::F654-2P::F884P::F756-1P::M863P::F663P::M478-P::F654-1P::F879-1P::M513-1P::M851P::F812-2P:: +31 chr6:54872200-54884700 1.00986111644481e-42 1.08039991542848e-37 Nod1, ::M513-3P::F959-2P::F879-1P::F654-3P::F673-2P::F859P::M628-1P::F756-2P::F947-2P::M513-2P::M513-1P::F957-2P::F654-2P::F663P::M619-1P::F879-2P::F771-2P::F947-4P::M651-2P::F991P::F876-2P::M562P::M863P::F806-2P::F756-1P::F715-3P::F750-1P::F983P::M1025P::M741P::F737-1P:: +30 chr4:86833900-86846400 5.60357105527688e-41 5.99498049348797e-36 Slc24a2, ::M910P::F649P::F1008-2P::F947-3P::F957-2P::F654-1P::F959-3P::F859P::F715-3P::F750-2P::M504P::F947-1P::M741P::M628-1P::M1025P::M620-1P::F663P::F737-1P::F756-1P::F760P::F825-22P::F806-4P::F673-2P::F806-2P::F812-1P::F959-2P::M513-5P::M625P::M513-1P::F704-1P:: +30 chr13:31719100-31731600 5.60357105527688e-41 5.99498049348797e-36 Foxf2, RP23-322J11.2, ::M725P::F859P::F879-2P::F715-2P::F991-P::F959-2P::M1022-P::F812-1P::M930-1P::F750-1P::F510P::F1008-2P::M741P::F704-1P::M704P::F812-2P::M1025P::F812-3P::F737-2P::F991P::F1023-P::F959-1P::F976-1P::M892-P::M930-2P::M570P::F876-2P::F803P::F750-2P::F812-4P:: +30 chr11:77388000-77400500 5.60357105527688e-41 5.99498049348797e-36 Taok1, ::M578P::F704-1P::M619-1P::F750-1P::F673-2P::F737-1P::M513-2P::F595P::F825-21P::F806-3P::F879-3P::MYSTERY-1P::F991-P::M570P::F812-1P::M704P::M725P::F812-2P::F812-4P::F649P::M892-P::M565P::F760P::F1023-P::M741P::F756-2P::M930-2P::M930-1P::F959-1P::F673-1P:: +30 chr1:147289800-147302300 5.60357105527688e-41 5.99498049348797e-36 No results within 2500 bp window ::F756-1P::F806-1P::F715-2P::M892-P::F649P::M499P::F991-P::M570P::F673-2P::F704-1P::M628-1P::F1023-P::F1026P::F959-2P::F715-1P::F959-1P::M851P::F947-2P::M1025P::F859P::F812-3P::F884P::M1022-P::M651-2P::M619-2P::F750-1P::F1008-2P::M619-1P::M625P::F1008-1P:: +28 chr5:22846400-22858900 1.56195031084823e-37 1.67105254006098e-32 No results within 2500 bp window ::M578P::F876-1P::F715-2P::M478-P::F825-21P::F959-2P::F585P::M620-2P::M741P::M504P::F976-1P::F737-2P::F947-2P::F673-1P::F756-2P::M910P::F806-1P::M513-1P::F947-1P::M620-1P::M625P::F825-22P::F750-2P::F959-1P::F991-P::F704-2P::F806-2P::F704-1P:: +28 chr16:67974600-67987100 1.56195031084823e-37 1.67105254006098e-32 No results within 2500 bp window ::M625P::F649P::M680P::F756-1P::F879-2P::F760P::M620-2P::F959-2P::M930-2P::F673-2P::F654-2P::F806-2P::F947-1P::M910P::MYSTERY-1P::M513-5P::F654-3P::F806-1P::F715-2P::F704-2P::F715-3P::F876-1P::F884P::M513-1P::F704-1P::M651-2P::F654-1P::F959-1P:: +28 chr9:3727700-3740200 1.56195031084823e-37 1.67105254006098e-32 Gucy1a2, ::F825-21P::F806-3P::M651-3P::F704-2P::M570P::F812-2P::M620-2P::F704-1P::F585P::F991P::M1022-P::F812-3P::M651-2P::F859P::M620-1P::F715-3P::M741P::F1008-2P::M619-2P::F1023-P::F959-3P::F876-1P::M625P::M504P::F1026P::F825-22P::F976-1P::M619-1P:: +51 chr11:79210000-79310000 1.07397660189692e-35 2.57077779196065e-31 Nf1, RP23-188A3.3, ::F510P::F1023-P::M1022-P::F704-2P::MYSTERY-2P::MYSTERY-1P::M499P::M620-1P::F595P::M578P::F812-2P::F983P::F859P::M628-1P::F825-21P::M930-1P::M725P::M851P::F654-2P::F825-22P::M680P::F737-2P::F750-1P::F630P::M504P::F750-2P::M562P::M619-1P::M619-2P::F585P::F957-2P::F673-1P::M930-2P::M628-3P::M593P::F771-1P::M741P::F879-1P::F947-1P::M651-2P::F991P::F1008-2P::F876-2P::F704-1P::F812-1P::F803P::F715-2P::M620-2P::F957-1P::F715-1P::F947-2P:: +26 chr2:120396000-120408500 3.78331138502683e-34 4.04757568527096e-29 Snap23, ::F654-2P::F991P::F1008-2P::F771-1P::F750-2P::F673-1P::F756-1P::M680P::F947-1P::M625P::M513-1P::F825-21P::MYSTERY-1P::F715-3P::F884P::F876-1P::F976-2P::F756-2P::F663P::F859P::M513-3P::F976-1P::F673-2P::F959-2P::F806-1P::F1023-P:: + +NF_0.01library +number pos pvalue bonferroni gene_name library_name +128 chr5:28496400-28696400 0 0 Cnpy1, AC129184.1, En2, Prr8, ::M626-10NF::M892-5NF::F802-2NF::F624-2NF::F976-5NF::M732-2NF::F735-1NF::M724-1NF::M878-1NF::F849-6NF::F877-1NF::F957-3NF::F957-1NF::F991-3NF::M892-1NF::F969-7NF::M920-5NF::F704-NF::M1008-2NF::F884-3NF::F885-1NF::F976-2NF::M1022-13NF::F1026-4NF::M988-4NF::F735-5NF::M878-4NF::F673-3NF::F849-7NF::F648-1NF::F849-3NF::F760-3NF::F601-NF::F959-5NF::F991-1NF::M1013-1NF::M952-4NF::F624-1NF::F849-2NF::F849-4NF::F879-4NF::F957-2NF::F969-1NF::F976-3NF::F1026-1NF::M920-3NF::F624-3NF::F695-2NF::M624-6NF::F1026-3NF::F1027-8NF::F652-NF::F729-3NF::F729-5NF::M626-7NF::F1026-5NF::M892-7NF::F1027-6NF::F850-5NF::M624-4NF::M724-2NF::M920-4NF::F695-4NF::F760-2NF::F796-NF::F841-6NF::F947-4NF::F957-11NF::F968-3NF::M1008-1NF::M626-5NF::M920-2NF::F729-1NF::F877-6NF::F884-2NF::F1027-5NF::F802-6NF::F877-3NF::F879-1NF::F947-2NF::F976-6NF::M1013-2NF::M988-3NF::F850-4NF::F879-6NF::F969-2NF::F976-4NF::M732-4NF::F1027-3NF::F624-4NF::F695-3NF::F760-6NF::F802-5NF::F850-7NF::F877-2NF::F959-4NF::F969-9NF::M624-7NF::M724-6NF::F1027-9NF::F850-2NF::M851-3NF::F1027-2NF::F802-3NF::F947-5NF::M624-5NF::M724-4NF::M892-2NF::F1027-7NF::F849-8NF::F879-2NF::F957-12NF::F968-4NF::M892-6NF::F729-4NF::F841-2NF::F959-3NF::M1008-3NF::M624-1NF::M892-9NF::F648-4NF::F947-3NF::F884-1NF::M732-5NF::F1027-4NF::F624-5NF::F760-1NF::F841-5NF:: +18 chr2:163468500-163481000 4.21198998728923e-61 2.69567359186511e-58 AL591488.2, 0610039K10Rik, Serinc3, ::F850-4NF::F802-4NF::F850-7NF::F959-4NF::F760-3NF::F802-2NF::F849-4NF::M892-1NF::F601-NF::F849-3NF::F849-5NF::F695-4NF::F994-7NF::M892-4NF::F1026-3NF::F729-1NF::F802-6NF::F849-7NF:: +5 chr3:158263500-158276000 3.46294052197872e-15 2.21628193406638e-12 No results within 2500 bp window ::F648-1NF::M851-1NF::F947-5NF::F841-2NF::F841-6NF:: +5 chr2:98502800-98515300 3.46294052197872e-15 2.21628193406638e-12 AL837506.1, AL837506.2, ::M732-3NF::F976-7NF::F624-6NF::F729-4NF::F729-5NF:: +5 chr10:57318100-57330600 3.46294052197872e-15 2.21628193406638e-12 No results within 2500 bp window ::F994-3NF::M552-NF::F994-4NF::F994-1NF::F994-8NF:: +3 chr13:16745300-16757800 6.20074597477398e-09 3.96847742385535e-06 No results within 2500 bp window ::F969-1NF::F969-4NF::F969-3NF:: +2 chr7:124704800-124717300 5.56608264893866e-06 0.00356229289532074 Xylt1, ::M910-2NF::F1027-6NF:: +2 chr9:21769300-21781800 5.56608264893866e-06 0.00356229289532074 Epor, Rgl3, ::F735-1NF::F735-5NF:: +2 chr7:126509000-126521500 5.56608264893866e-06 0.00356229289532074 No results within 2500 bp window ::M910-2NF::F849-3NF:: +2 chr7:35892300-35904800 5.56608264893866e-06 0.00356229289532074 Cebpa, ::F735-5NF::F735-1NF:: +2 chr2:101636000-101648500 5.56608264893866e-06 0.00356229289532074 Prr5l, ::M732-1NF::F796-NF:: +2 chr2:26322200-26334700 5.56608264893866e-06 0.00356229289532074 Notch1, ::F729-2NF::F729-3NF:: +2 chr14:121562700-121575200 5.56608264893866e-06 0.00356229289532074 Farp1, ::F969-3NF::F969-1NF:: +2 chrX:12148100-12173100 2.2190045895503e-05 0.0142016293731219 Atp6ap2, ::F850-4NF::F994-7NF:: +2 chr12:39202400-39227400 2.2190045895503e-05 0.0142016293731219 Dgkb, ::F673-3NF::F976-2NF:: +2 chr10:27294900-27319900 2.2190045895503e-05 0.0142016293731219 Lama2, ::F877-6NF::F849-6NF:: + +NF_0.001library +number pos pvalue bonferroni gene_name library_name +242 chr5:28412500-28612500 0 0 En2, Cnpy1, AC129184.1, ::M626-5NF::M952-2NF::M988-5NF::F1026-5NF::F850-5NF::F704-NF::F968-4NF::F885-1NF::M892-9NF::F1027-2NF::F959-6NF::F947-3NF::F850-2NF::F884-1NF::F735-4NF::F976-3NF::F877-5NF::F760-4NF::F969-7NF::F760-5NF::M624-6NF::M892-2NF::M724-1NF::M624-8NF::M920-2NF::M878-5NF::F1026-7NF::F957-9NF::F601-NF::F991-5NF::F850-6NF::F1027-10NF::F802-4NF::F969-9NF::M724-2NF::F652-NF::M626-6NF::F947-2NF::F1027-8NF::F877-3NF::F1026-6NF::F1026-8NF::F969-2NF::F648-2NF::M624-4NF::F968-1NF::M732-2NF::F959-10NF::F969-5NF::F1027-5NF::M628-2NF::F957-11NF::F877-1NF::F885-3NF::F729-4NF::M724-4NF::M920-3NF::M626-1NF::F695-4NF::F969-4NF::F648-3NF::F849-5NF::F976-5NF::M920-5NF::F1027-7NF::M892-3NF::M878-2NF::F879-5NF::F760-2NF::M952-3NF::F648-1NF::M724-6NF::F849-4NF::M626-9NF::M1013-2NF::F884-2NF::F968-2NF::F877-6NF::F959-1NF::F729-2NF::F802-5NF::M988-4NF::F850-1NF::F976-16NF::M626-10NF::F959-7NF::M892-5NF::F841-1NF::F841-2NF::M892-11NF::F735-5NF::F1026-10NF::F802-3NF::F969-6NF::F976-6NF::F1026-2NF::F624-4NF::F959-5NF::M988-6NF::F879-6NF::F976-1NF::F976-2NF::M892-6NF::F991-4NF::F737-NF::F841-5NF::M878-1NF::M732-5NF::F879-4NF::F849-2NF::F796-NF::M1013-1NF::M920-4NF::F729-1NF::F879-1NF::F649-3NF::F976-8NF::F849-3NF::F735-2NF::F991-3NF::M626-2NF::M952-4NF::M624-5NF::M732-4NF::M1013-5NF::F760-1NF::F991-1NF::M920-1NF::F760-3NF::M988-9NF::M851-2NF::F624-2NF::M1013-3NF::F850-7NF::F849-7NF::F959-4NF::F976-11NF::F735-1NF::F802-1NF::F695-3NF::M892-10NF::F735-3NF::F648-4NF::F624-3NF::F648-5NF::M952-1NF::F1027-1NF::F968-5NF::F983-1NF::F1026-4NF::M1008-4NF::M626-7NF::F991-2NF::F959-9NF::M626-3NF::M851-3NF::F959-2NF::M892-8NF::M988-3NF::F885-2NF::M1022-13NF::F968-6NF::F969-10NF::M624-1NF::F947-4NF::F959-8NF::M878-6NF::F850-4NF::F1023-NF::M892-1NF::M988-1NF::F757-1NF::M1008-2NF::F624-5NF::M878-3NF::M732-6NF::M988-8NF::F957-3NF::F802-2NF::F624-1NF::F884-3NF::M626-4NF::F849-6NF::M988-2NF::F729-3NF::F957-1NF::F957-2NF::M892-4NF::M988-7NF::F1027-3NF::F802-6NF::F695-2NF::F850-3NF::F969-1NF::F957-10NF::F976-4NF::F968-3NF::F1026-1NF::F959-3NF::M624-7NF::F879-2NF::M1008-1NF::F877-4NF::F735-7NF::F947-1NF::M878-4NF::F1026-3NF::F757-3NF::M1013-4NF::F976-7NF::F957-12NF::M724-5NF::M892-7NF::M626-11NF::F771-2NF::M851-1NF::M732-3NF::F673-3NF::F947-5NF::F1027-4NF::F771-5NF::M1008-3NF::F877-2NF::F729-5NF::M1008-5NF::F735-6NF::F760-6NF::F695-1NF::F1027-9NF::M624-2NF::F849-8NF::M626-8NF::F841-4NF::M724-3NF::F624-6NF::M624-3NF::F1027-6NF::F1026-9NF::F969-8NF::F969-3NF::F850-8NF::F841-6NF:: +132 chr2:163468400-163480900 0 0 AL591488.2, 0610039K10Rik, Serinc3, ::M892-4NF::F849-6NF::M878-4NF::M732-1NF::F947-2NF::F877-3NF::M626-7NF::F969-2NF::F760-4NF::F735-5NF::F1027-5NF::F884-3NF::M626-5NF::F729-4NF::F1026-4NF::F959-5NF::F849-2NF::M732-6NF::M878-5NF::M626-11NF::M1013-3NF::F757-1NF::F757-3NF::M952-1NF::M892-3NF::M892-9NF::F802-5NF::M988-8NF::M624-1NF::F735-1NF::F735-2NF::M626-9NF::M892-7NF::F877-6NF::F969-7NF::M892-2NF::F802-4NF::M724-1NF::F1027-1NF::F1026-3NF::M626-10NF::M952-3NF::F850-3NF::M988-9NF::F849-4NF::F735-4NF::F624-1NF::F841-4NF::F885-1NF::F652-NF::F879-4NF::F991-1NF::M724-5NF::M952-4NF::M626-2NF::F850-7NF::F879-1NF::F849-7NF::M878-2NF::F850-1NF::M920-1NF::M878-3NF::F849-3NF::F760-3NF::F695-4NF::F968-4NF::F957-12NF::F760-2NF::F802-6NF::F884-1NF::F802-2NF::F850-4NF::F991-4NF::M878-1NF::F969-9NF::F841-2NF::F959-1NF::F729-1NF::M1013-5NF::F957-3NF::F802-3NF::F968-3NF::M626-4NF::M724-4NF::F1027-4NF::M626-1NF::F968-2NF::M624-5NF::F1027-10NF::M1013-4NF::F976-7NF::F957-2NF::F841-1NF::F994-7NF::F695-1NF::M892-5NF::F1026-10NF::M920-4NF::M920-5NF::F885-2NF::M1022-13NF::F796-NF::F648-1NF::M851-1NF::M1013-2NF::F968-1NF::F850-5NF::M732-4NF::F959-3NF::M732-5NF::F771-5NF::F695-2NF::M732-2NF::M892-1NF::M952-2NF::F877-4NF::M920-3NF::M624-4NF::M892-11NF::F648-4NF::F624-4NF::F760-1NF::M1008-2NF::F968-6NF::M1013-1NF::M892-10NF::F601-NF::F849-5NF::M624-6NF::F879-2NF::F959-4NF::F976-9NF:: +130 chr2:98502500-98515000 0 0 AL837506.1, AL837506.2, ::F760-4NF::M920-3NF::F959-1NF::F976-11NF::M626-3NF::F850-6NF::M626-4NF::M626-6NF::M988-6NF::M1008-4NF::F1027-9NF::F841-2NF::F968-2NF::F729-2NF::F1026-4NF::M988-7NF::M732-6NF::F735-3NF::M988-5NF::M626-7NF::M626-1NF::F1026-2NF::F957-1NF::M988-4NF::M626-8NF::F968-1NF::M732-4NF::F760-6NF::F885-3NF::M724-4NF::F976-16NF::F991-3NF::M626-2NF::F1026-9NF::F959-2NF::F969-7NF::M988-3NF::F976-8NF::M878-2NF::M724-2NF::F850-1NF::F879-6NF::M952-3NF::F1026-6NF::F969-5NF::F957-12NF::F983-1NF::M920-1NF::F947-3NF::F991-2NF::F947-4NF::F624-3NF::F968-4NF::M988-2NF::F1026-5NF::F648-2NF::M624-5NF::F957-11NF::M988-1NF::F1027-1NF::F729-4NF::F959-9NF::F735-4NF::M624-6NF::M988-8NF::M624-1NF::F1027-4NF::F1026-10NF::M724-1NF::F885-2NF::F879-5NF::F884-1NF::F991-5NF::F729-3NF::F968-5NF::M732-5NF::F991-1NF::M624-3NF::M878-6NF::F1023-NF::M732-2NF::M920-5NF::F648-5NF::F1027-7NF::M724-3NF::F877-2NF::F957-9NF::F1027-6NF::M732-3NF::M952-4NF::F802-6NF::M952-1NF::M626-9NF::M892-9NF::F624-5NF::M624-4NF::M624-8NF::M1008-1NF::F877-3NF::F841-4NF::F968-6NF::F884-2NF::F969-9NF::F729-5NF::F959-8NF::F976-7NF::F1027-2NF::F1027-5NF::F991-4NF::F1027-8NF::F624-6NF::F976-4NF::F760-5NF::M988-9NF::F879-1NF::F1027-10NF::F760-2NF::M724-5NF::M892-2NF::F969-1NF::M892-11NF::F760-1NF::F850-2NF::F877-4NF::M851-3NF::F850-5NF::M892-7NF::F885-1NF::M628-2NF::M952-2NF:: +54 chr3:158263500-158276000 3.20306084987095e-128 5.61048138463395e-124 No results within 2500 bp window ::M988-6NF::F968-3NF::M988-3NF::M988-7NF::M851-1NF::F841-6NF::F760-2NF::M952-3NF::M624-6NF::F1027-8NF::F624-3NF::F648-1NF::M1013-3NF::M892-8NF::F648-5NF::F1027-2NF::F1026-5NF::F969-2NF::F850-8NF::F976-8NF::F1023-NF::F760-4NF::M952-1NF::F957-1NF::F947-5NF::F850-1NF::F1027-5NF::F737-NF::M1013-5NF::M1008-5NF::M988-9NF::F841-1NF::F735-7NF::F959-2NF::F885-2NF::F735-4NF::F841-2NF::F969-4NF::F704-NF::M988-1NF::M878-2NF::F879-4NF::F991-4NF::F983-1NF::M624-1NF::F1026-8NF::F649-3NF::F885-3NF::F879-6NF::M732-6NF::F884-1NF::M626-7NF::F969-6NF::F885-1NF:: +29 chrX:139917600-139930100 7.77287578133663e-62 1.36149692185892e-57 No results within 2500 bp window ::F1027-9NF::F624-1NF::M724-1NF::M988-8NF::M878-5NF::M988-1NF::M920-5NF::M988-3NF::M724-4NF::M892-5NF::F957-9NF::M988-6NF::M624-1NF::F976-3NF::F704-NF::F802-6NF::M920-3NF::F841-4NF::F991-2NF::F1026-7NF::F959-4NF::F1027-7NF::F1027-8NF::F760-1NF::M988-5NF::M952-2NF::M732-6NF::F957-11NF::F959-5NF:: +26 chr13:31719100-31731600 2.22684506229703e-54 3.90054181111947e-50 Foxf2, RP23-322J11.2, ::F735-5NF::F849-3NF::M624-4NF::M624-6NF::F1026-4NF::M626-7NF::F947-4NF::M1008-2NF::F968-4NF::F959-4NF::F849-2NF::F885-1NF::M988-9NF::M892-1NF::M732-3NF::F850-7NF::F729-4NF::M626-5NF::F879-2NF::F760-1NF::F695-2NF::F850-5NF::F976-16NF::F976-8NF::M1013-1NF::F760-5NF:: +13 chr10:57318100-57330600 4.59739825399024e-24 8.0528027816893e-20 No results within 2500 bp window ::F994-6NF::F994-5NF::F994-3NF::F994-7NF::F994-4NF::F994-8NF::M910-1NF::M910-4NF::M732-1NF::F994-2NF::M552-NF::M910-2NF::F994-1NF:: +13 chr10:16578700-16591200 4.59739825399024e-24 8.0528027816893e-20 No results within 2500 bp window ::F841-1NF::M920-1NF::F802-6NF::F976-16NF::F959-6NF::F959-2NF::F957-12NF::F957-3NF::F1027-10NF::M1008-1NF::F969-9NF::F695-2NF::F969-2NF:: +10 chr4:96180000-96192500 1.03090320653541e-17 1.80573005656742e-13 Cyp2j6, ::F968-4NF::F760-5NF::F994-6NF::M552-NF::F994-5NF::M910-2NF::F994-4NF::F994-3NF::M910-1NF::F994-1NF:: +16 chr11:3034900-3134900 1.55365707341515e-16 2.72138572979398e-12 RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Sfi1, Eif4enif1, Drg1, ::F959-9NF::F1027-10NF::F1027-9NF::M1013-2NF::F850-1NF::F969-4NF::M624-5NF::M878-1NF::F624-5NF::F796-NF::M624-7NF::F959-1NF::M952-4NF::F969-1NF::F877-7NF::F976-11NF:: +9 chr9:123968200-123980700 1.12706090111303e-15 1.97415987438959e-11 No results within 2500 bp window ::F735-5NF::F735-7NF::F735-6NF::F735-3NF::F735-1NF::F735-4NF::F735-2NF::M624-4NF::M626-7NF:: +9 chr6:53243100-53255600 1.12706090111303e-15 1.97415987438959e-11 Creb5, ::F735-1NF::F735-3NF::F735-4NF::F735-2NF::F735-6NF::M624-4NF::F735-5NF::M626-7NF::F735-7NF:: +9 chr16:57523800-57536300 1.12706090111303e-15 1.97415987438959e-11 2610528E23Rik, Filip1l, ::M626-7NF::F735-3NF::F735-1NF::M624-4NF::F735-7NF::F735-4NF::F735-5NF::F735-6NF::F735-2NF:: +8 chr7:35892300-35904800 1.10896895080778e-13 1.94247001423491e-09 Cebpa, ::F735-7NF::F735-1NF::F735-5NF::F735-3NF::F735-4NF::M626-7NF::F735-2NF::F735-6NF:: +8 chr9:21769300-21781800 1.10896895080778e-13 1.94247001423491e-09 Epor, Rgl3, ::M626-7NF::F735-4NF::F735-1NF::F735-2NF::F735-5NF::F735-7NF::F735-3NF::F735-6NF:: +8 chr16:42526200-42538700 1.10896895080778e-13 1.94247001423491e-09 No results within 2500 bp window ::M626-3NF::F849-8NF::F624-5NF::F1027-4NF::F695-4NF::F648-2NF::M626-1NF::F802-4NF:: +10 chrX:39578300-39628300 8.21571523440975e-12 1.43906468045921e-07 Stag2, ::F885-1NF::F884-3NF::F735-3NF::M892-7NF::M878-6NF::M626-10NF::M892-11NF::F1026-3NF::F695-3NF::F968-1NF:: +10 chrY:2850500-2900500 8.21571523440975e-12 1.43906468045921e-07 No results within 2500 bp window ::M626-7NF::M920-4NF::M732-5NF::M892-11NF::M878-5NF::M878-3NF::M624-5NF::M1022-13NF::M920-1NF::F994-7NF:: +7 chr1:81528400-81540900 9.69926594140133e-12 1.69892342229586e-07 No results within 2500 bp window ::M910-2NF::F994-1NF::M552-NF::F994-3NF::F994-4NF::F994-8NF::F994-5NF:: +9 chr8:35964600-36014600 2.24550941268798e-10 3.93323428726426e-06 Tnks, ::F850-2NF::F1026-4NF::M892-4NF::F1027-5NF::F849-7NF::F849-1NF::M952-4NF::F802-5NF::F959-6NF:: +9 chr9:3004800-3054800 2.24550941268798e-10 3.93323428726426e-06 AC131780.1, AC131780.11, AC131780.3, AC131780.7, AC131780.2, AC131780.4, AC131780.6, AC131780.12, AC131780.10, AC131780.9, AC131780.8, AC131780.5, ::F757-1NF::M920-1NF::F760-5NF::F760-6NF::M892-8NF::F884-2NF::F648-3NF::M851-3NF::M952-3NF:: +11 chr17:3134300-3234300 3.88165179924775e-10 6.79910129156235e-06 Rbm16, ::M1013-4NF::F704-NF::M892-11NF::M920-2NF::F959-7NF::F1027-9NF::M626-3NF::M626-1NF::M892-4NF::M892-2NF::F624-2NF:: +11 chr11:104197800-104297800 3.88165179924775e-10 6.79910129156235e-06 1700081L11Rik, AL593843.1, ::M1022-13NF::F850-4NF::F760-6NF::F648-1NF::F695-1NF::F994-6NF::F976-4NF::M892-5NF::M624-5NF::M626-6NF::F969-9NF:: +6 chr9:52994600-53007100 7.42277678440093e-10 1.30017358155567e-05 Ddx10, ::F802-5NF::F994-1NF::M910-1NF::F994-4NF::F994-5NF::F994-3NF:: +6 chr3:111049700-111062200 7.42277678440093e-10 1.30017358155567e-05 No results within 2500 bp window ::F976-8NF::F1027-5NF::F884-2NF::F957-1NF::F648-3NF::F1027-10NF:: + +NF_0.0001library +number pos pvalue bonferroni gene_name library_name +252 chr5:28496200-28546200 0 0 AC129184.1, En2, Cnpy1, ::F735-3NF::F959-9NF::M878-5NF::F729-4NF::F1027-3NF::M626-10NF::F976-1NF::F991-2NF::F849-5NF::F649-3NF::F771-2NF::F957-11NF::F879-4NF::M626-1NF::F957-10NF::M988-9NF::F976-4NF::F969-9NF::F1026-9NF::F969-2NF::F648-3NF::M892-7NF::M892-6NF::M624-5NF::M878-2NF::M1008-2NF::F735-4NF::F1023-NF::F1027-7NF::M732-5NF::M626-6NF::F947-2NF::F983-2NF::F976-11NF::F969-1NF::M724-4NF::F648-1NF::F850-2NF::F850-7NF::F994-8NF::M626-11NF::F884-3NF::F735-1NF::F959-3NF::M920-2NF::M732-2NF::M952-1NF::M910-4NF::M1013-3NF::F885-3NF::F991-1NF::F841-2NF::F1027-4NF::F1026-4NF::F802-2NF::F760-1NF::F849-8NF::M626-8NF::M988-7NF::M1013-2NF::F968-6NF::F1027-6NF::M851-3NF::M988-3NF::F959-1NF::F968-5NF::F969-6NF::F959-4NF::M624-2NF::F879-6NF::F976-2NF::F729-3NF::F624-5NF::F850-3NF::M892-8NF::F969-4NF::F877-1NF::F849-6NF::F771-5NF::F879-1NF::M626-3NF::F991-5NF::F976-8NF::F885-2NF::M952-4NF::F885-1NF::F959-5NF::M732-6NF::F959-7NF::F1027-10NF::F1026-5NF::F849-7NF::F757-1NF::F624-2NF::M878-3NF::M892-11NF::F976-6NF::F968-3NF::F735-5NF::M1013-5NF::F969-5NF::M626-7NF::F849-4NF::F850-5NF::F695-2NF::F1027-1NF::F760-2NF::F969-8NF::F1027-9NF::F1027-2NF::M724-1NF::F757-3NF::M988-4NF::F1026-10NF::F760-4NF::F957-2NF::M1008-5NF::F1026-1NF::M892-10NF::M920-3NF::F968-2NF::M624-8NF::F850-8NF::F1027-5NF::F648-4NF::M878-1NF::M892-9NF::F735-6NF::M1013-4NF::F1026-6NF::F796-NF::M626-9NF::M988-6NF::M624-1NF::F976-3NF::F1026-8NF::F959-8NF::M724-6NF::M878-6NF::F841-5NF::F850-1NF::F704-NF::M1022-13NF::M624-6NF::F957-12NF::F729-1NF::F695-4NF::M892-2NF::F1027-8NF::F947-3NF::M628-2NF::F760-3NF::M892-1NF::F729-2NF::F802-6NF::F991-4NF::F959-10NF::M624-3NF::F841-1NF::M892-5NF::M892-3NF::F969-3NF::F969-10NF::F877-6NF::F850-6NF::M1013-1NF::F624-4NF::F841-4NF::F648-5NF::M851-1NF::F877-3NF::F968-1NF::M920-1NF::F601-NF::M1025-1NF::M952-2NF::F652-NF::F994-1NF::F947-4NF::F969-7NF::F983-1NF::F877-5NF::F849-2NF::F976-5NF::F968-4NF::F947-5NF::F957-9NF::M988-1NF::F877-4NF::M624-4NF::F1026-7NF::F976-16NF::F624-1NF::M920-5NF::F802-1NF::M724-3NF::F959-6NF::M626-5NF::F879-5NF::F850-4NF::M626-2NF::M952-3NF::F802-4NF::F624-3NF::M1008-4NF::F802-3NF::M732-3NF::F695-1NF::F735-2NF::F957-1NF::M851-2NF::M988-8NF::M1008-1NF::F879-2NF::F802-5NF::F695-3NF::F648-2NF::F849-3NF::F957-3NF::M988-2NF::F737-NF::F884-1NF::M892-4NF::F760-5NF::F991-3NF::F1026-2NF::F976-7NF::M732-4NF::F884-2NF::M724-2NF::M624-7NF::F959-2NF::F735-7NF::M988-5NF::M920-4NF::M626-4NF::F841-6NF::F994-6NF::F976-9NF::F760-6NF::M878-4NF::F947-1NF::F673-3NF::F877-2NF::M1008-6NF::M1008-3NF::F1026-3NF::M724-5NF::F814-4NF::F994-4NF::F729-5NF::F624-6NF:: +211 chr2:163390800-163490800 0 0 Ttpal, Serinc3, 0610039K10Rik, Pkig, Hnf4a, AL591488.2, ::F652-NF::M892-3NF::F994-3NF::F968-4NF::M878-2NF::F1026-10NF::F969-6NF::M626-8NF::F850-2NF::M626-3NF::F648-3NF::M624-6NF::M626-4NF::F991-1NF::F1027-4NF::F877-6NF::F968-3NF::M1008-2NF::F884-1NF::M732-1NF::F802-3NF::F695-2NF::M892-1NF::F760-5NF::F849-2NF::M624-8NF::F802-6NF::M892-9NF::F976-7NF::M920-4NF::M920-3NF::F695-4NF::M724-1NF::F1026-3NF::F969-2NF::F947-2NF::F969-4NF::M892-11NF::F624-2NF::M626-9NF::F735-5NF::M732-4NF::F760-3NF::F969-7NF::F959-4NF::F849-7NF::F850-7NF::F735-1NF::F884-3NF::M724-6NF::M626-7NF::M892-4NF::F957-9NF::F802-4NF::M878-5NF::F729-2NF::M878-1NF::F757-3NF::F849-3NF::F1026-5NF::F849-4NF::M626-5NF::F729-4NF::F760-1NF::M626-2NF::M624-4NF::M626-1NF::F994-6NF::F849-6NF::F648-4NF::F802-2NF::F648-1NF::F802-5NF::M878-4NF::M732-6NF::M892-5NF::F796-NF::M892-2NF::F1026-4NF::M624-5NF::F729-1NF::M732-5NF::F879-2NF::M892-6NF::F695-3NF::F850-4NF::F879-4NF::M624-1NF::M878-3NF::F735-4NF::F849-5NF::F957-3NF::F850-8NF::M988-1NF::F841-1NF::F976-16NF::F885-1NF::F957-12NF::M920-5NF::M988-9NF::F969-8NF::M1013-1NF::F1026-7NF::M724-2NF::M988-4NF::F735-7NF::F737-NF::M892-10NF::M624-2NF::F969-10NF::M1022-13NF::F885-2NF::F850-3NF::M732-2NF::F624-5NF::F959-8NF::F959-5NF::F1027-10NF::M1008-5NF::M988-8NF::F969-1NF::F959-6NF::F1027-5NF::F877-4NF::M1013-2NF::F968-6NF::F771-2NF::F879-1NF::F994-7NF::F1026-6NF::F976-8NF::F877-3NF::M952-2NF::M851-3NF::F771-5NF::F885-3NF::F994-2NF::M724-3NF::F760-2NF::F649-3NF::F884-2NF::F947-1NF::F757-1NF::M626-11NF::M892-7NF::M988-2NF::M952-1NF::F959-1NF::F877-2NF::F959-3NF::M1013-3NF::F841-2NF::M626-10NF::F735-6NF::F991-5NF::F841-4NF::F735-3NF::F735-2NF::F976-11NF::F957-10NF::F1027-1NF::F969-9NF::M1008-1NF::M988-7NF::F969-3NF::F959-9NF::M724-4NF::M1013-5NF::F947-3NF::F947-4NF::F760-4NF::F968-2NF::M851-2NF::F879-6NF::F1027-9NF::M952-4NF::F959-2NF::M724-5NF::F601-NF::F624-3NF::F969-5NF::M878-6NF::F850-5NF::F850-6NF::F991-4NF::M1013-4NF::F968-1NF::M920-1NF::M920-2NF::M952-3NF::F695-1NF::F957-1NF::F976-9NF::F976-4NF::F1023-NF::M851-1NF::M988-5NF::F983-1NF::F850-1NF::F879-5NF::F624-4NF::F991-2NF::M988-6NF::F648-5NF::M626-6NF::F1026-8NF::F624-1NF::F957-11NF::M1008-4NF::F957-2NF::F877-1NF:: +216 chr2:98348500-98548500 0 0 RP23-100E6.1, AL837506.2, AL837506.1, ::M626-1NF::M988-5NF::M892-2NF::M1013-1NF::F959-5NF::F850-8NF::F968-1NF::F1026-5NF::F1026-9NF::M1013-4NF::F957-2NF::M988-2NF::F624-4NF::M1008-1NF::M724-3NF::M626-4NF::M952-4NF::F1026-8NF::F760-4NF::F1027-7NF::M732-4NF::F1027-4NF::F991-1NF::F969-5NF::M724-1NF::M878-2NF::F841-1NF::M892-3NF::M988-3NF::F850-1NF::F729-4NF::F841-6NF::F968-6NF::F735-3NF::F649-3NF::M624-1NF::M952-1NF::M892-10NF::M732-6NF::F976-11NF::F850-6NF::F648-5NF::M988-1NF::F957-12NF::F729-3NF::F802-4NF::F947-3NF::F983-1NF::F885-3NF::F1027-1NF::M626-8NF::M920-3NF::F735-7NF::F976-8NF::M624-4NF::F757-3NF::F957-3NF::F760-2NF::F968-4NF::F695-4NF::M724-2NF::M920-2NF::F879-4NF::M988-4NF::F624-3NF::M878-5NF::M626-7NF::M626-3NF::F1026-7NF::F735-6NF::F976-16NF::M892-8NF::M624-2NF::M624-6NF::M988-6NF::F802-5NF::F850-3NF::M732-5NF::F947-2NF::M626-2NF::F735-4NF::F1023-NF::M878-6NF::F884-1NF::M624-5NF::M624-3NF::F959-2NF::M732-2NF::F695-2NF::F879-5NF::F991-5NF::F624-1NF::F957-11NF::F735-2NF::F959-1NF::F947-4NF::M920-4NF::F760-6NF::M920-1NF::M624-7NF::F729-5NF::M910-1NF::F957-10NF::F771-5NF::M1008-5NF::F757-1NF::F969-2NF::F729-2NF::F648-4NF::F1026-10NF::F1027-8NF::M1008-4NF::M1025-1NF::F959-9NF::F959-6NF::F969-6NF::F841-2NF::F991-4NF::F976-1NF::F695-3NF::M626-6NF::M920-5NF::F957-1NF::F879-6NF::F1026-6NF::F991-3NF::F1027-9NF::F991-2NF::F877-4NF::F885-2NF::F1026-2NF::F983-2NF::F969-7NF::F968-2NF::F968-5NF::F1026-4NF::M626-11NF::F1027-3NF::M988-7NF::F648-2NF::F884-3NF::F969-3NF::M952-3NF::F959-8NF::M988-8NF::F969-8NF::M724-4NF::M732-3NF::M851-1NF::F1027-10NF::M1013-3NF::F969-10NF::F877-2NF::M724-6NF::F850-7NF::F959-7NF::F957-9NF::M626-9NF::F841-5NF::F760-5NF::M952-2NF::F968-3NF::F850-2NF::M892-6NF::F624-5NF::F959-10NF::M878-3NF::F1027-6NF::M1008-2NF::M892-9NF::F695-1NF::F969-4NF::F1026-1NF::F877-5NF::F802-6NF::F1027-2NF::M724-5NF::M1022-13NF::F969-1NF::F737-NF::M624-8NF::F796-NF::F1027-5NF::F884-2NF::F877-3NF::F976-3NF::F879-2NF::M1013-5NF::F648-3NF::F841-4NF::F976-7NF::F969-9NF::F624-6NF::F976-4NF::M1013-2NF::M988-9NF::F879-1NF::M892-11NF::F976-6NF::M892-4NF::F760-1NF::M851-2NF::M628-2NF::M626-10NF::M892-5NF::M892-7NF::F850-5NF::M851-3NF::F652-NF::F959-4NF::M626-5NF::F885-1NF::F1026-3NF::M878-1NF::F704-NF::F802-3NF:: +252 chr5:28311600-28511600 0 0 AC156021.1, Insig1, En2, ::M724-6NF::F983-1NF::F802-6NF::M624-4NF::M626-5NF::M624-7NF::F735-3NF::F959-9NF::M878-5NF::F729-4NF::F1027-3NF::M626-10NF::F976-1NF::F991-2NF::F849-5NF::F649-3NF::F771-2NF::F957-11NF::F879-4NF::M626-1NF::F957-10NF::M988-9NF::F976-4NF::F969-9NF::F1026-9NF::F969-2NF::F648-3NF::M892-7NF::M892-6NF::M624-5NF::M878-2NF::M1008-2NF::F735-4NF::F1023-NF::F1027-7NF::M732-5NF::M626-6NF::F947-2NF::F983-2NF::F976-11NF::F969-1NF::M724-4NF::F648-1NF::F850-2NF::F850-7NF::F994-8NF::M626-11NF::F884-3NF::F735-1NF::F959-3NF::M920-2NF::M732-2NF::M952-1NF::M910-4NF::M1013-3NF::F885-3NF::F991-1NF::F841-2NF::F1027-4NF::F1026-4NF::F802-2NF::F760-1NF::F849-8NF::M626-8NF::M988-7NF::M1013-2NF::F968-6NF::F1027-6NF::M851-3NF::M988-3NF::F959-1NF::F968-5NF::F969-6NF::F959-4NF::M624-2NF::F879-6NF::F976-2NF::F729-3NF::F624-5NF::F850-3NF::M892-8NF::F969-4NF::F877-1NF::F849-6NF::F771-5NF::F879-1NF::M626-3NF::F991-5NF::F976-8NF::F885-2NF::M952-4NF::F885-1NF::F959-5NF::M732-6NF::F959-7NF::F1027-10NF::F1026-5NF::F849-7NF::F757-1NF::F624-2NF::M878-3NF::M892-11NF::F976-6NF::F968-3NF::F735-5NF::M1013-5NF::F969-5NF::M626-7NF::F849-4NF::F850-5NF::F695-2NF::F1027-1NF::F760-2NF::F969-8NF::F1027-9NF::F1027-2NF::M724-1NF::F757-3NF::M988-4NF::F1026-10NF::F760-4NF::F957-2NF::M1008-5NF::F1026-1NF::M892-10NF::M920-3NF::F968-2NF::M624-8NF::F850-8NF::F1027-5NF::F648-4NF::M878-1NF::M892-9NF::F735-6NF::M1013-4NF::F1026-6NF::F796-NF::M626-9NF::M988-6NF::M624-1NF::F976-3NF::F1026-8NF::F959-8NF::M878-6NF::F841-5NF::F850-1NF::F704-NF::M1022-13NF::M624-6NF::F957-12NF::F729-1NF::F695-4NF::M892-2NF::F1027-8NF::F947-3NF::M628-2NF::F760-3NF::M892-1NF::F729-2NF::F991-4NF::F959-10NF::M624-3NF::F841-1NF::M892-5NF::M892-3NF::F969-3NF::F969-10NF::F877-6NF::F850-6NF::M1013-1NF::F624-4NF::F841-4NF::F648-5NF::M851-1NF::F877-3NF::F968-1NF::M920-1NF::F601-NF::M1025-1NF::M952-2NF::F652-NF::F994-1NF::F947-4NF::F969-7NF::F877-5NF::F849-2NF::F976-5NF::F968-4NF::F947-5NF::F957-9NF::M988-1NF::F877-4NF::F1026-7NF::F976-16NF::F624-1NF::M920-5NF::F802-1NF::M724-3NF::F959-6NF::F879-5NF::F850-4NF::M626-2NF::M952-3NF::F802-4NF::F624-3NF::M1008-4NF::F802-3NF::M732-3NF::F695-1NF::F735-2NF::F957-1NF::M851-2NF::M988-8NF::M1008-1NF::F879-2NF::F802-5NF::F695-3NF::F648-2NF::F849-3NF::F957-3NF::M988-2NF::F737-NF::F884-1NF::M892-4NF::F760-5NF::F991-3NF::F1026-2NF::F976-7NF::M732-4NF::F884-2NF::M724-2NF::F959-2NF::F735-7NF::M988-5NF::M920-4NF::M626-4NF::F841-6NF::F994-6NF::F976-9NF::F760-6NF::M878-4NF::F947-1NF::F673-3NF::F877-2NF::M1008-6NF::M1008-3NF::F1026-3NF::M724-5NF::F814-4NF::F994-4NF::F729-5NF::F624-6NF:: +147 chrX:139917600-139930100 1.0325038388214e-277 1.43566561276599e-272 No results within 2500 bp window ::M626-7NF::F735-4NF::F968-5NF::F983-1NF::M724-1NF::M626-4NF::F968-4NF::F879-5NF::F850-8NF::F648-5NF::F991-2NF::F947-3NF::M626-1NF::F771-5NF::F879-1NF::F757-1NF::F969-2NF::M624-6NF::F957-9NF::F796-NF::M1013-4NF::F983-2NF::M988-7NF::M952-2NF::M1008-4NF::M626-6NF::F1026-5NF::M988-3NF::M878-6NF::M920-1NF::M626-8NF::M988-4NF::M892-5NF::F1026-6NF::F957-11NF::F947-2NF::M892-8NF::F947-4NF::F968-6NF::F760-2NF::M724-3NF::F802-5NF::F850-2NF::M1008-1NF::F968-3NF::M878-5NF::M1013-1NF::M626-9NF::M1008-2NF::M732-4NF::F735-3NF::F969-3NF::F959-4NF::F1027-1NF::M892-10NF::F695-4NF::F976-16NF::F885-2NF::F1027-8NF::M988-6NF::F879-4NF::F704-NF::M920-3NF::F969-9NF::M988-1NF::F879-2NF::F760-3NF::M724-2NF::F1026-10NF::F1026-1NF::F735-7NF::F1027-4NF::F885-3NF::M624-2NF::F1027-2NF::M878-2NF::F959-2NF::M624-8NF::F968-1NF::M952-1NF::F969-5NF::M724-6NF::F959-9NF::F841-4NF::M724-5NF::F976-3NF::F841-1NF::M1025-1NF::M920-2NF::F959-5NF::F757-3NF::M624-1NF::M1008-5NF::M732-6NF::M892-3NF::F1026-4NF::F969-6NF::F959-1NF::F991-1NF::M626-11NF::F735-6NF::F877-4NF::M624-3NF::M624-4NF::F695-1NF::M988-9NF::F1026-7NF::M1013-3NF::F877-3NF::F991-5NF::F1023-NF::F652-NF::M988-5NF::F969-10NF::F959-6NF::F648-4NF::F1027-5NF::F1027-7NF::F648-2NF::F959-8NF::F841-6NF::F1026-8NF::M626-5NF::M1013-5NF::M920-5NF::M988-2NF::F624-1NF::F969-1NF::M724-4NF::F760-1NF::F969-8NF::F991-4NF::F850-6NF::F976-11NF::F850-3NF::M626-2NF::F802-6NF::F884-2NF::F737-NF::F957-2NF::F729-2NF::F735-2NF::M988-8NF::F1027-9NF::F976-8NF::M626-3NF::M920-4NF:: +118 chr13:31719100-31731600 4.08941890056485e-212 5.68621429866841e-207 Foxf2, RP23-322J11.2, ::M988-5NF::M1008-2NF::F850-7NF::F968-4NF::F841-2NF::F648-5NF::F947-2NF::F849-8NF::F957-2NF::M724-4NF::F1026-4NF::M626-10NF::F879-4NF::M724-1NF::F976-7NF::F760-5NF::F850-1NF::M892-7NF::F968-6NF::M892-1NF::M878-1NF::M626-11NF::F969-9NF::F695-3NF::F959-4NF::F849-7NF::F695-2NF::F841-5NF::M1013-3NF::F729-1NF::F969-5NF::F624-5NF::F849-3NF::F991-5NF::F735-5NF::F771-5NF::F760-4NF::F1026-5NF::F735-1NF::F885-2NF::F957-3NF::M920-4NF::F885-1NF::F959-7NF::M624-6NF::F879-2NF::F1023-NF::F969-2NF::F648-4NF::F969-7NF::F1026-8NF::M1022-13NF::M624-5NF::M892-6NF::F884-3NF::F957-12NF::F947-5NF::F957-1NF::M626-5NF::M624-4NF::F959-8NF::F760-3NF::F850-3NF::M626-7NF::M988-9NF::M988-6NF::M732-3NF::F648-1NF::F957-9NF::M724-6NF::M952-4NF::F1027-8NF::M624-1NF::M892-5NF::F849-2NF::F796-NF::M892-3NF::F957-11NF::F968-1NF::F757-3NF::M628-2NF::M626-4NF::F947-4NF::M920-5NF::M626-2NF::F729-4NF::F968-3NF::F991-1NF::M892-10NF::F976-11NF::F729-2NF::M878-3NF::F877-3NF::F624-3NF::M892-4NF::F850-5NF::F959-2NF::F959-5NF::F695-4NF::M878-5NF::F1027-1NF::M732-6NF::F850-6NF::F1026-10NF::M1013-1NF::F760-1NF::F877-4NF::M878-6NF::F976-16NF::M624-8NF::M626-9NF::M892-8NF::M892-2NF::F652-NF::F877-5NF::F850-4NF::F1027-2NF::F976-8NF:: +112 chr9:3025300-3037800 6.62041835394503e-199 9.20549310860994e-194 AC131780.5, AC131780.4, AC131780.6, AC131780.12, AC131780.2, AC131780.10, ::M952-3NF::F841-5NF::M892-8NF::M626-4NF::M878-5NF::F648-2NF::F737-NF::F969-7NF::F947-4NF::F968-6NF::M988-2NF::F1026-7NF::F760-6NF::F991-3NF::F1027-1NF::F991-2NF::F947-2NF::F850-5NF::F959-9NF::M626-1NF::M851-2NF::F957-12NF::M1013-1NF::F1026-6NF::M626-2NF::F735-2NF::F959-1NF::F1026-9NF::F969-2NF::M626-11NF::F757-3NF::M988-6NF::F969-10NF::M724-3NF::F757-1NF::M920-1NF::F652-NF::F959-2NF::M624-2NF::M851-1NF::F648-5NF::F1026-10NF::M892-3NF::F1026-8NF::F695-2NF::F841-6NF::M920-5NF::F959-8NF::F1026-2NF::F884-3NF::M624-5NF::M724-4NF::M878-6NF::F885-3NF::F735-6NF::F771-2NF::F957-11NF::F735-4NF::M626-6NF::F957-2NF::F1026-5NF::M988-8NF::F1027-5NF::F879-2NF::F884-2NF::M1013-3NF::F991-5NF::M988-1NF::F1027-2NF::M988-3NF::M988-9NF::M988-5NF::F991-1NF::M1008-1NF::F735-3NF::M732-6NF::F1027-4NF::F976-1NF::M892-9NF::M892-11NF::F1027-8NF::F884-1NF::F969-8NF::F976-16NF::F968-1NF::F802-4NF::M892-2NF::F624-1NF::F879-5NF::M952-4NF::F968-4NF::F983-1NF::F729-4NF::F850-3NF::F968-2NF::F802-5NF::M952-1NF::F1027-9NF::M851-3NF::F648-3NF::F877-4NF::F695-1NF::F760-5NF::M724-6NF::F877-5NF::M878-2NF::F879-6NF::F760-2NF::M626-9NF::M624-3NF::F850-6NF::F850-2NF:: +95 chr3:158263500-158276000 2.91939176379546e-162 4.05932666580467e-157 No results within 2500 bp window ::F969-2NF::F991-2NF::M1013-5NF::F850-3NF::M626-4NF::M1008-5NF::F969-8NF::F991-4NF::F1027-2NF::F695-3NF::M626-2NF::F1027-8NF::M1008-4NF::F885-1NF::M952-1NF::M626-7NF::M878-6NF::F957-1NF::F850-8NF::F968-3NF::F1026-7NF::F884-1NF::M1013-4NF::F879-4NF::F968-1NF::M878-2NF::M952-3NF::F735-2NF::M1013-3NF::F757-1NF::F648-2NF::F877-4NF::M988-6NF::F1023-NF::F969-3NF::F624-3NF::F885-3NF::F841-2NF::F760-2NF::F969-10NF::F976-8NF::F1026-10NF::M892-8NF::M988-9NF::F969-6NF::F796-NF::F649-3NF::F695-2NF::F850-1NF::M988-8NF::F735-6NF::F841-1NF::F704-NF::M624-2NF::F885-2NF::F968-6NF::F959-2NF::F760-4NF::F879-6NF::F695-4NF::M626-6NF::M624-1NF::F737-NF::F947-4NF::F983-1NF::F771-5NF::F959-6NF::F841-6NF::F947-5NF::M851-1NF::F757-3NF::F735-7NF::M732-6NF::M724-3NF::M988-2NF::F1026-8NF::F983-2NF::F648-1NF::F1027-5NF::M1013-1NF::M988-7NF::M988-1NF::F648-5NF::M624-4NF::M1025-1NF::F969-4NF::M988-3NF::F648-4NF::F957-2NF::M878-5NF::M626-8NF::M624-6NF::F735-4NF::M892-10NF::F1026-5NF:: +100 chr11:3001300-3101300 8.24103735876911e-85 1.97265711256856e-80 Pisd-ps1, Sfi1, RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Eif4enif1, Drg1, ::F968-1NF::M988-1NF::M892-11NF::F983-1NF::F771-5NF::F757-1NF::F1027-1NF::M892-6NF::M626-4NF::M724-6NF::F1026-3NF::M732-4NF::F850-7NF::F959-9NF::F1026-10NF::M988-2NF::F735-4NF::M624-3NF::M892-3NF::F976-11NF::M952-4NF::F1026-7NF::F1027-10NF::F850-3NF::F959-6NF::F1027-9NF::F850-6NF::F968-6NF::F957-2NF::F757-3NF::F991-4NF::M1013-3NF::M626-2NF::M626-6NF::M892-10NF::F959-1NF::F969-6NF::F850-2NF::F947-1NF::M1013-2NF::M624-8NF::F735-2NF::M988-3NF::F994-4NF::F969-8NF::M624-2NF::F850-1NF::F648-1NF::M626-7NF::F968-2NF::F969-4NF::M624-5NF::F969-2NF::F1023-NF::M626-5NF::F957-3NF::F969-3NF::M878-1NF::F624-5NF::F802-6NF::M732-2NF::F959-2NF::F849-2NF::F969-10NF::F879-4NF::F796-NF::F735-6NF::M624-7NF::M988-8NF::F648-5NF::M1008-4NF::M878-2NF::M920-4NF::F760-1NF::F947-4NF::F649-3NF::M724-4NF::F879-5NF::M878-5NF::M626-3NF::F729-2NF::F695-4NF::F1027-2NF::F976-7NF::F976-6NF::F841-6NF::F1027-7NF::F1026-1NF::F885-3NF::F1026-6NF::F947-2NF::M988-5NF::F968-4NF::F969-1NF::M878-6NF::F879-1NF::M892-4NF::F877-4NF::F729-4NF::F877-7NF:: +51 chr6:103588400-103600900 2.54021364915466e-74 3.53209087274008e-69 Chl1, ::F757-3NF::F983-1NF::F735-3NF::F957-1NF::F1026-8NF::M878-5NF::F879-6NF::M724-2NF::F802-4NF::M626-2NF::F969-3NF::F757-1NF::M1008-4NF::F968-4NF::M952-3NF::F959-8NF::F735-7NF::F624-1NF::F695-1NF::M724-6NF::F969-2NF::F1026-10NF::M1013-4NF::F695-2NF::M988-8NF::M892-2NF::M624-8NF::M626-3NF::M952-2NF::M988-9NF::F1027-4NF::F991-1NF::F850-8NF::M626-8NF::F877-4NF::M628-2NF::M624-2NF::F959-6NF::F969-5NF::M732-6NF::F771-5NF::M626-10NF::F841-1NF::F969-10NF::F877-3NF::M920-1NF::F947-3NF::M626-6NF::M892-8NF::F879-5NF::M1013-1NF:: +39 chr9:3733700-3746200 8.99422811983147e-53 1.25062043737821e-47 Gucy1a2, ::F959-7NF::M1022-13NF::M851-3NF::M732-6NF::F760-4NF::F849-5NF::F849-7NF::F695-1NF::F757-3NF::F624-4NF::M892-3NF::F1026-7NF::F877-5NF::F1026-2NF::F771-2NF::F879-2NF::M626-9NF::M1013-3NF::M920-4NF::F976-7NF::F802-4NF::M878-3NF::F968-2NF::F802-3NF::F1026-5NF::F1026-6NF::F735-1NF::M1008-2NF::F1027-9NF::F968-4NF::F850-6NF::M892-11NF::M892-1NF::M892-4NF::M724-3NF::M892-8NF::F652-NF::F1026-10NF::F1026-4NF:: +42 chrY:2859000-2884000 1.06360555521642e-45 2.54595261752153e-41 No results within 2500 bp window ::M732-5NF::M920-5NF::M920-1NF::M624-3NF::M1008-1NF::M952-1NF::M724-2NF::M988-7NF::M892-4NF::M892-7NF::M892-3NF::M878-2NF::M732-4NF::M1008-4NF::M892-10NF::M892-11NF::M626-10NF::M626-3NF::M624-6NF::M878-5NF::M851-3NF::M1013-4NF::M878-3NF::M1013-1NF::M626-6NF::M920-2NF::M624-5NF::M988-2NF::M988-3NF::M1022-13NF::F994-6NF::M724-3NF::M626-8NF::M624-8NF::M624-7NF::M851-2NF::M920-4NF::M1008-2NF::F976-16NF::F849-2NF::M1013-5NF::M892-8NF:: +35 chr10:16573800-16586300 6.38745059378905e-46 8.88155842714586e-41 No results within 2500 bp window ::F735-2NF::F652-NF::M892-6NF::F991-4NF::F1023-NF::F976-16NF::F648-4NF::F802-6NF::M988-5NF::F959-6NF::F959-9NF::F983-2NF::M920-1NF::M624-2NF::M892-10NF::F841-1NF::F695-2NF::F1026-8NF::F959-2NF::F1027-10NF::F969-2NF::F735-4NF::M1008-1NF::M988-6NF::F885-3NF::F957-12NF::F957-3NF::F1026-5NF::M724-2NF::M988-7NF::F969-9NF::F735-7NF::F879-4NF::M1008-5NF::M878-6NF:: +34 chr3:48818900-48831400 3.07892000247338e-44 4.28114589583916e-39 No results within 2500 bp window ::M626-7NF::F771-5NF::F1026-4NF::M624-1NF::F760-5NF::M878-1NF::M920-4NF::F1027-5NF::F796-NF::M878-2NF::F1026-8NF::F841-6NF::F735-5NF::F849-5NF::F976-2NF::M1013-3NF::F850-7NF::F850-6NF::F849-2NF::F1026-6NF::M851-1NF::M878-4NF::F1027-3NF::F841-5NF::F624-4NF::F1027-9NF::F802-2NF::F968-4NF::F695-1NF::F968-5NF::M626-3NF::F802-5NF::M952-4NF::F729-3NF:: +30 chr16:42526200-42538700 1.23286113288979e-37 1.71425641944926e-32 No results within 2500 bp window ::M724-3NF::M1013-5NF::F735-2NF::F1027-4NF::F624-5NF::F976-11NF::F850-6NF::F648-2NF::M626-1NF::F976-1NF::M920-1NF::F760-2NF::F976-9NF::M988-6NF::F802-4NF::F968-2NF::F879-4NF::M626-3NF::F695-4NF::F947-3NF::F757-1NF::F760-5NF::M892-10NF::F849-8NF::M952-4NF::F760-6NF::F969-5NF::F771-2NF::F850-3NF::M626-6NF:: +28 chr9:3000000-3012500 2.03441255540329e-34 2.82878962591161e-29 AC131780.8, AC131780.9, AC131780.5, AC131780.1, ::M878-5NF::M952-2NF::F983-1NF::M624-6NF::F968-4NF::F1027-5NF::F760-4NF::F729-2NF::M878-2NF::M892-10NF::F652-NF::F1027-4NF::M1008-4NF::F877-4NF::M724-6NF::F757-1NF::F976-8NF::F1026-1NF::F885-3NF::F959-3NF::F991-1NF::F735-3NF::M920-1NF::M892-8NF::M626-2NF::F757-3NF::F879-4NF::F969-7NF:: +52 chrX:39517400-39617400 2.00979839553522e-31 4.81085441939267e-27 Stag2, ::M920-4NF::F968-2NF::F947-3NF::M1013-3NF::F729-4NF::M624-3NF::M624-8NF::F841-2NF::M878-1NF::F969-2NF::M920-2NF::M920-5NF::M952-1NF::M892-7NF::M626-3NF::F850-6NF::F969-7NF::M732-4NF::F976-16NF::F757-1NF::F959-9NF::M892-5NF::F884-2NF::F760-3NF::F624-1NF::F735-3NF::F885-1NF::F884-3NF::F959-2NF::M626-6NF::F1027-5NF::M851-3NF::F760-1NF::F884-1NF::F879-5NF::F1026-8NF::F885-3NF::M624-4NF::M878-6NF::M892-8NF::M626-10NF::M626-4NF::M892-11NF::F877-4NF::F959-5NF::F1023-NF::F959-1NF::F959-10NF::M988-3NF::F1026-3NF::F695-3NF::F968-1NF:: +25 chr6:93722000-93734500 1.04458212828607e-29 1.45246011191793e-24 Magi1, ::F624-1NF::F969-10NF::F796-NF::M988-5NF::M1013-3NF::F976-16NF::M988-9NF::F1027-2NF::M920-2NF::F850-3NF::M878-6NF::M878-5NF::F983-2NF::F735-7NF::F850-8NF::F959-9NF::F802-6NF::F959-6NF::M724-1NF::F885-3NF::F735-6NF::F1023-NF::F1027-8NF::M988-3NF::F735-2NF:: +49 chr17:10393300-10493300 1.35967301588236e-28 3.25464929811762e-24 Qk, ::F957-12NF::F841-1NF::M626-8NF::M892-2NF::F969-3NF::F729-2NF::F991-1NF::F877-2NF::F850-4NF::M628-2NF::M920-3NF::F757-3NF::M988-8NF::F624-4NF::F849-5NF::F879-2NF::F760-5NF::F624-1NF::F648-2NF::M878-5NF::F729-3NF::M892-7NF::M626-1NF::F959-8NF::M920-1NF::F850-6NF::F1026-7NF::F976-1NF::M626-6NF::F695-2NF::M920-2NF::F1026-10NF::F969-7NF::M988-3NF::M892-3NF::M1013-2NF::F957-10NF::F735-2NF::M624-7NF::F850-3NF::F735-6NF::M952-3NF::F760-6NF::F704-NF::F968-2NF::F849-6NF::F983-1NF::M1013-1NF::F648-4NF:: +24 chr1:20633100-20645600 3.59654423912044e-28 5.0008868681698e-23 No results within 2500 bp window ::F968-2NF::M988-6NF::F983-2NF::M724-4NF::M988-7NF::F969-6NF::M878-5NF::M626-2NF::F695-1NF::F968-1NF::M952-1NF::F1027-1NF::M626-6NF::F969-3NF::F983-1NF::M988-2NF::M626-11NF::F695-3NF::F994-6NF::F959-6NF::F850-8NF::M988-8NF::M624-2NF::F879-2NF:: +24 chrY:2777700-2790200 3.59654423912044e-28 5.0008868681698e-23 No results within 2500 bp window ::M624-7NF::M952-3NF::M878-3NF::M626-1NF::F994-6NF::M626-9NF::M1008-4NF::M878-2NF::F976-16NF::M1013-2NF::M732-4NF::M626-6NF::M892-10NF::F976-4NF::M892-7NF::M1013-4NF::M624-6NF::M920-2NF::M878-6NF::M724-6NF::M624-2NF::M626-2NF::M1008-2NF::M624-4NF:: +36 chr19:32839900-32889900 6.88901694204691e-27 1.64902398541777e-22 Pten, ::M732-3NF::F735-3NF::F1026-6NF::F850-1NF::M1013-5NF::M892-6NF::F1026-7NF::F760-4NF::F704-NF::M724-4NF::F850-2NF::F849-5NF::F1026-10NF::M920-4NF::F771-5NF::M626-5NF::F1026-9NF::F885-3NF::M1013-4NF::F959-9NF::F802-4NF::M626-2NF::F624-1NF::M1025-1NF::F885-2NF::F850-3NF::F991-2NF::F1027-5NF::M626-8NF::M626-6NF::F1023-NF::F729-6NF::M724-3NF::M724-6NF::F959-2NF::M988-5NF:: +63 chr5:22924800-23124800 5.75016344598857e-26 1.37641662406628e-21 BC050254, Mll5, 7SK, Srpk2, ::F959-6NF::F1027-8NF::F879-5NF::F850-1NF::F957-9NF::M892-3NF::F735-2NF::F959-8NF::F624-1NF::F957-10NF::M624-2NF::M892-8NF::F968-4NF::F648-5NF::F959-10NF::M1013-1NF::M724-3NF::M952-1NF::F760-6NF::F1027-10NF::F850-6NF::F735-7NF::F947-1NF::M732-6NF::F735-3NF::F624-4NF::F957-11NF::M988-2NF::F695-4NF::F648-3NF::F735-1NF::M851-3NF::F969-7NF::F1023-NF::F969-1NF::M626-11NF::M626-4NF::M878-6NF::F1027-4NF::F1026-8NF::M892-10NF::M892-4NF::F1027-7NF::F877-4NF::F947-5NF::M892-6NF::M626-8NF::F957-3NF::M624-5NF::F1026-10NF::F968-6NF::M878-5NF::F849-2NF::M920-3NF::F850-3NF::F1026-7NF::M724-2NF::F850-2NF::F1026-5NF::F968-3NF::M628-2NF::M624-4NF::M626-6NF:: +46 chr11:104200400-104300400 7.66845923629501e-26 1.83559908739194e-21 1700081L11Rik, AL593843.1, ::F760-2NF::F760-4NF::M1013-2NF::M892-11NF::F959-7NF::M724-2NF::F968-6NF::F850-4NF::F796-NF::F649-3NF::F1027-2NF::F760-6NF::F648-1NF::F1026-6NF::F879-2NF::F991-2NF::F885-2NF::F695-1NF::M892-10NF::F968-1NF::F968-2NF::F760-5NF::F1026-1NF::F648-2NF::M626-6NF::F994-6NF::F735-4NF::F735-1NF::M1013-3NF::F976-4NF::F729-2NF::M892-5NF::F879-5NF::F969-8NF::M626-10NF::M1022-13NF::F976-8NF::F841-1NF::M624-5NF::F959-1NF::F735-3NF::M1013-5NF::F969-9NF::M624-7NF::F947-2NF::F850-6NF:: +44 chr17:3117100-3217100 4.70439845141935e-24 1.12609185731625e-19 Rbm16, ::F850-3NF::F1027-7NF::M626-8NF::M878-5NF::M626-2NF::M626-4NF::F624-3NF::M624-1NF::F771-5NF::M892-3NF::M892-7NF::F976-9NF::F802-2NF::F959-6NF::M624-2NF::M1013-4NF::F757-1NF::F704-NF::F968-1NF::M626-1NF::M892-11NF::F735-3NF::F879-4NF::M920-2NF::F959-7NF::F1026-8NF::F735-4NF::F1027-9NF::M626-3NF::F991-1NF::M878-1NF::F735-7NF::F969-8NF::F968-5NF::F976-11NF::F968-6NF::F976-8NF::M892-4NF::M892-2NF::M624-7NF::M851-3NF::F1026-7NF::F624-2NF::F969-3NF:: + +NF_0library +number pos pvalue bonferroni gene_name library_name +181 chr11:3009900-3209900 0 0 Pisd-ps1, Sfi1, RP23-191E3.1, RP23-191E3.2, Drg1, RP23-191E3.18, Fau-ps2, Eif4enif1, Patz1, RP23-191E3.14, RP23-191E3.17, ::M624-6NF::M892-6NF::F648-2NF::M626-4NF::M988-5NF::F947-1NF::M851-2NF::F991-2NF::M626-11NF::F969-3NF::M724-6NF::F850-2NF::F1023-NF::F1026-3NF::M624-7NF::M732-4NF::M1008-5NF::F1027-2NF::F850-7NF::F885-3NF::F850-6NF::F969-5NF::M988-6NF::M892-8NF::F959-9NF::F959-8NF::F729-2NF::F1026-10NF::F1026-7NF::F947-4NF::F850-3NF::F757-1NF::F737-NF::F969-9NF::M624-8NF::M988-2NF::M988-7NF::M878-5NF::F735-4NF::F969-1NF::M892-3NF::M624-2NF::F969-2NF::F648-5NF::F969-8NF::M624-3NF::F991-5NF::F695-2NF::M988-1NF::F976-11NF::F879-4NF::F757-3NF::F735-7NF::M724-4NF::F983-2NF::F879-5NF::M952-4NF::M988-3NF::M920-1NF::F1027-10NF::M878-2NF::F850-8NF::F760-2NF::F959-6NF::F1027-9NF::F968-6NF::M988-4NF::M1013-1NF::F957-2NF::F957-1NF::F969-7NF::M1025-1NF::F991-4NF::F841-2NF::M626-7NF::M878-6NF::F735-3NF::M1013-3NF::F957-10NF::F624-3NF::M892-2NF::M851-3NF::M626-2NF::F976-16NF::M626-9NF::M892-10NF::M626-6NF::F735-6NF::F969-6NF::F959-1NF::F624-1NF::F885-2NF::F983-1NF::F1027-8NF::F760-4NF::F735-2NF::M724-3NF::F968-2NF::M920-2NF::F968-3NF::M1013-2NF::F959-2NF::F760-5NF::M952-2NF::F976-8NF::F994-4NF::M626-1NF::F877-3NF::F947-3NF::F850-1NF::F624-4NF::F648-1NF::F884-2NF::M988-8NF::F877-4NF::M626-8NF::F771-5NF::F968-1NF::M624-5NF::F969-4NF::M892-7NF::F849-2NF::M626-5NF::F1027-1NF::M892-4NF::F957-3NF::M878-1NF::F624-5NF::F802-6NF::F1027-7NF::M1008-1NF::M732-2NF::F841-4NF::F1026-8NF::M952-3NF::F969-10NF::F796-NF::F947-2NF::F1026-1NF::M1008-4NF::F695-3NF::M920-4NF::F735-1NF::F959-10NF::F760-1NF::F884-3NF::F957-12NF::F649-3NF::M732-6NF::F648-4NF::M626-3NF::F959-3NF::F695-4NF::F976-7NF::F976-6NF::F1026-6NF::F879-6NF::F841-6NF::F841-5NF::F968-4NF::M920-5NF::F976-1NF::F849-3NF::F1026-9NF::F976-9NF::M988-9NF::F879-1NF::F957-9NF::F729-4NF::M1013-5NF::F877-6NF::F877-7NF::M724-2NF::M724-5NF::M1008-2NF::M1013-4NF::F879-2NF::F957-11NF::M626-10NF::M624-1NF::F994-8NF:: +255 chr5:28496200-28508700 0 0 En2, ::F735-3NF::F649-3NF::F704-NF::F1027-6NF::M892-6NF::F760-2NF::F959-3NF::F976-16NF::F968-2NF::F879-2NF::M988-4NF::F976-1NF::M732-4NF::F1023-NF::F968-1NF::F841-4NF::M1022-13NF::F1026-5NF::M732-6NF::F957-3NF::F969-2NF::F735-7NF::F802-5NF::F850-2NF::F760-3NF::F969-6NF::F1026-8NF::M624-5NF::M892-5NF::F957-1NF::M626-9NF::F695-3NF::F1026-2NF::M724-6NF::F877-5NF::M626-5NF::M920-3NF::F1027-1NF::M732-5NF::M626-10NF::F879-5NF::F947-1NF::F849-2NF::F648-4NF::F624-5NF::F648-3NF::M988-3NF::F850-7NF::F841-1NF::M878-1NF::F729-1NF::F1026-6NF::M988-9NF::F957-11NF::F879-4NF::F991-1NF::F879-1NF::F735-6NF::F968-5NF::M1013-3NF::M892-7NF::F1027-7NF::F968-4NF::F884-1NF::F1026-7NF::F959-6NF::M624-2NF::F1026-4NF::F841-5NF::F1027-10NF::F969-4NF::M920-4NF::F735-5NF::M1008-1NF::M952-1NF::F802-6NF::F648-5NF::F957-9NF::F802-4NF::F968-6NF::F976-9NF::F991-3NF::F760-1NF::M624-7NF::M626-3NF::M952-3NF::M988-2NF::F969-9NF::F959-10NF::F796-NF::F760-4NF::M724-4NF::F624-2NF::M626-4NF::M892-4NF::F624-3NF::F802-2NF::F737-NF::F802-1NF::M892-8NF::F735-4NF::F983-2NF::F947-4NF::F757-3NF::F976-5NF::M851-2NF::M724-1NF::F991-2NF::F735-2NF::F877-6NF::F1027-8NF::F1027-3NF::F959-4NF::F850-5NF::M851-3NF::M626-8NF::M1025-1NF::F879-6NF::F877-4NF::F959-1NF::F959-5NF::F991-5NF::M624-1NF::M1008-5NF::F695-4NF::M1008-2NF::F841-6NF::M1013-5NF::F969-1NF::F969-8NF::F850-4NF::F994-8NF::F1026-10NF::F885-3NF::F947-2NF::M1008-4NF::F969-7NF::M624-3NF::M988-7NF::M1008-3NF::F976-6NF::F802-3NF::M892-2NF::M892-10NF::F947-3NF::F976-11NF::F976-2NF::F729-3NF::F976-3NF::F850-1NF::M952-4NF::F849-8NF::F959-7NF::F968-3NF::F947-5NF::M724-2NF::M988-1NF::F957-2NF::M732-3NF::F735-1NF::F814-4NF::F849-7NF::F849-3NF::M892-9NF::F1026-1NF::F1027-5NF::M920-1NF::F760-6NF::F959-9NF::M892-3NF::F729-4NF::F1027-9NF::F976-4NF::F957-12NF::F841-2NF::F849-6NF::M892-11NF::F601-NF::F729-2NF::F695-2NF::M626-11NF::M724-5NF::F850-3NF::F850-6NF::M920-2NF::M626-2NF::F849-5NF::F957-10NF::F760-5NF::F648-1NF::M988-5NF::M892-1NF::F849-4NF::F983-1NF::M626-6NF::F969-3NF::M724-3NF::F624-1NF::F969-5NF::F771-5NF::F884-2NF::M1013-2NF::M628-2NF::F695-1NF::F959-8NF::M878-3NF::F624-4NF::F1026-9NF::M624-4NF::M910-4NF::F959-2NF::M988-8NF::F652-NF::M851-1NF::M1013-1NF::M878-5NF::F877-3NF::F885-2NF::F976-7NF::M920-5NF::M626-1NF::M732-2NF::M1013-4NF::M988-6NF::F1027-4NF::F969-10NF::F991-4NF::M952-2NF::M626-7NF::F1027-2NF::F850-8NF::F976-8NF::M624-8NF::M878-2NF::F648-2NF::F885-1NF::F757-1NF::M878-6NF::F884-3NF::M624-6NF::F771-2NF::F994-1NF::F877-1NF::M1008-6NF::F1026-3NF::F994-6NF::F877-2NF::F673-3NF::M878-4NF::F624-6NF::F729-6NF::F729-5NF::M732-1NF::F879-3NF::F994-4NF:: +255 chr5:28453700-28503700 0 0 En2, ::F652-NF::F879-5NF::M626-3NF::M626-5NF::F735-3NF::F649-3NF::F704-NF::F1027-6NF::M892-6NF::F760-2NF::F959-3NF::F976-16NF::F968-2NF::F879-2NF::M988-4NF::F976-1NF::M732-4NF::F1023-NF::F968-1NF::F841-4NF::M1022-13NF::F1026-5NF::M732-6NF::F957-3NF::F969-2NF::F735-7NF::F802-5NF::F850-2NF::F760-3NF::F969-6NF::F1026-8NF::M624-5NF::M892-5NF::F957-1NF::M626-9NF::F695-3NF::F1026-2NF::M724-6NF::F877-5NF::M920-3NF::F1027-1NF::M732-5NF::M626-10NF::F947-1NF::F849-2NF::F648-4NF::F624-5NF::F648-3NF::M988-3NF::F850-7NF::F841-1NF::M878-1NF::F729-1NF::F1026-6NF::M988-9NF::F957-11NF::F879-4NF::F991-1NF::F879-1NF::F735-6NF::F968-5NF::M1013-3NF::M892-7NF::F1027-7NF::F968-4NF::F884-1NF::F1026-7NF::F959-6NF::M624-2NF::F1026-4NF::F841-5NF::F1027-10NF::F969-4NF::M920-4NF::F735-5NF::M1008-1NF::M952-1NF::F802-6NF::F648-5NF::F957-9NF::F802-4NF::F968-6NF::F976-9NF::F991-3NF::F760-1NF::M624-7NF::M952-3NF::M988-2NF::F969-9NF::F959-10NF::F796-NF::F760-4NF::M724-4NF::F624-2NF::M626-4NF::M892-4NF::F624-3NF::F802-2NF::F737-NF::F802-1NF::M892-8NF::F735-4NF::F983-2NF::F947-4NF::F757-3NF::F976-5NF::M851-2NF::M724-1NF::F991-2NF::F735-2NF::F877-6NF::F1027-8NF::F1027-3NF::F959-4NF::F850-5NF::M851-3NF::M626-8NF::M1025-1NF::F879-6NF::F877-4NF::F959-1NF::F959-5NF::F991-5NF::M624-1NF::M1008-5NF::F695-4NF::M1008-2NF::F841-6NF::M1013-5NF::F969-1NF::F969-8NF::F850-4NF::F994-8NF::F1026-10NF::F885-3NF::F947-2NF::M1008-4NF::F969-7NF::M624-3NF::M988-7NF::M1008-3NF::F976-6NF::F802-3NF::M892-2NF::M892-10NF::F947-3NF::F976-11NF::F976-2NF::F729-3NF::F976-3NF::F850-1NF::M952-4NF::F849-8NF::F959-7NF::F968-3NF::F947-5NF::M724-2NF::M988-1NF::F957-2NF::M732-3NF::F735-1NF::F814-4NF::F849-7NF::F849-3NF::M892-9NF::F1026-1NF::F1027-5NF::M920-1NF::F760-6NF::F959-9NF::M892-3NF::F729-4NF::F1027-9NF::F976-4NF::F957-12NF::F841-2NF::F849-6NF::M892-11NF::F601-NF::F729-2NF::F695-2NF::M626-11NF::M724-5NF::F850-3NF::F850-6NF::M920-2NF::M626-2NF::F849-5NF::F957-10NF::F760-5NF::F648-1NF::M988-5NF::M892-1NF::F849-4NF::F983-1NF::M626-6NF::F969-3NF::M724-3NF::F624-1NF::F969-5NF::F771-5NF::F884-2NF::M1013-2NF::M628-2NF::F695-1NF::F959-8NF::M878-3NF::F624-4NF::F1026-9NF::M624-4NF::M910-4NF::F959-2NF::M988-8NF::M851-1NF::M1013-1NF::M878-5NF::F877-3NF::F885-2NF::F976-7NF::M920-5NF::M626-1NF::M732-2NF::M1013-4NF::M988-6NF::F1027-4NF::F969-10NF::F991-4NF::M952-2NF::M626-7NF::F1027-2NF::F850-8NF::F976-8NF::M624-8NF::M878-2NF::F648-2NF::F885-1NF::F757-1NF::M878-6NF::F884-3NF::M624-6NF::F771-2NF::F994-1NF::F877-1NF::M1008-6NF::F1026-3NF::F994-6NF::F877-2NF::F673-3NF::M878-4NF::F624-6NF::F729-6NF::F729-5NF::M732-1NF::F879-3NF::F994-4NF:: +188 chr10:57222400-57322400 0 0 Serinc1, Hsf2, ::M988-1NF::F991-4NF::F757-3NF::F735-7NF::M626-9NF::M624-2NF::M878-2NF::F1026-3NF::F885-2NF::M626-6NF::F735-4NF::M626-4NF::M624-7NF::M1008-2NF::F850-8NF::F760-2NF::M988-2NF::F969-8NF::M988-5NF::F1026-7NF::M878-6NF::F1027-3NF::M624-3NF::F879-5NF::M1022-13NF::F947-4NF::F968-2NF::F760-6NF::M952-2NF::F959-6NF::F957-12NF::M624-6NF::F757-1NF::M1008-4NF::F648-4NF::F729-2NF::F969-5NF::F802-4NF::F957-2NF::F877-5NF::M626-3NF::M626-5NF::M910-4NF::F1023-NF::F991-2NF::F994-1NF::F1026-1NF::F957-1NF::M892-2NF::F849-3NF::F771-2NF::F850-6NF::F968-6NF::M626-8NF::M1013-1NF::F849-1NF::F849-5NF::M892-4NF::F695-3NF::M878-5NF::F959-4NF::F802-3NF::F994-2NF::F849-2NF::F850-1NF::F884-2NF::F994-3NF::F771-5NF::F1026-9NF::F1027-2NF::F959-5NF::F849-8NF::F624-3NF::M910-1NF::F648-5NF::M851-1NF::F969-9NF::F994-4NF::M910-2NF::M878-1NF::M626-7NF::F994-6NF::F991-5NF::F994-5NF::M732-1NF::M626-11NF::F879-4NF::F947-2NF::F879-1NF::F994-8NF::M732-4NF::F959-1NF::M1008-1NF::F1027-10NF::F850-5NF::M624-4NF::M892-3NF::F735-1NF::M920-4NF::M628-2NF::F957-9NF::F976-11NF::M892-6NF::M892-1NF::M626-1NF::F969-10NF::F957-11NF::F1027-7NF::M952-3NF::F879-2NF::M892-7NF::F735-2NF::F994-7NF::F1027-5NF::F957-3NF::F760-1NF::F802-6NF::F648-2NF::F695-1NF::M624-8NF::F648-3NF::F729-3NF::M851-3NF::M952-4NF::F850-3NF::M624-1NF::F796-NF::F957-10NF::M1013-5NF::F976-9NF::F841-4NF::F1026-10NF::M920-2NF::F729-4NF::M851-2NF::F879-6NF::F673-3NF::F1027-6NF::F959-2NF::M552-NF::M626-2NF::F976-4NF::F737-NF::F976-5NF::F760-4NF::F991-3NF::F735-3NF::F649-3NF::F983-1NF::F968-3NF::F1026-8NF::F877-3NF::F976-3NF::F652-NF::F969-1NF::F760-5NF::F947-3NF::M988-7NF::F877-4NF::F969-6NF::F959-9NF::F968-1NF::F841-1NF::F959-8NF::F968-5NF::F968-4NF::M626-10NF::F976-7NF::F959-10NF::M892-8NF::M724-2NF::M724-6NF::F1027-1NF::F735-6NF::M920-5NF::M892-10NF::F624-4NF::F729-1NF::M892-11NF::F969-3NF::F648-1NF::M1008-5NF::M724-4NF::M988-3NF::M988-6NF::F802-5NF::M1013-3NF::F760-3NF:: +183 chr10:57289200-57339200 0 0 No results within 2500 bp window ::M1008-4NF::F648-4NF::F729-2NF::F757-3NF::F760-2NF::F969-5NF::F802-4NF::F968-2NF::F957-2NF::F877-5NF::M626-3NF::M626-5NF::M910-4NF::F1023-NF::F991-2NF::F994-1NF::F1026-1NF::F957-1NF::M892-2NF::F849-3NF::F771-2NF::F850-6NF::F968-6NF::M626-8NF::M1013-1NF::F849-1NF::F849-5NF::M624-6NF::M892-4NF::F760-6NF::F695-3NF::M878-5NF::M624-7NF::F959-4NF::F802-3NF::F994-2NF::F849-2NF::F850-1NF::F884-2NF::F994-3NF::F771-5NF::F1026-9NF::F1027-2NF::F959-5NF::F849-8NF::F624-3NF::M910-1NF::F648-5NF::M851-1NF::F969-9NF::F959-6NF::F994-4NF::F969-8NF::M910-2NF::M878-2NF::M878-6NF::M878-1NF::M626-7NF::M626-9NF::F994-6NF::F991-5NF::F994-5NF::M732-1NF::F957-12NF::M626-11NF::F879-4NF::F947-2NF::F879-1NF::F735-4NF::F994-8NF::M732-4NF::F959-1NF::M1008-1NF::F1027-10NF::M626-4NF::F850-5NF::M624-4NF::M892-3NF::F735-1NF::M920-4NF::M628-2NF::F957-9NF::F976-11NF::M892-6NF::M892-1NF::M626-1NF::F969-10NF::F957-11NF::F1027-7NF::M952-3NF::F879-2NF::M892-7NF::F735-2NF::F994-7NF::F1027-5NF::F957-3NF::M1022-13NF::F760-1NF::F802-6NF::F648-2NF::F695-1NF::M624-8NF::F648-3NF::F729-3NF::M624-2NF::M851-3NF::M952-4NF::F850-3NF::M624-1NF::F796-NF::F957-10NF::M1013-5NF::F1027-3NF::F976-9NF::F841-4NF::F991-4NF::F1026-10NF::M920-2NF::F729-4NF::M851-2NF::F735-7NF::F879-6NF::F879-5NF::F673-3NF::F1027-6NF::F959-2NF::M552-NF::M624-3NF::M626-2NF::F947-4NF::F976-4NF::F737-NF::F976-5NF::F760-4NF::F991-3NF::F735-3NF::F649-3NF::F983-1NF::F968-3NF::F1026-8NF::F877-3NF::M952-2NF::F976-3NF::F652-NF::F969-1NF::F760-5NF::F947-3NF::M988-7NF::F877-4NF::F969-6NF::F959-9NF::F968-1NF::F841-1NF::F959-8NF::F968-5NF::F968-4NF::M626-10NF::F976-7NF::F959-10NF::F757-1NF::M892-8NF::M724-2NF::M724-6NF::F1027-1NF::F735-6NF::M920-5NF::M892-10NF::F624-4NF::F729-1NF::M892-11NF::F969-3NF::M626-6NF::F885-2NF::F648-1NF::M1008-5NF::M988-5NF::M724-4NF::M988-3NF::M988-6NF::F802-5NF::M1013-3NF::F760-3NF::M920-1NF:: +243 chr2:163423100-163473100 0 0 Ttpal, Serinc3, 0610039K10Rik, AL591488.2, ::F879-4NF::M892-3NF::M892-2NF::M878-2NF::F994-3NF::F959-2NF::F968-4NF::F1023-NF::F1027-8NF::F969-3NF::F947-4NF::F969-8NF::F802-4NF::F850-8NF::F884-3NF::F1026-10NF::M732-6NF::F969-6NF::M626-11NF::F735-4NF::M626-10NF::F648-2NF::M988-1NF::M626-8NF::F879-5NF::M624-3NF::F624-1NF::F879-1NF::F1026-8NF::M624-5NF::M892-6NF::F735-1NF::F968-1NF::F695-2NF::M624-1NF::F957-1NF::M724-6NF::M920-1NF::F1026-2NF::M732-4NF::F1026-5NF::M892-9NF::F841-5NF::F841-2NF::F850-6NF::F1027-5NF::F991-4NF::F959-7NF::M878-5NF::F991-3NF::M988-3NF::F850-3NF::M724-4NF::M851-2NF::M624-2NF::F976-9NF::M892-7NF::F735-3NF::M952-4NF::M892-10NF::F877-4NF::M626-2NF::M626-6NF::F969-10NF::F624-5NF::F959-5NF::F735-6NF::F1026-9NF::F802-5NF::F959-4NF::M732-5NF::F648-5NF::F957-11NF::F624-2NF::F735-2NF::F802-6NF::M988-7NF::F959-10NF::F959-1NF::F976-8NF::F994-6NF::F695-4NF::F735-5NF::F648-1NF::F796-NF::F885-2NF::F850-5NF::F969-5NF::F1026-1NF::F850-2NF::F802-2NF::F879-2NF::F957-9NF::F976-4NF::F704-NF::F850-1NF::F884-2NF::F1027-7NF::F849-2NF::M732-1NF::F771-2NF::F957-2NF::F969-9NF::M851-1NF::F969-4NF::M1008-5NF::F729-5NF::M1022-13NF::F652-NF::M878-6NF::M892-11NF::F947-1NF::F959-8NF::M624-4NF::M988-5NF::M732-2NF::M1013-3NF::F957-10NF::M626-4NF::M724-2NF::F976-5NF::M892-4NF::M624-8NF::F969-1NF::M626-9NF::F877-1NF::F959-3NF::F737-NF::M1008-4NF::F976-16NF::F1027-4NF::F991-5NF::F729-3NF::F968-3NF::F729-4NF::F991-1NF::F976-1NF::M1013-2NF::F841-4NF::F884-1NF::F957-3NF::F814-4NF::F976-3NF::F729-1NF::F877-5NF::M1008-1NF::F877-3NF::M724-1NF::F757-3NF::M626-5NF::M1013-1NF::M952-1NF::M878-3NF::M988-6NF::F976-6NF::F849-4NF::F947-3NF::M626-3NF::F771-5NF::F976-11NF::F1026-7NF::F849-8NF::F976-7NF::M892-8NF::M892-5NF::M724-5NF::M626-7NF::F760-4NF::F649-3NF::M851-3NF::F695-3NF::M988-9NF::M878-4NF::M878-1NF::F877-6NF::F729-2NF::F760-2NF::F991-2NF::F760-1NF::M988-2NF::F1026-6NF::M892-1NF::F760-3NF::M626-1NF::F968-2NF::F648-4NF::F983-1NF::F850-4NF::M628-2NF::F849-5NF::F947-2NF::M920-4NF::F968-6NF::M1008-2NF::M1013-4NF::F850-7NF::M624-7NF::F648-3NF::F1027-1NF::F1026-4NF::F760-5NF::F1026-3NF::F849-7NF::F957-12NF::F959-9NF::M952-3NF::F969-2NF::M988-4NF::F969-7NF::M920-5NF::F1027-2NF::M952-2NF::M988-8NF::F735-7NF::F885-3NF::F624-4NF::M920-3NF::F976-2NF::F849-6NF::F802-3NF::F849-3NF::F1027-10NF::F879-6NF::F1027-9NF::F959-6NF::F841-1NF::F624-3NF::M624-6NF::F877-2NF::F757-1NF::M920-2NF::F994-7NF::F1027-3NF::M1025-1NF::F885-1NF::M724-3NF::F695-1NF::F729-6NF::F601-NF::M1013-5NF::F849-1NF::F994-2NF::F802-1NF:: +175 chr3:48804200-49004200 0 0 No results within 2500 bp window ::M1013-1NF::F757-3NF::F1026-7NF::F884-2NF::M1025-1NF::F968-1NF::F991-1NF::M988-1NF::F983-1NF::M878-2NF::M626-1NF::F850-8NF::F729-3NF::F991-4NF::F947-2NF::M626-2NF::M732-6NF::F849-5NF::F695-2NF::F879-4NF::F1027-10NF::F1027-4NF::F879-1NF::M624-3NF::F802-5NF::M626-10NF::F947-3NF::F976-2NF::F695-4NF::F957-12NF::M624-6NF::M892-9NF::F695-1NF::F1027-5NF::M920-1NF::F1027-1NF::F968-5NF::M1013-3NF::F802-2NF::M878-6NF::F757-1NF::F991-3NF::F959-3NF::F957-2NF::F760-1NF::M628-2NF::F969-4NF::M892-2NF::F735-5NF::M988-2NF::F771-5NF::M988-5NF::F976-9NF::F969-5NF::F735-6NF::F959-2NF::F957-10NF::F760-2NF::M1008-2NF::F850-3NF::F947-4NF::M920-2NF::M1008-5NF::F877-4NF::M988-6NF::F959-9NF::F648-5NF::M851-3NF::F849-2NF::M952-3NF::F735-1NF::M988-3NF::F802-4NF::M626-4NF::F735-4NF::F885-2NF::M988-8NF::M988-7NF::F879-5NF::M878-5NF::F991-5NF::F879-2NF::F957-11NF::M952-4NF::M851-1NF::F648-3NF::M624-4NF::F1026-6NF::M892-5NF::F1026-2NF::F976-16NF::F850-1NF::F976-8NF::F1026-5NF::F1026-4NF::F968-4NF::F652-NF::F959-8NF::M624-7NF::M892-8NF::F1026-10NF::M952-1NF::M892-3NF::F968-6NF::M724-4NF::M1008-1NF::M732-4NF::F947-1NF::M626-6NF::M1013-4NF::M732-5NF::M851-2NF::F1026-1NF::M892-4NF::M892-10NF::M626-9NF::M624-2NF::F957-9NF::F969-9NF::F1027-9NF::F850-2NF::F695-3NF::F624-1NF::M920-5NF::F969-10NF::F841-6NF::F968-2NF::F959-6NF::F648-4NF::F1026-8NF::M626-11NF::M878-4NF::F850-7NF::F1023-NF::F624-3NF::F969-3NF::M892-7NF::F649-3NF::F976-5NF::F1027-3NF::F850-6NF::F969-1NF::F957-3NF::M878-1NF::F735-3NF::F991-2NF::F841-4NF::M920-4NF::M1008-4NF::F737-NF::F735-7NF::M724-5NF::F760-4NF::F850-4NF::M724-3NF::F959-10NF::F624-4NF::F796-NF::F884-3NF::F771-2NF::F841-5NF::F957-1NF::M626-7NF::M624-1NF::M624-8NF::F760-5NF::M626-3NF::F885-3NF::F841-2NF::F735-2NF::F976-11NF::F760-3NF::F969-6NF::F1027-2NF::F983-2NF:: +233 chr2:98467900-98517900 0 0 AL837506.2, AL837506.1, ::F850-8NF::M988-2NF::M624-2NF::F968-1NF::F729-4NF::F648-5NF::M988-1NF::F1026-5NF::F969-8NF::M1013-4NF::M624-3NF::M732-6NF::F1026-10NF::F802-2NF::F1026-7NF::F968-3NF::F983-2NF::M626-2NF::M1025-1NF::F1026-9NF::M1013-5NF::M1008-1NF::F969-3NF::F648-2NF::F957-11NF::M724-3NF::F757-1NF::F991-4NF::F760-6NF::M1008-4NF::M892-10NF::F1026-8NF::M892-2NF::M626-6NF::M878-5NF::M724-4NF::F957-2NF::F1026-6NF::M988-6NF::F729-2NF::F959-9NF::M892-11NF::M952-4NF::F760-4NF::F796-NF::F879-5NF::F884-3NF::F983-1NF::M988-9NF::M626-4NF::F959-8NF::M988-7NF::F652-NF::F1027-8NF::M988-8NF::F850-5NF::F735-4NF::F624-4NF::M626-8NF::F1027-4NF::F1026-4NF::F969-10NF::F968-6NF::M626-11NF::M1008-5NF::F624-3NF::M732-5NF::M626-7NF::F969-6NF::M878-6NF::M626-10NF::F959-4NF::M851-2NF::M878-2NF::M1013-1NF::M988-5NF::F969-2NF::F1027-7NF::F850-6NF::M920-2NF::M624-6NF::F1027-9NF::F850-4NF::F959-1NF::F850-3NF::F991-2NF::M724-1NF::M920-5NF::F969-5NF::M988-3NF::F884-2NF::F735-7NF::F968-2NF::F991-1NF::F976-11NF::F885-3NF::F976-16NF::F841-1NF::M732-4NF::F877-5NF::M952-1NF::F729-6NF::F1027-10NF::M628-2NF::F877-4NF::M732-2NF::M626-1NF::F991-3NF::F729-5NF::F648-4NF::F624-1NF::F802-5NF::F969-7NF::F957-12NF::F1026-2NF::M724-6NF::F991-5NF::F959-6NF::F1027-5NF::F695-2NF::M624-1NF::F959-2NF::F1027-1NF::M952-3NF::F885-2NF::M892-3NF::F729-3NF::F957-10NF::F850-1NF::F976-1NF::F757-3NF::M851-3NF::F695-3NF::F877-3NF::M624-7NF::F969-4NF::F735-3NF::M878-3NF::F885-1NF::F735-2NF::F649-3NF::F1023-NF::F695-1NF::M920-3NF::M624-5NF::M892-9NF::M724-5NF::M624-8NF::F841-2NF::F968-4NF::F957-9NF::F879-6NF::M892-4NF::F735-6NF::F841-5NF::M920-1NF::F976-8NF::F802-4NF::F968-5NF::F957-3NF::M624-4NF::F771-5NF::F695-4NF::F947-2NF::M910-1NF::F947-3NF::M626-3NF::M1013-3NF::F947-4NF::F957-1NF::F884-1NF::M892-8NF::M724-2NF::F1027-3NF::F760-2NF::F879-4NF::M920-4NF::F648-1NF::M988-4NF::F841-6NF::F877-2NF::M626-9NF::F959-10NF::M1022-13NF::F760-5NF::F1027-2NF::M892-6NF::F704-NF::F1026-1NF::F1027-6NF::F624-5NF::M952-2NF::M851-1NF::M1013-2NF::F850-7NF::F959-7NF::M732-3NF::F959-5NF::F850-2NF::F729-1NF::F1026-3NF::F969-1NF::M892-7NF::F802-6NF::M1008-2NF::F976-4NF::F879-1NF::F879-2NF::F737-NF::F947-5NF::F735-1NF::F841-4NF::F976-3NF::F648-3NF::F969-9NF::F976-9NF::F976-7NF::F624-6NF::F735-5NF::F760-3NF::F976-6NF::F760-1NF::M892-5NF::F959-3NF::F877-1NF::M626-5NF::F947-1NF::F771-2NF::M878-1NF::F802-3NF::F849-2NF::F976-2NF::F849-5NF:: +177 chr6:103466000-103666000 0 0 Chl1, U7, ::M626-1NF::F969-3NF::F1026-6NF::F850-8NF::M624-2NF::F879-5NF::F969-8NF::F969-5NF::M626-8NF::F959-9NF::F969-2NF::F850-7NF::F760-2NF::F969-10NF::M626-6NF::F850-4NF::M988-1NF::F885-3NF::F1026-8NF::M626-11NF::M624-7NF::F850-2NF::F976-16NF::F1027-4NF::F850-1NF::F1023-NF::M628-2NF::M952-3NF::F735-6NF::M626-5NF::M988-6NF::F648-5NF::M626-10NF::M624-4NF::M1008-5NF::F976-11NF::F695-2NF::F760-1NF::F648-4NF::F959-2NF::F695-4NF::F1026-10NF::M988-7NF::F735-3NF::F729-4NF::F885-2NF::M892-10NF::M624-3NF::F648-2NF::M1013-1NF::F947-3NF::M892-1NF::F695-3NF::F877-3NF::F959-8NF::F841-1NF::M878-6NF::F957-10NF::F624-3NF::F879-2NF::F802-6NF::M952-1NF::F760-4NF::M732-4NF::F968-2NF::M988-5NF::M892-3NF::M624-6NF::F959-10NF::F624-1NF::M892-11NF::F968-6NF::M626-4NF::F735-7NF::M851-3NF::F757-3NF::F983-1NF::M892-7NF::F841-4NF::F957-1NF::M626-2NF::F1026-1NF::F957-9NF::M988-4NF::F879-6NF::F959-1NF::F879-1NF::M1008-4NF::M920-1NF::F1027-7NF::M624-5NF::M724-6NF::F991-4NF::F649-3NF::M724-1NF::F771-5NF::M624-8NF::F877-5NF::M988-2NF::F1026-2NF::F959-7NF::F968-1NF::F877-4NF::F735-4NF::M920-2NF::F1027-8NF::M952-4NF::M724-5NF::F729-6NF::M724-2NF::M851-2NF::F1027-6NF::F976-8NF::F976-1NF::F991-2NF::F735-2NF::M988-3NF::F947-4NF::M952-2NF::M626-3NF::F1026-5NF::F885-1NF::M1022-13NF::F1027-5NF::F991-5NF::F1026-4NF::F760-6NF::F1027-10NF::M920-3NF::F1026-7NF::M878-2NF::F1027-1NF::F969-6NF::F841-5NF::M878-5NF::F976-6NF::M1013-4NF::M892-8NF::F1027-2NF::F968-5NF::F695-1NF::F737-NF::F796-NF::F968-3NF::M626-9NF::F959-4NF::F983-2NF::F991-1NF::F850-6NF::F1027-9NF::M732-6NF::M892-2NF::F884-2NF::M1025-1NF::F760-3NF::F969-4NF::F957-11NF::F802-4NF::F729-2NF::M988-8NF::F969-1NF::M988-9NF::M920-5NF::F947-2NF::F968-4NF::F959-6NF::F879-4NF::F757-1NF::F850-3NF::F771-2NF::F624-4NF::M1013-3NF::M892-5NF::F994-3NF::M732-5NF::F957-2NF::M892-4NF:: +201 chr13:31676400-31776400 0 0 RP23-467M8.2, Foxf2, RP23-322J11.2, 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+173 chrX:139717900-139917900 0 0 Chrdl1, SNORA17, ::F735-3NF::M626-6NF::F735-1NF::F959-6NF::F695-3NF::F968-4NF::F957-3NF::F735-6NF::F991-4NF::F968-2NF::F841-1NF::F648-2NF::M892-10NF::F624-3NF::F968-6NF::F959-9NF::F976-11NF::F959-2NF::F991-5NF::M626-8NF::M1013-1NF::F884-2NF::F969-1NF::F1027-2NF::F850-3NF::M628-2NF::M624-3NF::M624-5NF::F735-2NF::F796-NF::M626-1NF::M624-6NF::F760-2NF::M1025-1NF::F983-2NF::M878-5NF::M724-4NF::M724-2NF::F947-4NF::F850-8NF::M626-2NF::M892-8NF::F885-2NF::M920-4NF::M920-1NF::F957-11NF::F802-4NF::M1013-5NF::F957-9NF::M952-3NF::F877-4NF::M626-3NF::F968-5NF::M952-2NF::F1026-10NF::F1027-1NF::M952-1NF::M724-6NF::F877-3NF::M892-1NF::F704-NF::F879-5NF::F1027-5NF::M920-3NF::F969-3NF::F771-5NF::F648-4NF::F729-2NF::F1026-5NF::M988-2NF::M988-7NF::F969-8NF::F1026-8NF::F1026-9NF::F757-1NF::F879-1NF::F959-1NF::M1008-3NF::F624-1NF::M624-8NF::F968-3NF::F1027-4NF::M988-3NF::M626-11NF::F737-NF::M724-1NF::F983-1NF::F802-5NF::M892-3NF::F879-2NF::F649-3NF::F841-6NF::M988-6NF::F976-16NF::F850-6NF::M988-8NF::M626-9NF::F760-6NF::M878-6NF::M626-5NF::F991-1NF::F1026-1NF::M892-7NF::F969-10NF::M624-4NF::F959-10NF::F947-5NF::F735-4NF::F695-4NF::F879-4NF::M920-2NF::M626-7NF::F1023-NF::F1026-4NF::M988-4NF::F652-NF::F1027-8NF::F991-2NF::F1027-7NF::F695-2NF::M1008-4NF::M988-9NF::M988-1NF::F1027-9NF::M988-5NF::M920-5NF::M732-4NF::F947-2NF::F802-6NF::F695-1NF::F969-5NF::F850-2NF::F841-4NF::F757-3NF::M624-1NF::F1026-7NF::M1008-5NF::M1008-1NF::F969-2NF::M724-5NF::F976-3NF::M892-11NF::M1013-4NF::M724-3NF::F735-7NF::M892-5NF::M851-2NF::M1013-3NF::M1008-2NF::F760-1NF::F760-3NF::F885-3NF::F959-8NF::F969-9NF::F957-2NF::F976-4NF::M878-2NF::F1026-6NF::F884-1NF::M851-3NF::M624-2NF::F959-5NF::F969-6NF::M878-3NF::F968-1NF::F959-4NF::F947-3NF::M624-7NF::F648-5NF::F976-8NF::M626-4NF::M732-6NF::F957-1NF:: +212 chr9:3000000-3100000 0 0 AC131780.5, AC131780.8, AC131780.9, AC131780.1, AC131780.11, AC131780.3, AC131780.7, AC131780.2, AC131780.4, AC131780.6, AC131780.12, AC131780.10, ::M878-5NF::F850-2NF::F957-9NF::F947-5NF::F1027-4NF::F884-1NF::M988-3NF::F879-2NF::M1013-4NF::M1008-5NF::F959-8NF::M626-4NF::F1026-7NF::M878-6NF::F991-5NF::F1027-7NF::F947-3NF::M626-6NF::M1008-1NF::F983-1NF::M988-1NF::F879-5NF::F879-4NF::M624-6NF::F695-4NF::F695-2NF::M952-2NF::M724-5NF::F957-2NF::M626-11NF::M624-3NF::F1027-5NF::F735-2NF::F735-4NF::F877-1NF::F968-4NF::F1026-6NF::M988-6NF::F968-3NF::F884-2NF::F957-12NF::M724-6NF::M920-2NF::F969-3NF::M988-7NF::F1027-2NF::F624-3NF::M1025-1NF::F673-3NF::F959-1NF::F983-2NF::M952-3NF::F885-3NF::F969-4NF::F729-2NF::F760-4NF::F1026-1NF::F735-7NF::M624-2NF::F976-8NF::F624-1NF::M724-2NF::M732-4NF::F850-8NF::M626-2NF::F968-2NF::M878-2NF::M892-10NF::F968-1NF::F959-9NF::F969-6NF::F991-4NF::F969-8NF::M1008-4NF::F877-4NF::F802-6NF::F652-NF::F729-5NF::F648-2NF::M624-4NF::F969-5NF::M1013-5NF::F1027-1NF::F1026-9NF::F959-2NF::F968-6NF::F850-5NF::M628-2NF::M920-3NF::F884-3NF::F841-1NF::M952-1NF::M624-7NF::F735-6NF::F757-1NF::F802-3NF::F957-10NF::M920-1NF::F757-3NF::F959-3NF::F735-3NF::M892-8NF::F1023-NF::F947-4NF::F991-1NF::F841-2NF::M920-4NF::F648-3NF::M851-3NF::F968-5NF::M988-4NF::M878-3NF::F969-7NF::M952-4NF::F976-1NF::F877-5NF::F879-1NF::F1027-8NF::F991-3NF::F969-10NF::F648-5NF::M1013-1NF::F1026-5NF::M988-5NF::F947-1NF::F1027-3NF::M988-2NF::F1027-6NF::M920-5NF::M892-3NF::M624-5NF::M1013-2NF::F760-5NF::F991-2NF::M892-4NF::F849-2NF::F969-9NF::M732-3NF::M1013-3NF::F957-1NF::M892-9NF::F771-5NF::F1026-10NF::F885-2NF::F695-1NF::M724-3NF::F624-5NF::F976-2NF::F969-2NF::M732-5NF::M626-8NF::F737-NF::F877-3NF::M892-7NF::F976-3NF::M626-3NF::F850-7NF::F1026-8NF::M732-2NF::M626-7NF::F1026-3NF::F1027-9NF::F879-6NF::F735-1NF::M892-11NF::M988-8NF::F760-3NF::M732-6NF::F850-6NF::M624-8NF::M988-9NF::F976-11NF::F959-4NF::F624-4NF::F841-4NF::F976-16NF::M851-2NF::F957-11NF::F959-10NF::F959-7NF::F802-4NF::F959-6NF::M851-1NF::F760-6NF::M626-1NF::F648-4NF::F649-3NF::F1026-4NF::F1026-2NF::F976-4NF::F695-3NF::F729-4NF::F841-6NF::F850-3NF::F947-2NF::M724-4NF::F841-5NF::F771-2NF::F704-NF::M892-2NF::F1027-10NF::F802-5NF::F729-3NF::M1022-13NF::F760-2NF::F850-1NF::F729-1NF::F796-NF::M724-1NF::M626-9NF::M624-1NF::F976-7NF:: +138 chr3:31845000-31857500 3.74837902630147e-171 8.97249487525783e-167 Kcnmb2, ::F947-5NF::F849-7NF::M920-2NF::M988-3NF::F959-6NF::M988-6NF::F841-5NF::F648-4NF::F879-5NF::F969-10NF::M892-10NF::F850-7NF::M988-7NF::F1026-6NF::M626-6NF::F976-5NF::F760-2NF::M878-2NF::F1026-4NF::M952-1NF::F695-4NF::M878-4NF::M892-8NF::F976-2NF::M624-2NF::F957-11NF::F959-8NF::M626-2NF::F1026-1NF::F849-2NF::F976-8NF::F879-2NF::M624-3NF::M732-5NF::F879-1NF::F729-3NF::F760-4NF::F850-1NF::M892-2NF::M892-9NF::F947-1NF::F735-5NF::F771-5NF::F841-6NF::M1022-13NF::M892-7NF::F957-1NF::F969-1NF::F1027-3NF::F735-6NF::F968-5NF::F947-4NF::M920-5NF::F879-4NF::F760-5NF::F884-2NF::F849-5NF::F991-4NF::M626-11NF::F991-5NF::M1013-3NF::F976-16NF::F771-2NF::F648-5NF::F1027-10NF::M626-10NF::F957-9NF::M626-9NF::M851-2NF::F850-8NF::F968-4NF::F796-NF::F648-3NF::F991-2NF::F1026-8NF::F649-3NF::F802-2NF::M624-4NF::F959-9NF::F850-3NF::F757-3NF::F957-12NF::M626-7NF::M952-4NF::F957-2NF::F976-9NF::F1027-5NF::F624-1NF::M626-4NF::F695-3NF::M626-1NF::F885-2NF::F957-10NF::M988-2NF::F969-3NF::F624-4NF::M624-1NF::M732-6NF::F735-3NF::F1023-NF::M724-3NF::F757-1NF::M920-4NF::M1025-1NF::F802-5NF::F968-2NF::F976-11NF::F695-1NF::F968-6NF::F983-1NF::F729-4NF::F959-10NF::M892-3NF::F850-6NF::F735-4NF::M624-8NF::M920-1NF::M628-2NF::M626-3NF::M878-5NF::F624-3NF::F1026-7NF::F947-2NF::F1026-10NF::F969-5NF::M892-5NF::M892-4NF::F735-2NF::F959-2NF::F1027-9NF::M878-1NF::F947-3NF::F1026-2NF::F968-1NF::F841-4NF::M988-5NF::M851-1NF::F969-8NF:: +134 chr9:3733700-3746200 1.41346846444311e-164 3.38341946333747e-160 Gucy1a2, ::F959-7NF::M892-10NF::M988-8NF::M626-8NF::M1022-13NF::F757-3NF::F969-1NF::F968-1NF::F850-3NF::F957-10NF::F850-6NF::F991-5NF::M626-2NF::F695-1NF::F947-3NF::F849-5NF::F969-8NF::M892-3NF::M626-11NF::M851-2NF::M851-3NF::F969-9NF::F849-7NF::F957-9NF::F885-2NF::F735-4NF::F969-10NF::F879-1NF::F1026-8NF::M892-2NF::M988-1NF::F959-3NF::M952-3NF::F879-5NF::F624-1NF::M626-3NF::M732-6NF::F850-1NF::F976-11NF::F735-7NF::F884-2NF::M892-8NF::F760-5NF::F1023-NF::F735-2NF::F959-2NF::F760-4NF::M988-7NF::F991-2NF::F737-NF::F735-3NF::M988-5NF::F957-2NF::M1008-2NF::F624-4NF::F841-4NF::M624-6NF::F968-6NF::F802-3NF::F1026-10NF::M988-2NF::F796-NF::F850-8NF::F771-2NF::F885-1NF::M920-2NF::M988-9NF::F983-2NF::M626-5NF::M724-2NF::M624-3NF::M920-4NF::F1027-10NF::F757-1NF::M892-4NF::F649-3NF::F969-5NF::F1026-5NF::F735-1NF::M626-6NF::F877-5NF::F1026-6NF::F959-5NF::F695-3NF::F1026-7NF::M878-3NF::F735-6NF::F1026-4NF::F976-7NF::F624-3NF::M1008-1NF::F879-2NF::M626-9NF::F959-8NF::M624-7NF::F1026-2NF::F1027-7NF::M1008-5NF::M1013-3NF::F648-4NF::F959-9NF::F802-4NF::F957-11NF::M920-1NF::M878-6NF::F969-3NF::F652-NF::F959-10NF::M1013-2NF::M626-1NF::F1027-9NF::F947-2NF::M732-4NF::M628-2NF::M1008-4NF::F959-6NF::M892-1NF::F735-5NF::M724-6NF::M724-3NF::F760-6NF::M626-4NF::M892-11NF::F968-2NF::F968-4NF::F983-1NF::F959-1NF::M626-7NF::M952-2NF::F850-2NF::F947-1NF::F884-3NF::M624-2NF::F947-4NF:: +113 chr11:36758000-36770500 6.16719810266137e-131 1.47624220983405e-126 Odz2, ::M892-1NF::F884-3NF::M724-6NF::F695-2NF::F877-3NF::F1026-8NF::M624-2NF::F976-11NF::F1026-10NF::M1008-2NF::F760-4NF::F849-7NF::F850-6NF::F968-6NF::M988-1NF::F976-7NF::F947-1NF::F802-4NF::F885-1NF::F969-8NF::M1013-1NF::F648-2NF::F1027-1NF::M626-3NF::M724-3NF::F968-2NF::F968-1NF::F1023-NF::F959-2NF::M626-7NF::F850-1NF::F850-3NF::F957-2NF::M626-11NF::F695-3NF::F1027-10NF::M626-1NF::M892-4NF::M724-2NF::F983-2NF::F969-10NF::F735-7NF::F947-4NF::F1026-7NF::M1022-13NF::F1026-2NF::F757-3NF::M851-3NF::M724-1NF::M1013-2NF::F991-5NF::M626-9NF::F959-5NF::M732-4NF::M626-2NF::M732-5NF::F991-2NF::M1013-3NF::F957-11NF::F879-1NF::F624-1NF::M626-6NF::F771-2NF::M892-3NF::M920-4NF::M988-7NF::F652-NF::F957-9NF::F957-3NF::F735-3NF::F957-10NF::F649-3NF::F959-10NF::M892-8NF::F884-2NF::F1026-4NF::F757-1NF::F968-4NF::M988-5NF::F885-2NF::F877-5NF::F735-4NF::F959-1NF::F1027-7NF::F879-4NF::F947-2NF::F969-5NF::F624-4NF::M892-11NF::F983-1NF::F969-3NF::F760-5NF::M732-6NF::M878-5NF::F802-3NF::F1026-6NF::F695-1NF::M878-3NF::M920-1NF::F841-1NF::F1026-5NF::M1008-5NF::M624-1NF::M952-3NF::F735-1NF::M988-9NF::M626-4NF::F850-2NF::F735-5NF::M892-10NF::F849-5NF::F1027-9NF::F735-2NF:: +109 chr1:147277600-147290100 1.03530979547173e-124 2.47822105742067e-120 No results within 2500 bp window ::F735-2NF::F969-10NF::F850-8NF::F735-4NF::M724-3NF::F959-5NF::M920-2NF::M988-2NF::M920-4NF::F648-3NF::M724-6NF::F976-11NF::F969-5NF::F695-3NF::F947-4NF::M851-3NF::F729-6NF::M1025-1NF::F879-4NF::F624-1NF::F1027-2NF::M724-2NF::F1027-7NF::F969-8NF::M1008-1NF::F959-1NF::F957-1NF::M626-1NF::M626-10NF::F959-4NF::F959-2NF::F991-5NF::F850-5NF::F802-6NF::F735-5NF::F624-3NF::F1026-7NF::M952-4NF::F947-3NF::M892-10NF::M988-5NF::F969-2NF::F1027-4NF::M988-6NF::M878-4NF::F735-1NF::F796-NF::M920-5NF::M732-4NF::M626-3NF::F968-1NF::F695-2NF::M988-7NF::F957-10NF::F877-4NF::F1027-6NF::M988-1NF::F729-2NF::M624-1NF::F968-6NF::F969-9NF::F968-2NF::F991-1NF::F969-1NF::M624-6NF::F735-7NF::F648-4NF::M624-7NF::F601-NF::F877-3NF::F648-5NF::M732-6NF::M1008-5NF::F976-16NF::F957-11NF::F947-2NF::F957-2NF::F879-1NF::F879-5NF::M851-2NF::F624-4NF::F760-4NF::F947-1NF::M920-1NF::F983-2NF::F850-7NF::F760-2NF::F879-2NF::M628-2NF::F729-4NF::M878-5NF::F1026-8NF::F757-1NF::F884-2NF::F735-6NF::F729-1NF::M1013-5NF::F1026-10NF::F771-5NF::F969-3NF::F976-9NF::F884-3NF::F991-2NF::M624-3NF::F1026-6NF::F885-3NF::M626-4NF::M892-2NF::M878-2NF:: +94 chr17:35136100-35148600 5.93072890935882e-102 1.41963857903322e-97 Vars, ::F760-4NF::M952-2NF::F957-3NF::M892-11NF::M1013-4NF::M892-7NF::F624-3NF::M624-4NF::F976-3NF::F729-3NF::F850-5NF::M624-1NF::M988-1NF::F1023-NF::M626-1NF::F841-2NF::F624-1NF::F879-6NF::F1026-5NF::M626-2NF::M892-2NF::F969-1NF::F976-1NF::M851-2NF::F983-1NF::M988-8NF::F885-2NF::M892-9NF::F884-2NF::M952-3NF::F1026-10NF::F877-3NF::F695-2NF::F969-4NF::M892-6NF::F1027-7NF::F885-3NF::M724-4NF::M624-6NF::F877-6NF::F959-1NF::F729-1NF::M952-4NF::F957-11NF::M878-3NF::M626-11NF::F1027-10NF::F1026-2NF::F695-4NF::M626-4NF::F959-5NF::F648-2NF::F735-4NF::M624-2NF::F850-4NF::F879-5NF::F760-1NF::M851-3NF::F969-9NF::F957-2NF::F729-4NF::F729-5NF::F959-3NF::M988-3NF::F704-NF::F884-1NF::F991-2NF::M988-9NF::F802-5NF::M724-6NF::F760-2NF::F957-1NF::F968-4NF::F695-3NF::F976-11NF::F879-2NF::M724-1NF::M626-9NF::M626-7NF::F976-4NF::M624-5NF::F947-2NF::M724-3NF::F976-6NF::F879-4NF::M732-2NF::F877-1NF::F735-1NF::F648-1NF::F729-2NF::M626-6NF::F959-2NF::M878-1NF::F1026-4NF:: +94 chr9:35107800-35120300 5.93072890935882e-102 1.41963857903322e-97 No results within 2500 bp window ::F624-1NF::M851-2NF::M920-2NF::F879-5NF::M878-5NF::M1013-2NF::F648-2NF::M988-1NF::M626-10NF::M624-7NF::M952-2NF::F1026-7NF::F735-4NF::M878-2NF::M732-3NF::M732-4NF::M724-1NF::F976-8NF::F991-5NF::M624-6NF::F1027-4NF::M624-4NF::F802-5NF::F1027-1NF::F969-3NF::M624-3NF::F757-3NF::F771-5NF::F802-6NF::F976-3NF::F976-1NF::M892-8NF::F850-8NF::M1013-3NF::F959-8NF::M988-5NF::M624-8NF::F885-2NF::F802-4NF::F735-7NF::F850-3NF::F735-2NF::F648-4NF::F983-2NF::F1026-5NF::F947-3NF::M732-2NF::F652-NF::F735-6NF::F1026-6NF::M878-6NF::F885-3NF::F1026-8NF::M892-10NF::M724-4NF::M626-8NF::F976-16NF::M626-11NF::F968-1NF::F729-2NF::M851-3NF::M1008-5NF::F1023-NF::F1026-9NF::F849-5NF::M626-6NF::F760-6NF::F983-1NF::M892-3NF::M988-7NF::F968-2NF::F968-6NF::F991-1NF::M724-6NF::F957-1NF::F969-5NF::M952-1NF::F760-5NF::M724-2NF::F969-9NF::F959-6NF::F1027-2NF::F1027-9NF::M624-2NF::M988-6NF::F695-2NF::F648-5NF::F879-4NF::F991-4NF::F624-5NF::M988-2NF::F1026-10NF::M626-2NF::M1025-1NF:: +111 chr3:158241700-158266700 9.53860407641406e-96 2.28325565777123e-91 No results within 2500 bp window ::F957-11NF::M878-5NF::M892-10NF::F991-5NF::F735-7NF::F957-2NF::M626-2NF::F850-3NF::F760-4NF::F969-6NF::F1027-5NF::M952-1NF::M988-9NF::F959-9NF::M1013-4NF::F991-4NF::F957-12NF::F695-4NF::M1013-5NF::M878-6NF::M624-8NF::M988-3NF::F695-2NF::F1027-2NF::M626-4NF::F885-3NF::F648-1NF::M988-5NF::F735-4NF::M988-1NF::F1023-NF::F841-1NF::F796-NF::M624-4NF::F841-2NF::M1008-4NF::F983-2NF::M732-6NF::F947-4NF::M626-6NF::M1025-1NF::F802-5NF::F757-3NF::F976-3NF::F802-6NF::F884-1NF::F737-NF::F1026-7NF::F624-3NF::F959-1NF::F648-4NF::F760-2NF::F648-2NF::F1026-10NF::M624-1NF::F968-3NF::F757-1NF::F976-8NF::M1013-3NF::F771-5NF::F885-1NF::F983-1NF::F969-8NF::F957-1NF::F695-3NF::M724-3NF::F652-NF::F1026-8NF::F879-4NF::M988-2NF::F735-2NF::F879-5NF::F877-4NF::F879-6NF::F969-2NF::F841-6NF::F850-8NF::M878-2NF::M626-11NF::F947-5NF::F1026-5NF::M988-6NF::F968-1NF::M624-6NF::F1027-8NF::F991-2NF::F704-NF::M988-7NF::M1013-1NF::F648-5NF::F969-3NF::F976-5NF::M1008-5NF::F959-6NF::M892-8NF::F959-2NF::F649-3NF::M624-3NF::M626-8NF::M988-8NF::M952-3NF::F969-4NF::F885-2NF::F735-6NF::F968-6NF::M626-7NF::M851-1NF::F969-10NF::F850-1NF::M724-4NF::M624-2NF:: +89 chr1:81516800-81529300 1.3701038028454e-94 3.27961747287104e-90 No results within 2500 bp window ::M724-2NF::F957-2NF::M624-2NF::F802-4NF::M892-10NF::F1027-2NF::M1013-3NF::F976-2NF::M952-2NF::M1013-2NF::F1026-7NF::F959-10NF::F802-3NF::M988-6NF::F735-3NF::F969-6NF::F850-1NF::F735-2NF::M892-3NF::F760-5NF::F969-4NF::M628-2NF::M626-2NF::M910-4NF::F976-4NF::F968-5NF::M624-6NF::F648-5NF::F969-8NF::M1013-1NF::F760-6NF::F1026-5NF::M910-2NF::F947-3NF::F649-3NF::F771-2NF::F673-3NF::F760-4NF::M624-7NF::M724-6NF::F994-7NF::F994-6NF::F994-5NF::F959-5NF::F959-9NF::F735-4NF::F957-11NF::F976-11NF::F849-2NF::F648-3NF::F652-NF::F1027-9NF::M892-7NF::F796-NF::M626-8NF::F1027-4NF::F968-3NF::F757-3NF::F850-3NF::F991-5NF::F983-2NF::M892-1NF::F879-1NF::F850-7NF::F850-6NF::M892-8NF::F994-1NF::F983-1NF::M732-5NF::F994-4NF::M988-5NF::M626-6NF::F648-2NF::M624-8NF::F994-8NF::F1027-3NF::F994-3NF::M552-NF::F957-9NF::F969-3NF::F1023-NF::M988-7NF::F968-1NF::F1026-10NF::F1027-5NF::F729-4NF::F885-2NF::F695-2NF::M878-2NF:: +85 chr9:25341200-25353700 8.72196115890513e-89 2.08777584260712e-84 Eepd1, SNORA70, ::M1013-2NF::M724-3NF::F757-3NF::F968-6NF::F968-3NF::M878-2NF::M624-4NF::F849-2NF::M624-8NF::F695-2NF::F884-2NF::M732-4NF::M892-6NF::F760-1NF::M920-5NF::F1026-1NF::F735-7NF::F849-1NF::F649-3NF::F968-1NF::F994-2NF::M910-4NF::F968-5NF::F802-5NF::F959-10NF::F994-1NF::F959-2NF::F991-5NF::M1013-3NF::F1026-9NF::M892-3NF::M988-1NF::F624-4NF::F695-3NF::F850-3NF::F879-1NF::M628-2NF::M626-8NF::F802-4NF::M910-2NF::F648-5NF::M910-1NF::F994-8NF::M892-7NF::F994-7NF::M988-6NF::M892-2NF::F735-4NF::M732-1NF::M1008-5NF::F994-3NF::M892-10NF::F648-2NF::F1023-NF::F879-6NF::F673-3NF::F850-1NF::F947-3NF::F735-3NF::M626-1NF::F771-5NF::F968-2NF::F1027-2NF::F1027-6NF::F729-4NF::M626-10NF::M624-3NF::F994-4NF::M626-7NF::F695-1NF::F624-1NF::F771-2NF::F850-6NF::F1027-3NF::M952-4NF::F957-9NF::M1013-1NF::F991-3NF::F994-6NF::M552-NF::M624-7NF::F729-3NF::F994-5NF::M1008-1NF::M988-7NF:: +79 chr8:62564800-62577300 3.10981641472006e-80 7.4439675519154e-76 No results within 2500 bp window ::F1026-5NF::F802-5NF::M878-2NF::M624-2NF::F957-12NF::F983-1NF::F735-7NF::M988-3NF::F649-3NF::F879-4NF::F885-1NF::F704-NF::F850-1NF::F1027-5NF::F991-4NF::F760-4NF::M1025-1NF::M1013-1NF::F879-6NF::M732-6NF::F969-4NF::F737-NF::M1008-5NF::M624-6NF::F648-5NF::M624-4NF::M988-1NF::F695-4NF::M892-10NF::F947-5NF::F1027-8NF::F850-3NF::F841-2NF::F1026-10NF::F957-2NF::F969-2NF::F991-2NF::F841-1NF::M988-7NF::M1008-4NF::F735-6NF::F885-2NF::M724-3NF::M1013-3NF::M878-6NF::F969-8NF::F983-2NF::F884-1NF::M724-4NF::F648-4NF::F735-4NF::F757-1NF::M851-1NF::F841-6NF::F976-8NF::F1026-8NF::F969-3NF::F771-5NF::F957-1NF::M626-7NF::F968-3NF::M988-2NF::F760-2NF::F969-6NF::M988-9NF::M626-3NF::F959-2NF::F648-2NF::M892-8NF::F885-3NF::M624-1NF::F1027-2NF::F624-3NF::F850-8NF::M988-6NF::F648-1NF::M952-3NF::F760-1NF::F968-2NF:: +78 chr9:52992800-53005300 7.93148334036717e-79 1.89855916718369e-74 Ddx10, ::M626-11NF::F802-5NF::F969-3NF::F802-6NF::F735-2NF::F959-2NF::F969-6NF::F760-2NF::M878-6NF::F994-1NF::F968-5NF::M988-5NF::M892-3NF::F994-2NF::F771-5NF::F879-2NF::M910-4NF::M624-1NF::F648-2NF::F850-7NF::M910-1NF::F771-2NF::F976-1NF::F976-2NF::F760-1NF::F735-6NF::F1023-NF::M724-6NF::F760-6NF::F957-9NF::F850-3NF::F947-3NF::M851-3NF::F969-4NF::F850-2NF::F624-4NF::F802-4NF::F969-7NF::M552-NF::M910-2NF::M732-1NF::F652-NF::F695-2NF::F994-6NF::M892-8NF::M626-10NF::F1027-3NF::M952-2NF::M626-6NF::F648-5NF::F624-3NF::F849-4NF::M878-2NF::M988-2NF::F802-3NF::F959-7NF::M1013-1NF::F994-5NF::F1027-2NF::F850-6NF::M626-9NF::M988-6NF::F959-1NF::F735-4NF::M952-4NF::F729-4NF::F850-1NF::F968-1NF::F877-4NF::F994-3NF::F994-7NF::F648-4NF::F994-4NF::F991-4NF::F884-2NF::M626-1NF::M624-2NF::F968-2NF:: +76 chr5:22835400-22847900 4.96506445986629e-76 1.18848747975819e-71 No results within 2500 bp window ::M878-1NF::F1027-8NF::F994-6NF::F735-2NF::F959-1NF::F968-1NF::F976-16NF::M732-4NF::M878-5NF::F976-3NF::F735-4NF::F969-6NF::F879-1NF::F735-3NF::F994-1NF::M892-4NF::M626-5NF::F760-6NF::F1023-NF::F994-5NF::M724-6NF::F771-2NF::F850-1NF::M626-10NF::F695-3NF::F802-4NF::M988-7NF::M624-8NF::F959-9NF::M892-6NF::M626-4NF::F729-4NF::F947-2NF::M910-4NF::F968-5NF::M910-1NF::M910-2NF::M626-1NF::M892-3NF::F652-NF::F695-2NF::F994-7NF::M892-8NF::F969-3NF::M624-3NF::F624-3NF::F673-3NF::F994-4NF::F735-7NF::F624-4NF::F601-NF::F1027-2NF::F994-8NF::F957-9NF::M1013-1NF::M626-6NF::F947-4NF::F885-2NF::F849-1NF::M920-3NF::F648-1NF::M988-5NF::F969-1NF::F648-5NF::F994-3NF::M892-11NF::F879-6NF::F968-6NF::F991-5NF::F1027-3NF::F771-5NF::M552-NF::F624-1NF::M732-1NF::M626-8NF::M892-10NF:: +73 chr1:31953200-31965700 7.04707976115755e-72 1.68685948242828e-67 No results within 2500 bp window ::F885-2NF::F877-4NF::M952-1NF::F648-5NF::M724-6NF::M1008-1NF::M732-5NF::F991-2NF::F729-2NF::F991-4NF::F1023-NF::F1026-8NF::F735-3NF::F991-1NF::F1026-7NF::M920-4NF::F968-4NF::F959-6NF::M1025-1NF::F969-10NF::F947-4NF::F879-5NF::F968-2NF::M732-6NF::F695-3NF::F991-5NF::M920-2NF::F947-2NF::F850-3NF::F760-6NF::F885-3NF::F1027-7NF::F959-1NF::M892-4NF::M624-3NF::M878-5NF::M626-8NF::M988-1NF::F1027-10NF::M878-2NF::F735-7NF::F1027-1NF::F959-5NF::M988-2NF::M624-7NF::F968-6NF::F957-9NF::F649-3NF::M988-5NF::M892-10NF::F957-10NF::M892-2NF::F976-9NF::F1027-2NF::M626-1NF::M626-2NF::F757-1NF::F957-11NF::M628-2NF::F737-NF::F947-3NF::M892-3NF::M892-7NF::M1013-1NF::F1027-5NF::F1027-4NF::F884-2NF::F879-1NF::F947-1NF::F735-4NF::F735-5NF::M626-6NF::M626-7NF:: + +PNSTQUINT_0.01library +number pos pvalue bonferroni gene_name library_name + +PNSTQUINT_0.001library +number pos pvalue bonferroni gene_name library_name + +PNSTQUINT_0.0001library +number pos pvalue bonferroni gene_name library_name + +PNSTQUINT_0library +number pos pvalue bonferroni gene_name library_name +77 chr5:28496400-28508900 1.85110014611045e-136 1.81702139242055e-131 En2, ::F812-3P::F806-4P::M930-1P::M988-P::M562P::M930-2P::F812-2P::F957-2P::F983P::M704P::F812-4P::M651-2P::F859P::F704-2P::F756-1P::F947-3P::F879-1P::F715-3P::M570P::F704-1P::M513-2P::F876-2P::M1025P::M565P::F1008-1P::F947-4P::F771-1P::M1022-P::F715-1P::F976-2P::F976-1P::M628-3P::F947-1P::M863P::F884P::F654-1P::F750-2P::F1008-2P::F959-1P::M651-3P::F654-2P::M478-P::F663P::F825-22P::M628-1P::F737-2P::F1026P::F750-1P::F812-1P::F991-P::M741P::F1023-P::F715-2P::M578P::M593P::M725P::F959-2P::F947-2P::F803P::F771-2P::F879-2P::M619-1P::F991P::F876-1P::F654-3P::F1027P::F806-3P::M680P::F825-21P::F649P::F806-1P::M851P::MYSTERY-2P::F879-3P::F806-2P::M513-3P::M950P:: +56 chr10:57312100-57324600 4.70324514632341e-92 4.6166584031796e-87 No results within 2500 bp window ::M851P::F756-2P::M513-4P::F595P::F825-22P::M741P::F976-2P::F976-1P::M628-3P::M651-2P::M513-2P::F959-2P::F704-1P::F991-P::F715-2P::F737-2P::M725P::MYSTERY-1P::M619-2P::M863P::F947-2P::M910P::F947-1P::M930-2P::M478-P::F704-2P::F673-2P::F750-2P::F876-1P::F959-1P::F673-1P::F654-1P::F806-3P::F715-3P::F991P::F812-2P::F825-21P::M988-P::F1008-2P::F806-2P::F756-1P::F884P::M1025P::F771-1P::M513-1P::M680P::F812-1P::F715-1P::F663P::M704P::F806-4P::F859P::F654-2P::F806-1P::M578P::F750-1P:: +51 chr6:69880000-69892500 6.09246199545918e-82 5.98029977012277e-77 AC154006.7, ::M628-1P::F1008-2P::M741P::F825-21P::M478-P::M578P::M930-2P::F806-3P::F750-2P::M1025P::F715-3P::F806-1P::F673-2P::F959-3P::F715-2P::F879-1P::F991P::F959-2P::F737-1P::M513-5P::MYSTERY-1P::M513-1P::F947-3P::F756-2P::M851P::F673-1P::M628-3P::F756-1P::M988-P::F663P::F947-1P::F947-2P::F654-2P::M513-4P::F806-2P::F654-1P::F959-1P::F976-1P::M680P::F812-2P::M910P::F704-2P::F771-1P::F957-2P::M513-2P::F704-1P::F649P::F884P::F859P::F825-22P::F812-1P:: +50 chr2:98500900-98513400 6.06174006714234e-80 5.95014343250625e-75 AL837506.2, AL837506.1, ::F876-2P::F771-1P::F991-P::M570P::F1023-P::F859P::F704-2P::M988-P::M863P::M851P::M1025P::M513-4P::F812-4P::F756-2P::F812-2P::M619-2P::F1026P::F704-1P::F715-3P::F756-1P::F825-22P::F750-1P::M593P::M628-1P::M704P::F715-2P::F737-2P::F812-1P::M725P::F876-1P::F976-1P::M651-3P::M478-P::F812-3P::F976-2P::M1022-P::F947-2P::F947-1P::M578P::M651-2P::F959-1P::F715-1P::F1008-2P::F884P::F959-2P::F806-1P::M741P::F825-21P::M619-1P::F879-2P:: +46 chr2:163461900-163474400 4.85332872335483e-72 4.76397894155787e-67 AL591488.2, 0610039K10Rik, Serinc3, ::F1026P::F1023-P::F704-1P::F879-1P::F750-1P::M988-P::F884P::F812-3P::M628-3P::F806-1P::F715-1P::F737-2P::F983P::M513-5P::F947-1P::M950P::M513-4P::F959-1P::M570P::F991P::M513-2P::M578P::F756-1P::F812-2P::F1008-2P::M930-2P::F750-2P::F825-22P::M1025P::M651-2P::M741P::F825-21P::F812-4P::F649P::F595P::F991-P::M680P::M704P::F715-3P::F879-2P::M1022-P::F756-2P::M725P::F976-2P::F812-1P::F803P:: +45 chr1:81528400-81540900 4.35543808182929e-70 4.27525446674281e-65 No results within 2500 bp window ::F806-3P::F654-1P::M628-3P::F715-3P::F673-1P::F756-1P::M513-2P::F806-1P::M593P::F959-2P::M1025P::F884P::F983P::M741P::M910P::F947-1P::F976-1P::M478-P::M513-5P::F750-1P::F715-2P::F715-1P::F876-1P::F1008-2P::F737-2P::M565P::M499P::F673-2P::M513-3P::F654-2P::MYSTERY-1P::F879-1P::F806-4P::F704-1P::M513-1P::F959-1P::F859P::F825-21P::M851P::F947-3P::F750-2P::F771-1P::F812-1P::F991P::F825-22P:: +50 chr19:32863000-32888000 4.08775169017508e-65 9.7848512207721e-61 Pten, ::M988-P::F879-1P::F715-3P::M704P::F812-3P::F812-2P::F876-2P::F750-1P::F812-1P::F704-1P::M680P::F876-1P::F715-1P::M499P::F806-1P::F991P::F673-2P::F756-1P::F806-4P::F649P::F825-21P::F654-3P::F806-2P::F1008-1P::F806-3P::F879-3P::M578P::F771-2P::F663P::M741P::F983P::M570P::M725P::M1022-P::F1026P::M910P::M619-2P::M651-2P::F947-1P::M930-2P::M930-1P::F825-22P::F715-2P::M851P::F673-1P::M593P::M619-1P::M628-3P::F756-2P::F957-1P:: +40 chr3:48818900-48831400 1.80455515383733e-60 1.77133329345519e-55 No results within 2500 bp window ::F750-2P::F825-22P::F876-1P::M619-2P::M619-1P::M851P::F1026P::F715-2P::M988-P::M1022-P::F771-1P::F991P::F976-2P::F704-1P::F715-1P::M1025P::F812-3P::F806-1P::F663P::F673-1P::M741P::F1023-P::F704-2P::F959-2P::F812-2P::MYSTERY-2P::M680P::F947-1P::F1008-2P::M628-1P::F750-1P::M570P::M513-4P::F959-3P::M651-3P::F825-21P::F983P::F649P::F806-3P::F991-P:: +40 chr1:96848800-96861300 1.80455515383733e-60 1.77133329345519e-55 No results within 2500 bp window ::F812-3P::F825-22P::M513-1P::F976-1P::F825-21P::MYSTERY-1P::F673-1P::F859P::F879-1P::M741P::M478-P::F947-1P::M1025P::M513-2P::F663P::F649P::F806-1P::F884P::F959-1P::F812-1P::F806-2P::F947-4P::M680P::F756-1P::F654-2P::F876-1P::M651-3P::F1008-2P::M513-4P::F750-1P::M863P::M910P::F756-2P::F673-2P::F879-3P::F654-1P::F959-2P::F715-2P::F750-2P::F715-3P:: +34 chr3:31845000-31857500 2.74951727233906e-49 2.6988986593553e-44 Kcnmb2, ::F812-2P::M725P::M570P::F976-2P::F704-1P::F750-2P::F673-1P::M619-2P::F715-2P::M741P::F1023-P::F825-22P::M851P::F1026P::F959-3P::F771-1P::F649P::F825-21P::F663P::M680P::F884P::MYSTERY-2P::F806-3P::F750-1P::F991-P::M1025P::M628-1P::F991P::F806-1P::M513-4P::F1008-2P::F715-1P::F704-2P::F983P:: +34 chr9:17524300-17536800 2.74951727233906e-49 2.6988986593553e-44 No results within 2500 bp window ::M910P::F812-1P::F756-1P::F959-3P::F884P::F991P::F806-2P::F1008-2P::M930-2P::M513-1P::F959-2P::F654-2P::F959-1P::F737-1P::F947-3P::F715-2P::M578P::F806-4P::F859P::F876-1P::M1025P::F825-21P::F750-2P::F715-3P::F806-3P::F947-1P::MYSTERY-1P::F957-2P::F649P::F654-1P::F663P::M741P::M513-4P::M513-5P:: +32 chr9:3024700-3037200 1.17413468704426e-45 1.15251886745578e-40 AC131780.5, AC131780.4, AC131780.6, AC131780.12, AC131780.10, AC131780.2, ::F771-1P::M988-P::F1026P::F991-P::F737-2P::M863P::F715-1P::F983P::F959-1P::M593P::M651-2P::F756-1P::M513-4P::F859P::F704-2P::F1008-2P::F673-1P::M851P::M619-1P::M680P::M1025P::F884P::F1023-P::F812-2P::F825-22P::F825-21P::M619-2P::M628-1P::F750-2P::M651-3P::F715-3P::F715-2P:: +31 chr6:54872200-54884700 7.32997007158077e-44 7.19502532256297e-39 Nod1, ::F983P::M1025P::M513-1P::F959-2P::M513-2P::M863P::F879-1P::F756-1P::F750-1P::F859P::F715-3P::M619-1P::M741P::F947-2P::F957-2P::M628-1P::F654-3P::F673-2P::M562P::F879-2P::F947-4P::F771-2P::F756-2P::M513-3P::F991P::F654-2P::F876-2P::F663P::M651-2P::F806-2P::F737-1P:: +30 chr1:109142400-109154900 4.43300478305661e-42 4.35139316500054e-37 AC157660.1, ::M1022-P::M513-3P::M851P::M680P::F756-2P::M741P::F704-1P::F976-1P::F673-1P::F654-1P::F991P::F812-2P::F756-1P::F654-2P::F959-2P::F957-2P::M513-1P::F715-2P::F750-2P::F947-1P::M988-P::F673-2P::F812-1P::F947-3P::F806-3P::F859P::M628-3P::F715-3P::M1025P::MYSTERY-1P:: +30 chr9:53003600-53016100 4.43300478305661e-42 4.35139316500054e-37 Ddx10, ::F879-1P::MYSTERY-1P::F959-2P::M863P::F859P::F654-2P::F976-1P::F663P::F654-1P::F756-1P::F806-3P::F825-21P::M851P::M513-2P::M1025P::F649P::M619-1P::F959-1P::F771-1P::M513-1P::F947-3P::F825-22P::M513-5P::F947-1P::M478-P::F806-1P::M565P::F884P::F806-4P::F812-2P:: +29 chr4:96179500-96192000 2.5945005031305e-40 2.54673574886787e-35 Cyp2j6, ::F715-1P::M680P::F991P::M863P::F715-2P::F704-2P::M513-1P::F959-2P::F654-2P::F806-3P::F673-2P::F825-22P::M570P::F812-2P::F976-1P::F825-21P::F715-3P::MYSTERY-1P::F756-2P::M513-4P::M478-P::F806-4P::F704-1P::F976-2P::F806-1P::F859P::F756-1P::F947-1P::F1008-2P:: +28 chr13:31719100-31731600 1.46786481942381e-38 1.44084142809822e-33 Foxf2, RP23-322J11.2, ::F704-1P::F737-2P::F859P::F879-2P::F991-P::M725P::F959-2P::F1008-2P::M1022-P::F812-1P::M930-2P::F715-2P::M1025P::F812-3P::F1023-P::F812-2P::F991P::F750-1P::M704P::M930-1P::F959-1P::M741P::F976-1P::F876-2P::F803P::F750-2P::F812-4P::M570P:: +28 chr11:77388000-77400500 1.46786481942381e-38 1.44084142809822e-33 Taok1, ::M578P::M513-2P::F595P::MYSTERY-1P::F704-1P::F750-1P::F673-2P::F825-21P::F806-3P::F879-3P::M619-1P::F737-1P::F991-P::M570P::M725P::F812-1P::M704P::F812-4P::F812-2P::F649P::M565P::F1023-P::M741P::F756-2P::F673-1P::F959-1P::M930-2P::M930-1P:: +28 chr1:147289800-147302300 1.46786481942381e-38 1.44084142809822e-33 No results within 2500 bp window ::F806-1P::M499P::M651-2P::F991-P::F1023-P::F750-1P::F1026P::F756-1P::F649P::F715-2P::F959-2P::F959-1P::M628-1P::F673-2P::F704-1P::F947-2P::M1025P::M619-1P::M619-2P::F812-3P::F859P::F1008-2P::M851P::F715-1P::M570P::F884P::M1022-P::F1008-1P:: +26 chr4:86833900-86846400 4.2235385894228e-35 4.14578324399153e-30 Slc24a2, ::F806-2P::F812-1P::F959-2P::F1008-2P::F663P::F756-1P::F737-1P::F673-2P::F947-3P::F957-2P::F859P::F649P::F959-3P::F947-1P::M910P::M513-1P::F654-1P::M1025P::M513-5P::F715-3P::F750-2P::M741P::M628-1P::F825-22P::F806-4P::F704-1P:: +25 chr2:120396000-120408500 2.14231889970288e-33 2.10287880875935e-28 Snap23, ::F756-2P::MYSTERY-1P::F959-2P::F1008-2P::F806-1P::F663P::F991P::M513-1P::F673-2P::F771-1P::F654-2P::F947-1P::F750-2P::F825-21P::M513-3P::F673-1P::F884P::F756-1P::M680P::F876-1P::F976-2P::F859P::F976-1P::F715-3P::F1023-P:: +25 chr16:67974600-67987100 2.14231889970288e-33 2.10287880875935e-28 No results within 2500 bp window ::F654-3P::F959-1P::MYSTERY-1P::M910P::M651-2P::F715-2P::F704-2P::F715-3P::F704-1P::F654-1P::F879-2P::M680P::F649P::M513-5P::F947-1P::F959-2P::M513-1P::F756-1P::F806-2P::F806-1P::F654-2P::F673-2P::F876-1P::F884P::M930-2P:: +24 chr9:25345000-25357500 1.04486079141122e-31 1.02562490424134e-26 Eepd1, SNORA70, ::M578P::M565P::M704P::M863P::M628-3P::F704-1P::F959-2P::F771-1P::F976-2P::M910P::F715-3P::F673-2P::M930-2P::F859P::F663P::M513-1P::F750-2P::F976-1P::F884P::F756-1P::F806-2P::M741P::F715-1P::F991-P:: +45 chr11:79213700-79313700 5.24557568187694e-31 1.25563345097088e-26 Nf1, RP23-188A3.3, Omg, ::F1023-P::M1022-P::F704-2P::M499P::MYSTERY-2P::MYSTERY-1P::F595P::M578P::F812-2P::F983P::F859P::M628-1P::F825-21P::M930-1P::M725P::M851P::F654-2P::F825-22P::F750-2P::M680P::F737-2P::M562P::F750-1P::M619-1P::M619-2P::F957-2P::F673-1P::M930-2P::M628-3P::M593P::F771-1P::M741P::F879-1P::F947-1P::M651-2P::F991P::F1008-2P::F704-1P::F876-2P::F803P::F812-1P::F957-1P::F715-2P::F715-1P::F947-2P:: +23 chr5:22846400-22858900 4.89219747179889e-30 4.80213211634307e-25 No results within 2500 bp window ::F959-1P::F991-P::F806-2P::M910P::F750-2P::F876-1P::M478-P::F825-21P::F704-2P::M513-1P::F959-2P::F704-1P::F947-2P::F976-1P::F715-2P::F806-1P::M741P::F947-1P::F737-2P::F673-1P::F825-22P::M578P::F756-2P:: + +NFQUINT_0.01library +number pos pvalue bonferroni gene_name library_name +67 chr5:28496400-28508900 6.73724474185922e-281 2.18960454110424e-278 En2, ::F849-6NF::F885-1NF::F976-5NF::M1022-13NF::F991-3NF::F704-NF::F969-7NF::F1026-4NF::F957-3NF::F976-2NF::M988-4NF::F957-1NF::M878-1NF::F884-3NF::M1008-2NF::F849-3NF::M878-4NF::F673-3NF::F849-7NF::F947-3NF::M1008-3NF::F1027-5NF::F884-1NF::F959-5NF::M851-3NF::F1027-3NF::F879-4NF::F957-2NF::M1013-1NF::F1027-9NF::F849-8NF::F976-6NF::M988-3NF::F1027-2NF::F841-2NF::F969-2NF::F976-4NF::F1027-7NF::F969-9NF::F947-4NF::F957-11NF::F841-5NF::F884-2NF::M1008-1NF::F652-NF::F849-2NF::F849-4NF::F879-1NF::F947-2NF::F1027-4NF::F879-6NF::M1013-2NF::F959-4NF::F1026-1NF::F1026-3NF::F1027-8NF::F841-6NF::F947-5NF::F991-1NF::M952-4NF::F1026-5NF::F1027-6NF::F879-2NF::F957-12NF::F969-1NF::F976-3NF::F959-3NF:: +6 chr2:163468500-163481000 3.3131723579069e-20 1.07678101631974e-17 AL591488.2, 0610039K10Rik, Serinc3, ::F959-4NF::F1026-3NF::F849-7NF::F849-4NF::F849-3NF::F849-5NF:: +4 chr3:158263500-158276000 3.45086064823729e-13 1.12152971067712e-10 No results within 2500 bp window ::F841-6NF::F947-5NF::M851-1NF::F841-2NF:: +3 chr13:16745300-16757800 8.13333166271099e-10 2.64333279038107e-07 No results within 2500 bp window ::F969-1NF::F969-4NF::F969-3NF:: +2 chr14:121562700-121575200 1.43770838666248e-06 0.000467255225665307 Farp1, ::F969-3NF::F969-1NF:: +2 chr7:126509000-126521500 1.43770838666248e-06 0.000467255225665307 No results within 2500 bp window ::M910-2NF::F849-3NF:: +2 chr7:124704800-124717300 1.43770838666248e-06 0.000467255225665307 Xylt1, ::M910-2NF::F1027-6NF:: +2 chr12:39202400-39227400 5.7410818325909e-06 0.00186585159559204 Dgkb, ::F673-3NF::F976-2NF:: + +NFQUINT_0.001library +number pos pvalue bonferroni gene_name library_name +135 chr5:28496400-28546400 0 0 AC129184.1, En2, Cnpy1, ::F969-6NF::F976-6NF::F947-4NF::F959-8NF::F704-NF::F737-NF::F976-16NF::F976-2NF::M851-3NF::F991-4NF::M988-6NF::F957-1NF::F957-3NF::F1026-10NF::F1026-2NF::M878-6NF::F976-1NF::F884-3NF::F959-3NF::F879-2NF::F957-2NF::M878-3NF::F976-8NF::F957-10NF::F991-3NF::F885-1NF::F849-5NF::M952-4NF::F849-4NF::F959-6NF::F947-3NF::M988-9NF::F884-1NF::F991-1NF::M1013-2NF::F841-1NF::F841-2NF::F957-9NF::F976-11NF::M952-1NF::F885-3NF::F947-2NF::F652-NF::M628-2NF::F983-1NF::F841-5NF::M878-5NF::F757-1NF::F959-10NF::F1027-1NF::F991-2NF::F957-11NF::M988-3NF::F1026-4NF::F849-2NF::M1013-1NF::M988-1NF::F969-10NF::F849-3NF::M1013-5NF::M988-8NF::F879-5NF::F1023-NF::F884-2NF::M988-2NF::F959-1NF::F969-1NF::M1013-3NF::F976-4NF::M988-7NF::M878-2NF::F959-7NF::F849-7NF::F1027-3NF::M952-2NF::M988-5NF::F959-5NF::F879-6NF::F1026-1NF::F879-1NF::F976-3NF::F1026-5NF::F879-4NF::F969-7NF::M1008-4NF::F1027-2NF::F991-5NF::M878-1NF::F649-3NF::M1022-13NF::F969-9NF::F969-2NF::F959-4NF::F969-5NF::F1026-7NF::M1008-2NF::F1027-10NF::F849-6NF::F1027-8NF::F969-4NF::F1026-6NF::F976-5NF::M1008-1NF::F1026-8NF::F1027-5NF::M988-4NF::F885-2NF::M952-3NF::F959-9NF::F1027-7NF::M851-2NF::F959-2NF::F976-7NF::M851-1NF::M1013-4NF::F947-1NF::M878-4NF::F771-2NF::F1027-4NF::F957-12NF::F757-3NF::F771-5NF::F1026-3NF::M1008-3NF::F673-3NF::F947-5NF::F1027-6NF::F1026-9NF::F849-8NF::F841-4NF::F969-8NF::F969-3NF::F841-6NF::F1027-9NF::M1008-5NF:: +70 chr2:98502700-98515200 1.90827595103524e-192 1.79454270435354e-188 AL837506.1, AL837506.2, ::F885-2NF::F969-7NF::F976-8NF::F976-16NF::M988-3NF::F991-3NF::F969-5NF::F879-5NF::M952-3NF::F841-2NF::F1026-9NF::M1008-4NF::F884-1NF::F1026-6NF::F983-1NF::M878-6NF::F991-2NF::F959-1NF::M988-2NF::M988-1NF::F1026-5NF::F1027-1NF::F957-1NF::M988-8NF::F885-3NF::F991-5NF::F1027-4NF::F1026-10NF::F991-1NF::F959-2NF::F957-12NF::F879-6NF::F1023-NF::F976-11NF::F1027-7NF::M878-2NF::M988-6NF::F947-3NF::F947-4NF::F1027-9NF::M988-7NF::F1026-4NF::M988-4NF::M988-5NF::F957-11NF::F959-9NF::F1026-2NF::F1027-6NF::F957-9NF::M952-1NF::M952-4NF::F969-9NF::M1008-1NF::F976-7NF::F1027-2NF::F841-4NF::F1027-5NF::F991-4NF::F1027-8NF::F884-2NF::F959-8NF::F976-4NF::F879-1NF::M988-9NF::F1027-10NF::F969-1NF::M851-3NF::F885-1NF::M628-2NF::M952-2NF:: +61 chr2:163468400-163480900 2.71148879587285e-164 2.54988406363883e-160 AL591488.2, 0610039K10Rik, Serinc3, ::M878-4NF::F849-6NF::M1013-3NF::F849-2NF::F991-4NF::F969-9NF::M851-1NF::F879-2NF::F959-4NF::F849-4NF::F841-4NF::F947-2NF::F976-7NF::F849-7NF::F884-3NF::F849-3NF::F1027-4NF::F959-5NF::F1027-10NF::M878-5NF::F885-1NF::M1013-5NF::F879-4NF::F841-2NF::F1026-10NF::F879-1NF::F652-NF::F957-12NF::M1013-4NF::M952-2NF::F841-1NF::M878-2NF::M878-3NF::F884-1NF::F976-9NF::F969-2NF::F757-1NF::F757-3NF::F959-1NF::F771-5NF::M878-1NF::M1022-13NF::F957-3NF::F1027-5NF::M1013-2NF::M952-1NF::F1026-4NF::M988-8NF::F969-7NF::F957-2NF::M952-3NF::M988-9NF::F1027-1NF::F1026-3NF::F885-2NF::M1008-2NF::F849-5NF::M952-4NF::M1013-1NF::F991-1NF::F959-3NF:: +39 chr3:158263500-158276000 4.20598027409595e-98 3.95530384975983e-94 No results within 2500 bp window ::F1027-2NF::F1026-5NF::F649-3NF::F879-6NF::F841-6NF::M952-1NF::F1023-NF::F884-1NF::F737-NF::F885-1NF::M1013-3NF::M988-9NF::F1027-5NF::F969-4NF::M988-1NF::F991-4NF::F983-1NF::M851-1NF::M1013-5NF::F1026-8NF::F841-1NF::M1008-5NF::F957-1NF::F969-6NF::F841-2NF::M988-6NF::F947-5NF::F704-NF::M988-3NF::M988-7NF::F885-2NF::M952-3NF::F959-2NF::F879-4NF::F1027-8NF::F969-2NF::F885-3NF::M878-2NF::F976-8NF:: +19 chrX:139917600-139930100 1.06021483750882e-42 9.97026033193291e-39 No results within 2500 bp window ::F959-5NF::F991-2NF::F1026-7NF::F1027-7NF::F1027-8NF::M988-5NF::F841-4NF::F704-NF::M952-2NF::M878-5NF::F957-9NF::F959-4NF::F1027-9NF::M988-8NF::M988-1NF::M988-3NF::F976-3NF::M988-6NF::F957-11NF:: +12 chr13:31719100-31731600 3.90943684457939e-25 3.67643440864246e-21 Foxf2, RP23-322J11.2, ::F879-2NF::F849-3NF::M1008-2NF::M988-9NF::F849-2NF::F947-4NF::F959-4NF::F885-1NF::F1026-4NF::F976-8NF::F976-16NF::M1013-1NF:: +10 chr10:16578700-16591200 2.13989149153668e-20 2.01235395864109e-16 No results within 2500 bp window ::F969-9NF::F1027-10NF::F959-6NF::F969-2NF::M1008-1NF::F959-2NF::F957-12NF::F957-3NF::F976-16NF::F841-1NF:: +10 chr11:3034900-3134900 1.62930272123883e-11 1.532196279053e-07 RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Sfi1, Eif4enif1, Drg1, ::F959-9NF::F1027-10NF::F1027-9NF::M1013-2NF::F969-4NF::M878-1NF::F959-1NF::M952-4NF::F969-1NF::F976-11NF:: +7 chr2:141310500-141360500 1.83957821011689e-09 1.72993934879393e-05 Macrod2, ::F1027-3NF::F849-5NF::F969-10NF::F1027-2NF::F1026-9NF::F976-8NF::M878-5NF:: +5 chr4:8718500-8731000 2.2658574627886e-09 2.1308123580064e-05 Chd7, ::F1026-4NF::F1026-10NF::F1026-2NF::F1026-1NF::F1026-7NF:: +5 chr3:111049700-111062200 2.2658574627886e-09 2.1308123580064e-05 No results within 2500 bp window ::F1027-10NF::F884-2NF::F976-8NF::F957-1NF::F1027-5NF:: +5 chr11:115523400-115535900 2.2658574627886e-09 2.1308123580064e-05 Grb2, ::F969-4NF::F969-3NF::F969-1NF::F976-16NF::F976-8NF:: +6 chr8:35967100-36017100 6.55553461486058e-08 0.000616482475181489 Tnks, ::F1026-4NF::F1027-5NF::F849-7NF::F849-1NF::M952-4NF::F959-6NF:: +6 chr12:8699900-8749900 6.55553461486058e-08 0.000616482475181489 Pum2, ::F1027-2NF::F1027-9NF::F1027-5NF::F957-10NF::M1022-13NF::F841-4NF:: +9 chr16:4070000-4270000 1.43356241948461e-07 0.00134812209928333 AC132380.1, Crebbp, RP24-425F2.2, Gm5766, Trap1, ::M851-1NF::F879-5NF::M878-6NF::F849-3NF::F849-2NF::F849-4NF::F879-2NF::F771-2NF::F884-1NF:: +4 chr5:39599200-39611700 2.30703615301761e-07 0.00216953679829776 No results within 2500 bp window ::F969-7NF::M628-2NF::F969-10NF::F969-1NF:: +4 chr3:107552400-107564900 2.30703615301761e-07 0.00216953679829776 Csf1, ::F849-2NF::F849-8NF::F976-16NF::F976-1NF:: +4 chr2:54470600-54483100 2.30703615301761e-07 0.00216953679829776 Galnt13, ::M851-3NF::F969-9NF::M952-1NF::F841-2NF:: +4 chr18:37849200-37861700 2.30703615301761e-07 0.00216953679829776 Pcdhga2, Pcdhga11, ::M851-2NF::F976-1NF::F957-9NF::F991-3NF:: +4 chr12:111506800-111519300 2.30703615301761e-07 0.00216953679829776 AL591207.1, Dio3, ::F969-3NF::F976-8NF::F976-11NF::F969-1NF:: +4 chr11:84677200-84689700 2.30703615301761e-07 0.00216953679829776 Gm10374, Pigw, Ggnbp2, ::F884-3NF::F991-5NF::F884-2NF::M1013-4NF:: +4 chr11:72403500-72416000 2.30703615301761e-07 0.00216953679829776 No results within 2500 bp window ::F1026-7NF::F1026-4NF::F1026-5NF::F1026-2NF:: +4 chr10:57318100-57330600 2.30703615301761e-07 0.00216953679829776 No results within 2500 bp window ::M910-2NF::M552-NF::M910-1NF::M910-4NF:: +4 chr1:136827700-136840200 2.30703615301761e-07 0.00216953679829776 Ppp1r12b, ::F1026-5NF::F1026-10NF::F1026-4NF::F1026-2NF:: +4 chr1:80258200-80270700 2.30703615301761e-07 0.00216953679829776 Cul3, ::F849-3NF::F976-7NF::F849-2NF::F849-1NF:: + +NFQUINT_0.0001library +number pos pvalue bonferroni gene_name library_name + +NFQUINT_0library +number pos pvalue bonferroni gene_name library_name +142 chr5:28496400-28508900 2.74269223072785e-211 6.56518239269327e-207 En2, ::F959-3NF::F704-NF::F1026-7NF::F1027-1NF::F959-8NF::F976-1NF::F841-4NF::F1027-6NF::F1027-5NF::M988-5NF::M1008-4NF::F1026-5NF::M1013-1NF::F991-5NF::F841-5NF::F969-6NF::F841-2NF::F957-1NF::F879-2NF::M1008-1NF::F1027-2NF::M878-5NF::F957-3NF::M1008-3NF::F849-2NF::F976-16NF::F969-10NF::F849-8NF::M988-7NF::F976-11NF::F879-4NF::F841-6NF::F884-2NF::F957-10NF::F976-3NF::F976-9NF::F879-5NF::F1026-4NF::F1027-4NF::M1013-3NF::F959-6NF::M878-3NF::F1023-NF::F885-3NF::M851-2NF::M1008-6NF::F976-8NF::F1027-9NF::F1026-1NF::F1027-8NF::F879-1NF::F884-3NF::F959-7NF::M1013-4NF::M952-2NF::F991-2NF::M878-6NF::M988-8NF::F976-4NF::F849-3NF::F969-1NF::F976-7NF::F969-2NF::F947-5NF::M1022-13NF::M1025-1NF::F771-2NF::F947-2NF::F976-2NF::F1027-3NF::M1008-5NF::F849-6NF::M952-1NF::F849-7NF::M988-1NF::M988-2NF::F884-1NF::F1026-8NF::F947-4NF::F969-4NF::F652-NF::F757-3NF::M851-1NF::F976-6NF::F959-9NF::F771-5NF::M1013-2NF::M988-9NF::F969-9NF::F879-6NF::F959-5NF::F649-3NF::F959-2NF::M910-4NF::F849-4NF::M988-6NF::F969-8NF::F991-1NF::F957-9NF::M1008-2NF::F957-2NF::F983-1NF::M851-3NF::F983-2NF::M878-1NF::F757-1NF::F947-3NF::M952-4NF::F1026-2NF::M952-3NF::F969-5NF::F814-4NF::F1027-10NF::F991-3NF::M628-2NF::F1026-6NF::F957-11NF::F991-4NF::F1026-10NF::F885-1NF::F957-12NF::F959-4NF::M878-2NF::F969-7NF::F841-1NF::F976-5NF::F959-10NF::F1026-9NF::F947-1NF::M988-4NF::F737-NF::M1013-5NF::F849-5NF::F969-3NF::F885-2NF::M988-3NF::F959-1NF::F1027-7NF::M878-4NF::F1026-3NF::F673-3NF::F879-3NF:: +134 chr2:163456300-163468800 3.64124574715009e-196 8.71604994495316e-192 AL591488.2, Serinc3, 0610039K10Rik, ::F969-8NF::F884-3NF::F1026-10NF::F969-6NF::M988-1NF::F879-5NF::F879-1NF::F885-3NF::M1013-3NF::M988-8NF::M988-2NF::F814-4NF::F959-7NF::F1026-5NF::M988-6NF::F849-3NF::M878-4NF::F969-3NF::F1026-2NF::M1008-5NF::M851-2NF::F879-6NF::F1026-9NF::F969-4NF::M878-1NF::F1026-3NF::M988-4NF::F1027-9NF::F849-6NF::F947-3NF::F884-1NF::F1027-8NF::F841-4NF::F849-5NF::F957-12NF::F737-NF::F969-5NF::M988-7NF::F976-11NF::M878-3NF::F849-2NF::M1008-4NF::M1013-4NF::F1027-1NF::F1026-8NF::F957-11NF::F879-4NF::F849-4NF::F652-NF::F976-7NF::M988-3NF::F991-2NF::M878-2NF::M1013-2NF::F983-1NF::F976-4NF::F959-4NF::F976-2NF::F1027-4NF::F1026-6NF::F757-3NF::M1008-2NF::F879-2NF::M878-5NF::M1013-1NF::F957-9NF::F849-8NF::F1023-NF::M952-2NF::F959-2NF::M851-1NF::F991-1NF::F976-3NF::F771-5NF::M878-6NF::F976-1NF::F959-9NF::F957-1NF::F885-2NF::M1008-1NF::F1027-10NF::F1027-2NF::F969-7NF::F959-10NF::F947-2NF::M851-3NF::F841-2NF::M952-1NF::F884-2NF::F841-1NF::F957-2NF::F969-2NF::F1026-7NF::F969-1NF::F959-6NF::F1026-1NF::F976-6NF::M952-3NF::F991-5NF::M628-2NF::F849-7NF::F976-9NF::F947-4NF::F976-8NF::F991-4NF::F771-2NF::M1022-13NF::F1027-7NF::F959-3NF::F969-9NF::M988-9NF::F976-16NF::M952-4NF::F991-3NF::F1026-4NF::F969-10NF::F959-1NF::F959-8NF::F976-5NF::F704-NF::F841-5NF::F649-3NF::M988-5NF::F947-1NF::F957-3NF::F1027-5NF::F957-10NF::F959-5NF::M1013-5NF::F849-1NF::F1027-3NF::M1025-1NF::F757-1NF::F885-1NF:: +130 chr2:98502400-98514900 1.11180033854048e-188 2.66131647036435e-184 AL837506.1, AL837506.2, ::F1026-5NF::M988-2NF::F969-8NF::M988-1NF::F879-5NF::M1008-4NF::F969-3NF::F1026-9NF::F959-9NF::M988-8NF::M1025-1NF::M988-9NF::F884-3NF::M1008-1NF::M1013-5NF::F1027-8NF::F652-NF::F991-4NF::F1026-10NF::F957-2NF::M988-7NF::F1026-6NF::M952-4NF::M1013-4NF::F983-2NF::F957-11NF::F757-1NF::M988-6NF::F983-1NF::F1026-8NF::F959-8NF::F1026-7NF::M878-5NF::F991-2NF::M1008-5NF::F1027-4NF::F1027-7NF::F969-5NF::M1013-1NF::F976-16NF::F1027-9NF::F959-4NF::F969-6NF::F976-11NF::M988-3NF::F959-1NF::M878-2NF::M851-2NF::F991-1NF::F841-1NF::M988-5NF::F1026-4NF::F884-2NF::F885-3NF::M878-6NF::F969-2NF::F969-10NF::M851-3NF::F649-3NF::F1026-2NF::F1027-1NF::M952-3NF::F969-7NF::M988-4NF::F841-2NF::M878-3NF::F947-3NF::F1023-NF::F757-3NF::F884-1NF::M628-2NF::F771-5NF::M952-1NF::M1013-3NF::F841-6NF::M910-1NF::F885-2NF::F957-12NF::F885-1NF::F957-1NF::F947-2NF::F957-9NF::F841-5NF::F1027-5NF::F991-5NF::F879-4NF::F969-4NF::F991-3NF::F976-8NF::F959-6NF::F959-2NF::F957-3NF::F1027-3NF::F1027-10NF::F976-1NF::F947-4NF::F957-10NF::F879-6NF::M1013-2NF::F1026-1NF::M851-1NF::F959-10NF::F959-7NF::M952-2NF::M1022-13NF::F1026-3NF::F704-NF::F1027-6NF::F1027-2NF::F959-5NF::F969-1NF::M1008-2NF::F879-2NF::F737-NF::F879-1NF::F969-9NF::F976-7NF::F947-5NF::F976-9NF::F976-4NF::F976-3NF::F841-4NF::F976-6NF::F959-3NF::F947-1NF::F771-2NF::M878-1NF::F849-2NF::F976-2NF::F849-5NF:: +112 chr13:31718600-31731100 1.10445866264708e-155 2.64374270077832e-151 Foxf2, RP23-322J11.2, ::M1008-1NF::F884-3NF::F969-3NF::F1027-4NF::F737-NF::F959-3NF::F885-2NF::M1013-5NF::F947-5NF::F959-4NF::F1026-8NF::M952-2NF::F841-2NF::M851-3NF::F959-8NF::M878-2NF::M988-5NF::F841-6NF::F879-2NF::F841-4NF::F884-1NF::M878-1NF::F1026-10NF::F959-2NF::F976-11NF::M851-1NF::M851-2NF::F879-6NF::M1013-3NF::F959-6NF::F957-10NF::F957-9NF::F991-4NF::F969-7NF::F957-12NF::F957-1NF::F1027-8NF::F947-1NF::F947-2NF::F991-5NF::F1023-NF::M988-2NF::F969-8NF::M952-4NF::F969-10NF::F957-3NF::F885-3NF::F959-1NF::F1026-4NF::F991-1NF::M988-1NF::F652-NF::F841-5NF::F959-5NF::M952-3NF::F991-2NF::F969-9NF::M988-6NF::F976-8NF::M988-7NF::M878-6NF::F1026-6NF::M1008-2NF::M878-3NF::F957-11NF::F969-5NF::F976-16NF::M1008-5NF::F969-2NF::F884-2NF::F1027-2NF::F957-2NF::F947-4NF::F969-4NF::F969-1NF::F959-7NF::F1027-7NF::F885-1NF::F757-3NF::F879-5NF::F1026-9NF::M988-9NF::F771-2NF::M628-2NF::F771-5NF::F849-7NF::F849-8NF::F849-2NF::F947-3NF::F976-7NF::F1027-10NF::M1022-13NF::F1026-5NF::F849-3NF::F879-1NF::F879-4NF::F1026-7NF::M1008-4NF::F976-6NF::M1013-2NF::M1013-1NF::M878-5NF::F969-6NF::F1026-1NF::F1027-1NF::F1026-3NF::M952-1NF::M988-4NF::F983-2NF::F976-9NF::F959-9NF::F1027-5NF:: +112 chr9:3018300-3030800 1.10445866264708e-155 2.64374270077832e-151 AC131780.5, AC131780.7, AC131780.2, AC131780.4, AC131780.6, AC131780.3, AC131780.11, AC131780.12, ::F969-9NF::M988-1NF::F969-2NF::F1027-2NF::F1026-10NF::F991-2NF::F1026-6NF::F969-6NF::F983-2NF::F983-1NF::F885-2NF::F1027-1NF::F976-2NF::F957-1NF::M1013-3NF::F884-2NF::F771-5NF::F969-8NF::M878-2NF::F976-8NF::F959-1NF::M878-5NF::M1013-2NF::F957-2NF::F737-NF::M1008-5NF::M988-2NF::M878-6NF::F976-3NF::F879-2NF::F991-4NF::F1023-NF::F1026-5NF::F1026-9NF::F879-5NF::F879-1NF::F947-3NF::F1026-8NF::F879-6NF::F1026-7NF::F1026-3NF::F1027-9NF::M851-3NF::F1027-5NF::M988-8NF::F957-10NF::M1008-1NF::F969-5NF::F991-1NF::F959-9NF::M952-3NF::M988-7NF::F969-10NF::F976-11NF::F947-4NF::M988-9NF::F884-1NF::M952-1NF::F771-2NF::M988-6NF::M628-2NF::F969-7NF::F879-4NF::F757-1NF::F704-NF::M1013-1NF::F885-3NF::F1026-2NF::F976-4NF::F841-5NF::M1025-1NF::F959-8NF::F757-3NF::F947-1NF::F959-2NF::F1027-8NF::F969-3NF::M1013-4NF::M851-1NF::F1026-1NF::F841-1NF::M952-2NF::M988-4NF::F1026-4NF::F959-3NF::M988-5NF::F976-1NF::F1027-4NF::M1008-4NF::M851-2NF::F841-6NF::M952-4NF::F991-5NF::F957-11NF::F991-3NF::F884-3NF::F652-NF::F959-10NF::F957-12NF::F959-4NF::F947-2NF::F976-16NF::F649-3NF::F841-4NF::F959-7NF::M988-3NF::F959-6NF::M1013-5NF::F1027-10NF::F1027-6NF::M1022-13NF::F957-9NF:: +98 chr3:48818900-48831400 7.08194681354571e-131 1.69520560875844e-126 No results within 2500 bp window ::F959-6NF::F884-2NF::F1027-3NF::F1026-2NF::F757-3NF::F841-4NF::F969-4NF::F947-4NF::M878-2NF::F841-2NF::F976-9NF::F1026-10NF::F957-3NF::F976-11NF::F885-3NF::M952-1NF::F957-1NF::F1027-4NF::F771-5NF::F841-5NF::F957-2NF::F969-9NF::M988-1NF::F1023-NF::F976-8NF::M952-3NF::F957-11NF::F879-1NF::M988-2NF::M628-2NF::M1013-1NF::F976-2NF::M851-1NF::F1026-1NF::F1027-5NF::M988-7NF::F879-4NF::F879-5NF::F1027-1NF::F957-9NF::F991-2NF::F969-10NF::F1026-8NF::F879-2NF::F947-2NF::F957-10NF::F991-1NF::F1027-10NF::F849-2NF::F959-9NF::F947-3NF::F983-1NF::M878-4NF::F969-5NF::M988-5NF::F771-2NF::F652-NF::F959-3NF::M1008-5NF::F957-12NF::F649-3NF::F1026-7NF::F737-NF::F969-3NF::F991-4NF::M1008-2NF::M952-4NF::F1026-4NF::F959-10NF::F757-1NF::F885-2NF::M851-3NF::M878-1NF::M851-2NF::F1026-5NF::F959-2NF::M988-3NF::M1013-3NF::F959-8NF::F1027-9NF::M878-5NF::F991-3NF::F991-5NF::M1008-4NF::M1008-1NF::M878-6NF::F976-16NF::F969-1NF::F884-3NF::F976-5NF::M988-6NF::F841-6NF::M988-8NF::F947-1NF::F1026-6NF::F849-5NF::M1013-4NF::M1025-1NF:: +97 chrX:139917600-139930100 3.89378997685331e-129 9.32056506759378e-125 No results within 2500 bp window ::F1027-8NF::F879-1NF::F1027-9NF::F957-11NF::F884-1NF::M878-2NF::M1013-1NF::F959-9NF::F879-4NF::M952-3NF::M988-2NF::F947-4NF::F841-6NF::M1013-4NF::M1008-1NF::M1008-5NF::F652-NF::M1008-3NF::F976-11NF::F1027-2NF::M851-3NF::F957-2NF::F737-NF::F969-5NF::F969-3NF::F969-1NF::F959-4NF::M988-1NF::M988-8NF::F1026-6NF::F1026-5NF::F757-1NF::F1026-1NF::F1027-4NF::F947-2NF::F1026-7NF::F884-2NF::F983-1NF::F976-4NF::M952-1NF::F991-5NF::F976-3NF::M1008-2NF::F879-2NF::M988-3NF::F959-8NF::F969-2NF::F1027-5NF::M1008-4NF::M988-7NF::F969-9NF::F704-NF::M878-3NF::F649-3NF::F1027-1NF::M851-2NF::F1026-8NF::F969-10NF::M1013-5NF::F983-2NF::F969-8NF::F991-2NF::M952-2NF::M988-6NF::F1027-7NF::F1023-NF::F959-2NF::F976-8NF::F959-10NF::F969-6NF::F991-1NF::F947-5NF::F991-4NF::F959-5NF::F879-5NF::F885-3NF::F841-4NF::F771-5NF::F841-1NF::M1025-1NF::F1026-10NF::M878-5NF::F959-1NF::M878-6NF::F1026-4NF::F1026-9NF::M988-9NF::F976-16NF::F757-3NF::M988-5NF::F885-2NF::F959-6NF::M988-4NF::F957-9NF::F947-3NF::M1013-3NF::F957-1NF:: +95 chr10:57314000-57326500 1.14130852919205e-125 2.73195022632701e-121 No results within 2500 bp window ::F757-3NF::F969-5NF::M1008-1NF::F976-4NF::F879-2NF::F879-1NF::F849-8NF::F849-5NF::F1027-2NF::F957-1NF::F1027-3NF::F959-8NF::F957-2NF::F885-2NF::F969-6NF::M910-2NF::F771-2NF::M1008-5NF::F957-9NF::F959-2NF::F673-3NF::F649-3NF::F957-3NF::M851-1NF::F969-9NF::M988-7NF::F1027-1NF::M878-2NF::F884-2NF::M910-1NF::F976-3NF::M910-4NF::F849-2NF::F947-4NF::F976-7NF::F947-2NF::F849-3NF::F879-4NF::M952-3NF::M851-3NF::M1022-13NF::F969-10NF::M1013-1NF::F771-5NF::F652-NF::F1026-1NF::F1026-9NF::F969-1NF::F959-6NF::M851-2NF::M1013-5NF::F947-3NF::F991-2NF::F1026-8NF::F849-1NF::F991-3NF::F957-11NF::M952-2NF::M628-2NF::F969-8NF::F1027-5NF::F737-NF::F957-10NF::F959-4NF::F841-1NF::F959-9NF::F879-5NF::F1026-10NF::M878-1NF::F1027-7NF::M552-NF::M988-6NF::F976-11NF::F991-5NF::M878-5NF::F1027-6NF::M878-6NF::M1013-3NF::F841-4NF::F976-9NF::M988-5NF::F991-4NF::F879-6NF::F959-10NF::F983-1NF::F757-1NF::M988-3NF::F959-5NF::F959-1NF::F976-5NF::M952-4NF::F969-3NF::F957-12NF::F1023-NF::F1027-10NF:: +90 chr6:103587700-103600200 4.41098541357449e-117 1.05585757844733e-112 Chl1, ::M851-3NF::F1023-NF::F757-3NF::F983-1NF::F841-4NF::F957-1NF::M988-6NF::F649-3NF::F959-1NF::F1026-6NF::F969-6NF::M988-3NF::F1027-8NF::F879-1NF::F976-1NF::F841-5NF::M878-5NF::M952-1NF::F991-5NF::M952-3NF::M952-2NF::F1027-6NF::F1027-5NF::F1026-10NF::F969-3NF::M878-6NF::F976-16NF::M1022-13NF::M1013-4NF::F1026-2NF::F959-2NF::M1008-4NF::F991-4NF::F1026-8NF::F1026-4NF::M851-2NF::F1027-7NF::F976-8NF::F771-5NF::F1026-5NF::M988-5NF::M988-2NF::F1027-10NF::F1026-1NF::M988-7NF::F737-NF::F1026-7NF::F885-1NF::M988-4NF::F947-3NF::F957-9NF::F969-2NF::F947-4NF::F879-5NF::F959-7NF::M878-2NF::F879-6NF::F1027-1NF::F991-2NF::M952-4NF::F959-8NF::F1027-2NF::F976-6NF::F841-1NF::F1027-4NF::F969-8NF::M1025-1NF::F1027-9NF::F959-9NF::F959-6NF::F885-3NF::F957-11NF::M988-9NF::F959-4NF::F969-5NF::F879-4NF::M1008-5NF::F885-2NF::M988-8NF::F983-2NF::F757-1NF::F884-2NF::M628-2NF::F991-1NF::M1013-1NF::F969-4NF::M988-1NF::F969-10NF::F947-2NF::F969-1NF:: +77 chr3:31845000-31857500 2.46305773808358e-95 5.89582130765067e-91 Kcnmb2, ::F947-5NF::F849-7NF::F991-2NF::F957-10NF::F957-2NF::F983-1NF::F957-9NF::F959-10NF::F947-2NF::F957-11NF::F976-11NF::F957-12NF::F957-1NF::F976-8NF::F976-5NF::F976-16NF::F976-2NF::F976-9NF::F959-2NF::F947-1NF::F991-4NF::F947-3NF::F947-4NF::F879-1NF::M952-1NF::M988-3NF::M878-4NF::F879-5NF::F1026-7NF::F1026-2NF::M988-5NF::F841-6NF::F959-9NF::M851-1NF::M988-7NF::F649-3NF::M988-2NF::F1026-8NF::M851-2NF::F959-6NF::F969-3NF::M988-6NF::F1027-9NF::F1027-5NF::F1026-1NF::M1013-3NF::F849-2NF::F771-2NF::F969-1NF::F849-5NF::M1025-1NF::F841-4NF::F879-2NF::F1027-3NF::F771-5NF::F969-5NF::F757-1NF::F757-3NF::F959-8NF::M878-5NF::M952-4NF::F879-4NF::F841-5NF::M1022-13NF::F991-5NF::F1023-NF::F1026-6NF::F1026-10NF::F969-10NF::M628-2NF::F884-2NF::F885-2NF::F1027-10NF::F1026-4NF::M878-2NF::M878-1NF::F969-8NF:: +76 chr9:3733700-3746200 1.06404281639442e-93 2.54699928960333e-89 Gucy1a2, ::F959-7NF::M988-8NF::M1022-13NF::F969-8NF::F885-2NF::F1026-8NF::F959-2NF::M1008-2NF::F884-2NF::F947-3NF::F957-10NF::F969-1NF::F969-9NF::M851-2NF::M988-7NF::F757-3NF::F879-5NF::F959-3NF::F957-9NF::F976-11NF::F991-2NF::F849-7NF::M988-1NF::F991-5NF::M952-3NF::F1023-NF::F879-1NF::F957-2NF::F849-5NF::F737-NF::F969-10NF::M851-3NF::M988-5NF::F841-4NF::M1008-4NF::M1008-1NF::F1027-10NF::F1026-5NF::F771-2NF::F983-2NF::F947-2NF::F947-4NF::F879-2NF::M1008-5NF::F959-1NF::F976-7NF::M952-2NF::M878-6NF::F1026-10NF::F885-1NF::M1013-3NF::F959-8NF::F652-NF::F969-5NF::F1026-4NF::F1027-7NF::M878-3NF::M628-2NF::F757-1NF::F884-3NF::F959-5NF::F969-3NF::F649-3NF::F947-1NF::F1026-7NF::F983-1NF::F1027-9NF::M1013-2NF::F959-9NF::F1026-2NF::F1026-6NF::M988-9NF::F959-10NF::F957-11NF::F959-6NF::M988-2NF:: +69 chr9:3000000-3012500 2.05132243139437e-82 4.91025050402869e-78 AC131780.8, AC131780.9, AC131780.5, AC131780.1, ::M878-5NF::F957-9NF::F1026-7NF::F1027-7NF::F947-5NF::F991-5NF::M1008-5NF::M1013-4NF::F879-2NF::F1027-4NF::M988-3NF::M878-6NF::F947-3NF::F884-1NF::F959-8NF::F957-2NF::M1008-1NF::M952-2NF::F983-1NF::F1027-5NF::M988-1NF::F879-5NF::F879-4NF::F1026-6NF::M988-6NF::F884-2NF::F957-12NF::M988-7NF::F885-3NF::M952-3NF::F1027-2NF::F983-2NF::F969-3NF::F673-3NF::M1025-1NF::F959-1NF::F969-4NF::F1026-1NF::F976-8NF::F969-6NF::M878-2NF::F959-9NF::F991-4NF::M1008-4NF::F969-8NF::F652-NF::M1013-5NF::F959-2NF::F1026-9NF::F969-5NF::F1027-1NF::M628-2NF::F884-3NF::F841-1NF::F757-1NF::M952-1NF::F957-10NF::F959-3NF::F1023-NF::F841-2NF::F947-4NF::F757-3NF::F991-1NF::M851-3NF::M988-4NF::M878-3NF::F969-7NF::M952-4NF::F976-1NF:: +62 chr11:36761400-36773900 1.95164604234797e-71 4.67165513156834e-67 Odz2, ::F884-3NF::F1026-8NF::F959-10NF::F976-7NF::F849-7NF::F959-1NF::F1026-10NF::F969-5NF::F959-5NF::F957-9NF::F959-2NF::F771-2NF::F991-5NF::F1026-7NF::F957-10NF::F1027-10NF::M1013-2NF::F1026-5NF::F991-2NF::F947-2NF::F976-11NF::F879-4NF::M878-3NF::F947-1NF::M851-3NF::F1027-9NF::F885-1NF::M878-5NF::F957-11NF::M1013-1NF::M952-3NF::M1008-2NF::F879-1NF::F849-5NF::F1026-2NF::F885-2NF::F969-8NF::F652-NF::M988-1NF::F1027-7NF::F957-3NF::M1008-5NF::M1013-3NF::M1022-13NF::F841-1NF::M988-5NF::F983-2NF::F757-3NF::F947-4NF::F1023-NF::F969-10NF::F1027-1NF::M988-7NF::F649-3NF::F1026-4NF::F884-2NF::F983-1NF::F969-3NF::F957-2NF::F757-1NF::M988-9NF::F1026-6NF:: +59 chr1:147286600-147299100 7.82087219929013e-67 1.87208217834408e-62 No results within 2500 bp window ::F969-10NF::M878-4NF::M988-2NF::M851-3NF::F1026-6NF::F969-3NF::F1027-4NF::F1026-8NF::F757-1NF::F879-1NF::F959-4NF::M878-5NF::F884-3NF::F976-9NF::M628-2NF::F969-2NF::M1013-5NF::F879-5NF::F991-2NF::F957-1NF::M988-6NF::M1008-5NF::F885-3NF::M1008-1NF::F879-4NF::F1026-10NF::F957-11NF::F959-1NF::F947-2NF::F976-16NF::F947-1NF::F947-4NF::F959-2NF::F771-5NF::F969-9NF::F1026-7NF::F957-10NF::M952-4NF::M851-2NF::F969-1NF::F1027-2NF::F879-2NF::M988-7NF::M878-2NF::F991-5NF::F991-1NF::M988-1NF::M1025-1NF::F947-3NF::F957-2NF::F1027-7NF::F969-8NF::F969-5NF::M988-5NF::F976-11NF::F1027-6NF::F884-2NF::F959-5NF::F983-2NF:: +90 chr11:3049700-3099700 3.21863246568986e-65 7.70444053312182e-61 RP23-191E3.2, RP23-191E3.18, Fau-ps2, Sfi1, Drg1, ::M988-2NF::M988-7NF::F947-1NF::M1013-2NF::F959-2NF::M952-4NF::F879-5NF::M952-2NF::F1026-7NF::F976-8NF::F879-4NF::F947-4NF::M988-3NF::F969-3NF::F969-8NF::F1026-10NF::F959-9NF::M988-1NF::F976-11NF::F983-2NF::F957-2NF::F947-3NF::F959-8NF::F884-2NF::M988-8NF::M1025-1NF::F991-2NF::M1013-3NF::F771-5NF::M1008-5NF::F969-6NF::M988-5NF::F757-1NF::F969-4NF::F969-2NF::M851-3NF::F1023-NF::F849-2NF::F969-5NF::M851-2NF::M1013-1NF::F1027-1NF::F957-3NF::F959-6NF::M878-1NF::F991-4NF::F959-1NF::F957-10NF::M878-6NF::F885-3NF::F1027-7NF::M1008-1NF::F841-4NF::F1026-8NF::F991-5NF::M988-6NF::F885-2NF::M952-3NF::F969-10NF::F947-2NF::F1026-1NF::F983-1NF::M1008-4NF::M878-2NF::F959-10NF::F884-3NF::F957-12NF::F649-3NF::M878-5NF::F737-NF::F841-2NF::F959-3NF::F1027-2NF::F976-7NF::F976-6NF::F1026-6NF::F879-6NF::F841-5NF::F841-6NF::F849-3NF::F976-1NF::F1026-9NF::F976-9NF::M988-9NF::F879-1NF::F969-1NF::F957-9NF::F1027-10NF::M1013-5NF::M1008-2NF:: +70 chr3:158241700-158266700 1.0374184832703e-63 2.48326862340412e-59 No results within 2500 bp window ::F957-11NF::M878-5NF::F991-5NF::F957-2NF::F737-NF::F969-2NF::F1027-2NF::F884-1NF::M1013-3NF::M1013-5NF::F959-6NF::F879-6NF::M988-5NF::M1013-4NF::F1026-7NF::F1026-5NF::M988-6NF::F969-6NF::F1027-8NF::F969-4NF::F757-3NF::F885-3NF::M988-9NF::F652-NF::F976-5NF::M851-1NF::F879-4NF::M1013-1NF::F957-12NF::F879-5NF::F969-8NF::M952-1NF::M1008-5NF::M988-8NF::F969-10NF::F991-4NF::M1008-4NF::M988-3NF::M1025-1NF::F947-5NF::F983-1NF::F1026-10NF::F947-4NF::F704-NF::M878-2NF::M988-7NF::F959-9NF::M878-6NF::F1026-8NF::F976-3NF::F885-1NF::F959-1NF::F957-1NF::F991-2NF::F649-3NF::F757-1NF::M988-1NF::F1027-5NF::F841-2NF::F959-2NF::M952-3NF::F841-1NF::F976-8NF::F969-3NF::F885-2NF::F841-6NF::M988-2NF::F771-5NF::F1023-NF::F983-2NF:: +51 chr9:35112200-35124700 6.86410677043711e-55 1.64306123763953e-50 No results within 2500 bp window ::M851-2NF::M878-5NF::F879-5NF::M1013-2NF::F1026-5NF::F969-3NF::M988-1NF::F976-3NF::F947-3NF::F991-5NF::M1013-3NF::F757-3NF::F976-8NF::F1026-7NF::F885-2NF::F983-2NF::M988-5NF::F771-5NF::F976-1NF::M952-2NF::F959-8NF::F1027-4NF::M878-2NF::F1027-1NF::F1026-6NF::M1008-5NF::F976-16NF::M851-3NF::M878-6NF::F1026-8NF::F1023-NF::F652-NF::F885-3NF::F1027-9NF::F969-9NF::F879-4NF::F1026-9NF::F849-5NF::M988-7NF::M952-1NF::F959-6NF::F957-1NF::F983-1NF::M988-6NF::F969-5NF::F991-1NF::F1027-2NF::M1025-1NF::M988-2NF::F1026-10NF::F991-4NF:: +50 chr8:62557900-62570400 1.96402943700095e-53 4.70129726334918e-49 U6, ::F1026-8NF::F983-2NF::F1026-5NF::F884-1NF::F771-5NF::M988-1NF::M1013-3NF::F841-6NF::F959-2NF::F957-12NF::F957-2NF::F983-1NF::F841-2NF::M988-3NF::F1027-8NF::M952-3NF::M1025-1NF::M1013-1NF::F947-5NF::F969-2NF::F649-3NF::M878-2NF::M988-7NF::F757-1NF::F991-2NF::M988-6NF::F969-3NF::F879-6NF::M1008-4NF::F737-NF::F885-2NF::F991-4NF::M988-2NF::F969-8NF::M1008-5NF::F969-6NF::F879-4NF::F957-1NF::M878-6NF::F885-1NF::F1027-5NF::F1026-10NF::M988-9NF::F885-3NF::F704-NF::M851-1NF::F841-1NF::F1027-2NF::F969-4NF::F976-8NF:: +48 chr17:35137100-35149600 1.51461289432772e-50 3.62552888515227e-46 Vars, ::M952-2NF::F957-3NF::F976-1NF::M851-2NF::F884-2NF::F959-1NF::M952-4NF::F969-1NF::F879-2NF::F969-9NF::F959-3NF::F1023-NF::F879-6NF::F976-4NF::M988-9NF::F957-2NF::F1027-10NF::F884-1NF::F1026-5NF::F976-6NF::M851-3NF::F983-1NF::F957-11NF::M878-1NF::F947-2NF::F976-3NF::M988-1NF::F1027-7NF::F959-2NF::F879-4NF::F879-5NF::F1026-10NF::F1026-2NF::F991-2NF::F841-2NF::F957-1NF::F969-4NF::M878-3NF::F959-5NF::F704-NF::F976-11NF::M952-3NF::M988-8NF::F1026-4NF::F885-3NF::M1013-4NF::M988-3NF::F885-2NF:: +46 chr1:81517000-81529500 1.07554433654815e-47 2.5745304783953e-43 No results within 2500 bp window ::F957-2NF::F969-4NF::M988-5NF::F976-4NF::F1027-2NF::F1027-9NF::F771-2NF::F649-3NF::F1026-5NF::M910-4NF::F947-3NF::M988-6NF::F959-5NF::F1027-3NF::F957-9NF::M628-2NF::F1023-NF::M910-2NF::F959-9NF::F991-5NF::F976-2NF::M952-2NF::F957-11NF::M988-7NF::M878-2NF::M1013-3NF::F1026-7NF::M1013-1NF::M1013-2NF::F959-10NF::F885-2NF::F969-8NF::F983-1NF::F673-3NF::F969-6NF::F1027-4NF::F849-2NF::F1026-10NF::F976-11NF::F652-NF::F983-2NF::F969-3NF::F879-1NF::F1027-5NF::M552-NF::F757-3NF:: +46 chr11:3034900-3047400 1.07554433654815e-47 2.5745304783953e-43 Sfi1, RP23-191E3.1, RP23-191E3.2, ::F959-9NF::F959-8NF::F1026-10NF::F1026-7NF::F947-4NF::M1008-5NF::F737-NF::F757-1NF::F969-9NF::M988-2NF::M988-7NF::M878-5NF::F969-1NF::F969-2NF::F969-8NF::F991-5NF::M988-1NF::F976-11NF::F757-3NF::F879-4NF::F983-2NF::F879-5NF::M988-3NF::F1027-10NF::M878-2NF::M952-4NF::F969-5NF::F1027-9NF::F959-6NF::M988-4NF::M1013-1NF::F957-1NF::F957-2NF::M1025-1NF::F969-7NF::F991-4NF::F841-2NF::M878-6NF::F957-10NF::M1013-3NF::M988-6NF::M851-3NF::F976-16NF::F991-2NF::F959-1NF::F969-6NF:: +43 chr1:31953200-31965700 1.72994660475409e-43 4.14097318779987e-39 No results within 2500 bp window ::F885-2NF::M952-1NF::F947-1NF::F1027-2NF::F884-2NF::F1027-5NF::F885-3NF::F991-4NF::F957-9NF::F757-1NF::F1026-8NF::F991-2NF::F649-3NF::F947-4NF::F1027-1NF::M1025-1NF::F1027-10NF::F1027-7NF::F969-10NF::F1026-7NF::F947-3NF::F1027-4NF::M988-1NF::F947-2NF::F959-1NF::M988-5NF::F879-1NF::F959-5NF::F976-9NF::F957-11NF::M628-2NF::M878-2NF::F879-5NF::F959-6NF::F991-1NF::F1023-NF::F737-NF::F957-10NF::M1008-1NF::M878-5NF::M1013-1NF::F991-5NF::M988-2NF:: +42 chr5:6158300-6170800 4.17344736538259e-42 9.9899809585163e-38 No results within 2500 bp window ::F1027-7NF::F1026-10NF::M1013-1NF::F649-3NF::M988-3NF::M1008-4NF::F1027-5NF::F969-4NF::F1027-2NF::F959-2NF::F885-3NF::F957-1NF::F957-12NF::M988-7NF::M1013-4NF::M878-5NF::F885-1NF::F841-2NF::F757-1NF::F771-5NF::F704-NF::F991-4NF::F841-6NF::M878-2NF::F884-1NF::F879-4NF::F947-5NF::F969-6NF::M952-3NF::F969-2NF::M988-1NF::F1023-NF::F983-1NF::F879-6NF::M952-1NF::F1026-8NF::F991-2NF::F969-8NF::M851-2NF::F885-2NF::M988-2NF::M988-6NF:: +42 chr10:47101800-47114300 4.17344736538259e-42 9.9899809585163e-38 No results within 2500 bp window ::M1008-4NF::F1026-8NF::F957-2NF::F959-6NF::M1013-1NF::F885-3NF::M878-6NF::F757-1NF::M952-3NF::M851-1NF::F885-2NF::F1026-5NF::M1013-3NF::F959-2NF::F959-8NF::M1013-5NF::F983-2NF::F969-2NF::M1008-5NF::F991-4NF::F841-2NF::F991-5NF::F959-1NF::F1027-2NF::F879-6NF::F771-5NF::F841-6NF::M1013-4NF::F969-6NF::F957-1NF::F947-5NF::M988-9NF::F983-1NF::M988-7NF::F969-4NF::F957-12NF::F991-2NF::M878-5NF::F1023-NF::F976-8NF::F947-4NF::M988-1NF:: +39 chr18:3004600-3017100 5.07655900194202e-38 1.21517592829486e-33 No results within 2500 bp window ::M988-5NF::F1026-8NF::F1027-2NF::M988-1NF::F969-6NF::M952-2NF::M1008-4NF::M1008-1NF::F959-8NF::F757-1NF::F959-6NF::F959-2NF::F879-4NF::F969-7NF::M1013-5NF::F1026-7NF::F991-2NF::F969-8NF::F885-2NF::M1025-1NF::F969-3NF::F959-1NF::F969-10NF::F957-2NF::F969-4NF::M988-2NF::F947-2NF::M1008-2NF::F771-5NF::M1008-5NF::M1013-1NF::F976-11NF::M1013-4NF::F969-2NF::F879-1NF::M952-3NF::M878-2NF::F885-3NF::M878-5NF:: + +PNSTQUAD-E_0.01library +number pos pvalue bonferroni gene_name library_name + +PNSTQUAD-E_0.001library +number pos pvalue bonferroni gene_name library_name + +PNSTQUAD-E_0.0001library +number pos pvalue bonferroni gene_name library_name + +PNSTQUAD-E_0library +number pos pvalue bonferroni gene_name library_name +9 chr5:28496400-28508900 2.47204676339557e-18 2.18207567804927e-14 En2, ::F510P::M504P::M892-P::M620-2P::M620-1P::F585P::F760P::F630P::M625P:: +8 chr10:57318100-57330600 4.82670209412034e-16 4.26052993848002e-12 No results within 2500 bp window ::M620-1P::F510P::F585P::F630P::M625P::M620-2P::M504P::F760P:: +7 chr2:163468400-163480900 8.37706307011232e-14 7.39443357198814e-10 AL591488.2, 0610039K10Rik, Serinc3, ::M892-P::F630P::M620-1P::F510P::F760P::F585P::M620-2P:: +8 chr19:32873100-32898100 1.17997255344759e-13 1.04156177292819e-09 Pten, ::F630P::M620-2P::M620-1P::F510P::M625P::M504P::F585P::F760P:: +6 chr9:17524300-17536800 1.27215822052408e-11 1.1229340612566e-07 No results within 2500 bp window ::M504P::F630P::F585P::M620-2P::M625P::F760P:: +6 chr6:69880000-69892500 1.27215822052408e-11 1.1229340612566e-07 AC154006.7, ::M504P::F630P::M625P::M620-1P::F585P::F760P:: +6 chr3:48818900-48831400 1.27215822052408e-11 1.1229340612566e-07 No results within 2500 bp window ::M504P::M625P::M892-P::F510P::F585P::M620-2P:: +6 chr3:31855800-31880800 7.77503849724701e-10 6.86302648151994e-06 Kcnmb2, ::M620-2P::M504P::M892-P::F585P::M625P::F510P:: +6 chr2:98484100-98509100 7.77503849724701e-10 6.86302648151994e-06 AL837506.2, AL837506.1, ::M620-2P::F585P::F630P::M620-1P::M892-P::M504P:: +7 chr11:3051500-3101500 1.19524259257415e-09 1.0550406364652e-05 RP23-191E3.18, Fau-ps2, RP23-191E3.2, Eif4enif1, Sfi1, Drg1, ::M625P::M620-2P::F630P::F510P::M504P::M892-P::F585P:: +5 chr9:3022100-3034600 1.65593651327795e-09 1.46169516027045e-05 AC131780.5, AC131780.2, AC131780.4, AC131780.6, AC131780.12, AC131780.7, ::M620-1P::M892-P::F585P::M625P::F630P:: +5 chr9:3739300-3751800 1.65593651327795e-09 1.46169516027045e-05 Gucy1a2, ::M620-2P::F585P::M625P::M504P::M620-1P:: +5 chr5:22846400-22858900 1.65593651327795e-09 1.46169516027045e-05 No results within 2500 bp window ::M620-1P::M625P::F585P::M504P::M620-2P:: +5 chr4:96181600-96194100 1.65593651327795e-09 1.46169516027045e-05 Cyp2j6, ::F630P::M620-1P::M625P::M504P::F760P:: +5 chr11:36769600-36782100 1.65593651327795e-09 1.46169516027045e-05 Odz2, ::M504P::M625P::M620-1P::F585P::F510P:: +5 chr1:81528400-81540900 1.65593651327795e-09 1.46169516027045e-05 No results within 2500 bp window ::F630P::M625P::F760P::M620-2P::F510P:: +5 chr1:96856200-96868700 1.65593651327795e-09 1.46169516027045e-05 No results within 2500 bp window ::F760P::M625P::F630P::F585P::M620-1P:: +6 chr11:79199700-79249700 4.53780064963545e-08 0.000400551663343321 Nf1, ::F760P::F510P::M620-1P::M504P::F630P::F585P:: +5 chr7:91691600-91716600 5.06028650053809e-08 0.000446671489402497 AC129605.1, ::M892-P::F510P::M620-2P::M620-1P::F585P:: +5 chr16:17173800-17198800 5.06028650053809e-08 0.000446671489402497 Ube2l3, ::M620-1P::F510P::F630P::M625P::M620-2P:: +7 chr16:4107400-4207400 1.27230669453346e-07 0.00112306511926468 Crebbp, ::M892-P::M620-2P::M620-1P::F510P::F585P::M625P::M504P:: +4 chr8:58426500-58439000 1.79624259242265e-07 0.00158554333633148 Glra3, ::M504P::F510P::F760P::M620-2P:: +4 chr6:42047500-42060000 1.79624259242265e-07 0.00158554333633148 No results within 2500 bp window ::F585P::M620-2P::M504P::M892-P:: +4 chr4:86833900-86846400 1.79624259242265e-07 0.00158554333633148 Slc24a2, ::M620-1P::F760P::M625P::M504P:: +4 chr2:69796600-69809100 1.79624259242265e-07 0.00158554333633148 Ubr3, ::F760P::M620-2P::M504P::F585P:: + +NFQUAD-E_0.01library +number pos pvalue bonferroni gene_name library_name +57 chr5:28496400-28508900 3.38534186210771e-239 9.37739695803837e-237 En2, ::F624-2NF::F735-5NF::F802-2NF::M892-5NF::M920-5NF::F735-1NF::M626-10NF::M732-2NF::M892-1NF::M724-1NF::F648-1NF::F601-NF::F760-3NF::M624-7NF::M892-9NF::F695-2NF::F760-1NF::M732-4NF::M624-5NF::M724-6NF::F968-4NF::F695-4NF::F729-3NF::F729-5NF::M624-1NF::M724-4NF::F624-4NF::F760-2NF::F796-NF::M892-7NF::F729-1NF::F695-3NF::F802-6NF::M732-5NF::F850-5NF::M624-6NF::F648-4NF::F760-6NF::F802-5NF::M626-7NF::M920-3NF::M624-4NF::F624-5NF::F802-3NF::F968-3NF::M626-5NF::F624-1NF::F850-4NF::M724-2NF::M920-4NF::F624-3NF::F729-4NF::F850-7NF::M892-2NF::M920-2NF::F850-2NF::M892-6NF:: +12 chr2:163468500-163481000 1.74911716915585e-43 4.8450545585617e-41 AL591488.2, 0610039K10Rik, Serinc3, ::F601-NF::F729-1NF::F802-6NF::F802-4NF::F760-3NF::F802-2NF::F695-4NF::F850-4NF::M892-1NF::F850-7NF::F994-7NF::M892-4NF:: +4 chr2:98502800-98515300 1.82146953791886e-13 5.04547062003523e-11 AL837506.1, AL837506.2, ::M732-3NF::F624-6NF::F729-4NF::F729-5NF:: +4 chr10:57318100-57330600 1.82146953791886e-13 5.04547062003523e-11 No results within 2500 bp window ::F994-3NF::F994-4NF::F994-1NF::F994-8NF:: +2 chr2:101636000-101648500 1.04465402141864e-06 0.000289369163932964 Prr5l, ::M732-1NF::F796-NF:: +2 chr7:35892300-35904800 1.04465402141864e-06 0.000289369163932964 Cebpa, ::F735-5NF::F735-1NF:: +2 chr9:21769300-21781800 1.04465402141864e-06 0.000289369163932964 Epor, Rgl3, ::F735-1NF::F735-5NF:: +2 chr2:26322200-26334700 1.04465402141864e-06 0.000289369163932964 Notch1, ::F729-2NF::F729-3NF:: +2 chrX:12148100-12173100 4.17257613411576e-06 0.00115580358915006 Atp6ap2, ::F850-4NF::F994-7NF:: +2 chr18:15705800-15805800 6.61843091560081e-05 0.0183330536362142 Chst9, ::F729-3NF::M732-1NF:: + +NFQUAD-E_0.001library +number pos pvalue bonferroni gene_name library_name + +NFQUAD-E_0.0001library +number pos pvalue bonferroni gene_name library_name + +NFQUAD-E_0library +number pos pvalue bonferroni gene_name library_name +107 chr5:28496200-28508700 2.28754584596777e-161 5.47569849149305e-157 En2, ::F735-3NF::M724-6NF::F695-1NF::F802-4NF::F802-2NF::M732-3NF::F850-5NF::M732-2NF::F968-3NF::F850-3NF::M892-5NF::M724-3NF::M892-2NF::M892-4NF::M724-1NF::F802-1NF::M732-4NF::F648-1NF::F648-2NF::F968-4NF::F760-2NF::M624-2NF::F850-1NF::F648-5NF::M724-2NF::F735-7NF::F760-4NF::M624-4NF::M626-9NF::M624-5NF::M892-6NF::F850-4NF::M624-1NF::M626-10NF::M624-7NF::F735-1NF::M920-4NF::F760-6NF::F624-3NF::F968-1NF::F968-2NF::F802-3NF::F648-3NF::M732-5NF::F729-2NF::M626-1NF::M892-1NF::F994-1NF::M920-1NF::M892-10NF::F695-3NF::M626-11NF::F695-2NF::F850-2NF::M892-7NF::F850-8NF::F802-6NF::F760-5NF::M892-3NF::M920-3NF::M626-3NF::M624-6NF::F735-5NF::M732-6NF::F760-3NF::F648-4NF::F624-1NF::M626-6NF::F968-6NF::M920-2NF::F850-6NF::M892-11NF::M624-8NF::F729-3NF::F735-4NF::M626-5NF::F735-2NF::M626-7NF::M892-8NF::F601-NF::F624-4NF::M624-3NF::F729-1NF::M626-2NF::M724-5NF::M626-4NF::F729-4NF::M920-5NF::M724-4NF::F735-6NF::F796-NF::M626-8NF::F624-2NF::F994-8NF::F760-1NF::F850-7NF::F695-4NF::F624-5NF::M892-9NF::F802-5NF::F968-5NF::F994-6NF::F994-4NF::M732-1NF::F729-5NF::F729-6NF::F624-6NF:: +102 chr2:163456600-163469100 8.01464802583763e-152 1.91846629794475e-147 AL591488.2, Serinc3, 0610039K10Rik, ::F802-4NF::F850-8NF::M732-6NF::M626-11NF::F735-4NF::M626-10NF::F648-2NF::M626-8NF::M624-3NF::F624-1NF::F994-6NF::F729-3NF::M732-2NF::F850-4NF::M892-4NF::M732-1NF::F648-4NF::F735-3NF::F729-5NF::F802-5NF::M920-4NF::M892-10NF::M892-9NF::M920-3NF::F648-1NF::M624-6NF::M892-11NF::F802-3NF::F850-5NF::F648-3NF::M724-5NF::F850-3NF::F760-5NF::M626-6NF::F624-2NF::M892-1NF::M892-5NF::M624-8NF::F968-1NF::F695-2NF::F624-3NF::F624-4NF::M626-5NF::F802-2NF::F760-2NF::F850-7NF::M624-2NF::M626-1NF::M624-7NF::F729-1NF::F968-4NF::F695-3NF::F850-1NF::M624-1NF::M732-4NF::F760-1NF::M892-6NF::F968-2NF::M624-5NF::F729-4NF::M626-2NF::F760-3NF::M724-2NF::M892-2NF::F850-2NF::M724-6NF::F624-5NF::F648-5NF::M626-3NF::M626-9NF::M626-7NF::M920-5NF::F735-5NF::M732-5NF::M892-3NF::F796-NF::M626-4NF::F695-4NF::F802-6NF::F760-4NF::M892-7NF::M624-4NF::F729-2NF::F968-6NF::F968-3NF::F850-6NF::M724-1NF::F735-1NF::M724-4NF::F735-6NF::M920-1NF::M892-8NF::F735-7NF::F735-2NF::F994-2NF::F695-1NF::F601-NF::M920-2NF::F729-6NF::F802-1NF::M724-3NF::F994-7NF:: +98 chr2:98495200-98507700 2.90705539823292e-144 6.95861850675014e-140 AL837506.2, AL837506.1, ::F729-4NF::F968-1NF::F648-5NF::M724-3NF::F729-2NF::F850-5NF::F968-3NF::F760-6NF::M626-8NF::F735-4NF::M626-4NF::M626-2NF::F796-NF::M732-6NF::F760-4NF::M626-6NF::F648-2NF::M624-2NF::F802-2NF::M892-2NF::M624-3NF::F624-4NF::M892-11NF::M724-4NF::M892-10NF::M920-5NF::F850-4NF::F968-6NF::M626-10NF::F735-7NF::F968-2NF::F624-3NF::M920-2NF::F850-3NF::M724-1NF::M732-5NF::M626-11NF::F850-6NF::M732-4NF::M624-6NF::M626-7NF::F648-4NF::M732-2NF::M892-4NF::M920-1NF::M892-8NF::F624-1NF::F968-5NF::F802-5NF::F968-4NF::M624-1NF::F802-4NF::M892-9NF::F695-2NF::M624-4NF::F735-3NF::F729-6NF::F850-1NF::M624-8NF::F695-4NF::F735-6NF::F760-2NF::F729-5NF::M626-1NF::M624-7NF::M724-2NF::F735-2NF::F695-3NF::M724-5NF::M892-3NF::F729-3NF::M920-3NF::M920-4NF::F850-8NF::M626-3NF::M724-6NF::F648-1NF::F695-1NF::M624-5NF::F624-5NF::F760-5NF::F850-2NF::M892-6NF::F850-7NF::M732-3NF::F729-1NF::M626-9NF::M892-7NF::F802-6NF::F648-3NF::F735-1NF::F624-6NF::F735-5NF::F760-3NF::F760-1NF::M892-5NF::M626-5NF::F802-3NF:: +84 chr13:31719100-31731600 2.21809525424525e-118 5.30945461008685e-114 Foxf2, RP23-322J11.2, ::M624-8NF::F735-3NF::M626-4NF::F968-4NF::M626-8NF::M724-5NF::M920-1NF::F802-3NF::M724-4NF::F760-5NF::M624-5NF::M724-6NF::F695-2NF::M892-7NF::M892-5NF::F648-1NF::F968-6NF::F850-2NF::M920-2NF::M724-1NF::F850-1NF::F735-4NF::F695-3NF::M624-6NF::M624-1NF::F850-7NF::F735-5NF::F760-4NF::F624-3NF::F729-1NF::M626-7NF::F729-4NF::M892-4NF::F850-8NF::M724-2NF::F735-6NF::M626-2NF::F624-4NF::M626-5NF::M920-4NF::F624-5NF::F648-5NF::M892-3NF::F735-2NF::M732-3NF::F796-NF::F760-2NF::M626-11NF::M624-4NF::M892-6NF::M920-5NF::F760-3NF::F968-1NF::M892-2NF::F850-3NF::M892-1NF::F802-5NF::M624-2NF::F735-1NF::M732-6NF::M626-10NF::M732-4NF::F968-2NF::M626-1NF::F802-6NF::F648-4NF::F850-6NF::F968-3NF::M624-7NF::M624-3NF::M892-8NF::F802-2NF::F624-1NF::M626-3NF::M724-3NF::F695-4NF::F729-2NF::F850-4NF::F850-5NF::M626-9NF::F760-1NF::M892-10NF::M920-3NF::F802-4NF:: +83 chr10:57314000-57326500 1.43884001408482e-116 3.44415134171484e-112 No results within 2500 bp window ::F760-2NF::F850-1NF::F648-5NF::F695-3NF::M624-1NF::M892-10NF::F968-1NF::F968-3NF::M626-10NF::F729-1NF::M626-9NF::F994-3NF::F796-NF::F994-2NF::M624-6NF::F648-3NF::M626-3NF::M624-2NF::F850-6NF::F994-1NF::M892-6NF::F802-6NF::F760-4NF::F735-1NF::M624-8NF::M724-6NF::M892-4NF::F968-4NF::F735-3NF::F760-3NF::M624-4NF::F729-2NF::F802-4NF::M626-11NF::M892-7NF::F968-6NF::M732-1NF::F735-4NF::F802-3NF::M624-7NF::M892-1NF::F695-1NF::F968-5NF::M626-1NF::F648-4NF::F729-4NF::M920-2NF::M732-4NF::F850-5NF::M626-6NF::M724-2NF::F624-3NF::M892-2NF::F850-3NF::F994-8NF::M892-11NF::F802-5NF::M892-3NF::F760-6NF::M626-8NF::M892-8NF::M920-5NF::F760-1NF::F994-6NF::M724-4NF::M626-5NF::F735-7NF::F994-7NF::F735-2NF::F729-3NF::F648-2NF::F994-4NF::M920-4NF::F735-6NF::F624-4NF::F968-2NF::M624-3NF::F760-5NF::F994-5NF::M626-7NF::M626-2NF::M626-4NF::F648-1NF:: +76 chr9:3020500-3033000 4.93131874846967e-104 1.18040976882118e-99 AC131780.5, AC131780.2, AC131780.4, AC131780.6, AC131780.12, AC131780.7, AC131780.3, ::M626-3NF::F850-7NF::M626-11NF::M892-10NF::M624-2NF::F968-3NF::M626-7NF::M732-2NF::F735-1NF::M892-11NF::F760-3NF::F968-2NF::M732-6NF::M626-2NF::M624-6NF::F968-1NF::F968-6NF::M624-7NF::F850-6NF::M626-4NF::M624-8NF::M624-3NF::F695-4NF::F850-8NF::M892-3NF::M724-4NF::M724-3NF::F850-2NF::F735-2NF::F735-3NF::F850-3NF::M920-1NF::F695-3NF::M920-2NF::F648-5NF::F729-4NF::F802-4NF::F648-2NF::F729-2NF::F624-1NF::M626-8NF::M626-6NF::F695-1NF::F850-5NF::M892-7NF::M892-9NF::F968-4NF::F735-4NF::F802-3NF::M892-4NF::F695-2NF::F735-7NF::M626-1NF::F735-6NF::M920-5NF::M624-5NF::F760-5NF::F760-6NF::F729-5NF::F760-4NF::M724-2NF::F624-3NF::F648-4NF::M892-8NF::F624-4NF::M732-5NF::M724-6NF::M724-5NF::M892-2NF::F624-5NF::F729-3NF::F802-5NF::F648-3NF::M920-4NF::M624-4NF::F760-2NF:: +72 chr3:48818900-48831400 5.40013508712852e-97 1.29263033580595e-92 No results within 2500 bp window ::F760-4NF::F850-2NF::F735-4NF::F624-1NF::M724-5NF::M732-6NF::F729-3NF::F968-5NF::M626-2NF::F850-7NF::M624-4NF::M920-4NF::M732-5NF::F735-1NF::M624-6NF::F695-4NF::M920-2NF::F695-3NF::F735-2NF::M626-4NF::F850-6NF::M624-1NF::F695-2NF::F735-6NF::F802-4NF::M892-2NF::M892-5NF::M626-3NF::F802-2NF::F735-3NF::F802-5NF::M624-3NF::F850-1NF::M626-6NF::F850-8NF::M626-7NF::M626-9NF::M892-9NF::M724-3NF::F968-2NF::F648-4NF::F760-2NF::F648-3NF::M624-7NF::M624-2NF::M892-8NF::F968-6NF::F760-1NF::M724-4NF::M892-7NF::M892-10NF::M732-4NF::F968-1NF::M626-11NF::F735-5NF::M624-8NF::F968-4NF::F695-1NF::M920-5NF::F760-5NF::M626-1NF::F796-NF::M892-4NF::F735-7NF::F648-5NF::F624-4NF::F850-4NF::M626-10NF::F624-3NF::M892-3NF::M920-1NF::F850-3NF:: +69 chrX:139915200-139927700 8.89923334025304e-92 2.13020948465637e-87 No results within 2500 bp window ::M892-10NF::M920-2NF::F695-2NF::F850-2NF::F729-2NF::M920-5NF::F648-5NF::M626-4NF::F648-2NF::F624-3NF::F695-1NF::M626-11NF::M724-1NF::F735-4NF::F648-4NF::M920-4NF::F735-1NF::F796-NF::M724-2NF::M626-8NF::F760-6NF::F802-4NF::F850-6NF::F968-3NF::F695-4NF::M920-1NF::M626-9NF::M724-5NF::M626-1NF::F968-1NF::F735-7NF::M892-7NF::M624-8NF::F735-3NF::M624-4NF::F735-2NF::M732-6NF::F735-6NF::M624-6NF::F760-2NF::M626-7NF::M624-2NF::F850-3NF::M892-5NF::M920-3NF::M892-1NF::M624-3NF::M724-4NF::F802-6NF::F850-8NF::F968-6NF::M892-11NF::M626-6NF::M624-1NF::F624-1NF::M892-8NF::M626-2NF::F968-4NF::F802-5NF::M724-6NF::M626-5NF::F760-3NF::M724-3NF::F968-5NF::M626-3NF::M624-7NF::F760-1NF::M892-3NF::M732-4NF:: +62 chr3:31851200-31863700 7.92564132372876e-80 1.89716076366095e-75 Kcnmb2, ::M920-2NF::F802-5NF::M892-8NF::F850-3NF::M892-2NF::M920-1NF::M626-2NF::M626-6NF::F760-5NF::F850-8NF::F735-4NF::M626-1NF::F802-2NF::F968-5NF::F968-4NF::M892-4NF::M626-7NF::M624-1NF::F624-3NF::M624-4NF::F648-5NF::F648-3NF::F968-1NF::M626-10NF::F735-6NF::F760-2NF::M892-7NF::F850-1NF::F968-2NF::F624-4NF::M732-6NF::F648-4NF::M892-9NF::F796-NF::F695-1NF::F729-3NF::M624-2NF::F735-5NF::M732-5NF::F729-4NF::F850-7NF::M892-10NF::M892-3NF::F695-4NF::M920-4NF::F968-6NF::F760-4NF::F735-2NF::F695-3NF::F735-3NF::M892-5NF::M626-4NF::M626-11NF::F624-1NF::M724-3NF::M626-3NF::M624-3NF::M626-9NF::F850-6NF::M920-5NF::M624-8NF::F648-2NF:: +58 chr6:103587500-103600000 3.7737342568552e-73 9.03318769063428e-69 Chl1, ::F735-7NF::M892-7NF::M892-3NF::F735-3NF::M626-11NF::M626-2NF::M724-1NF::F695-1NF::F968-5NF::M724-2NF::F968-2NF::M920-3NF::F648-5NF::F695-2NF::M626-4NF::M626-3NF::M920-1NF::F968-1NF::F760-6NF::F735-6NF::M724-6NF::F735-2NF::M724-5NF::M920-2NF::M626-1NF::M892-8NF::M624-8NF::F850-8NF::F735-4NF::M624-5NF::F729-6NF::F760-2NF::M892-10NF::F850-6NF::M626-8NF::M624-6NF::F760-4NF::M624-7NF::F760-3NF::M732-6NF::F968-6NF::F648-2NF::M626-9NF::F624-1NF::M920-5NF::F968-4NF::M626-10NF::F968-3NF::M624-2NF::M626-6NF::F729-4NF::M892-2NF::M624-4NF::F802-4NF::F729-2NF::F695-4NF::F796-NF::F695-3NF:: +57 chr9:3736500-3749000 1.6902554158522e-71 4.0459643889254e-67 Gucy1a2, ::M892-10NF::M626-8NF::F760-4NF::M626-3NF::F760-5NF::F624-1NF::F850-1NF::M626-2NF::F850-3NF::F624-4NF::M892-2NF::M624-6NF::M892-3NF::F968-6NF::F735-2NF::F735-4NF::M626-11NF::F968-1NF::M732-6NF::F695-1NF::M892-8NF::F850-6NF::F735-7NF::F735-3NF::F648-4NF::M724-2NF::M626-4NF::M920-2NF::M892-11NF::M724-3NF::M892-1NF::M626-7NF::M626-6NF::M624-2NF::M624-7NF::F735-6NF::M920-4NF::F695-3NF::M732-4NF::M892-4NF::F802-4NF::F802-3NF::M626-9NF::F968-2NF::F735-5NF::M624-3NF::F968-4NF::F624-3NF::F760-6NF::F735-1NF::M724-6NF::M626-5NF::F850-8NF::M626-1NF::F850-2NF::F796-NF::M920-1NF:: +49 chr11:36758000-36770500 1.42434530552752e-58 3.40945535784122e-54 Odz2, ::M892-1NF::M724-6NF::F695-2NF::F624-4NF::M920-4NF::M626-7NF::M732-4NF::F760-4NF::M892-8NF::F968-4NF::M624-2NF::M920-1NF::F760-5NF::F735-3NF::F850-2NF::M732-5NF::M626-2NF::M892-11NF::F695-1NF::M724-1NF::M624-1NF::M626-6NF::F802-3NF::F735-5NF::M626-9NF::F968-2NF::F624-1NF::M626-4NF::F648-2NF::F735-2NF::F968-1NF::F735-1NF::M724-2NF::F735-4NF::M626-11NF::M892-3NF::F850-6NF::M892-4NF::M626-3NF::M892-10NF::M626-1NF::M724-3NF::F735-7NF::F695-3NF::F850-1NF::F802-4NF::F968-6NF::M732-6NF::F850-3NF:: +48 chr1:147277600-147290100 5.38969757528497e-57 1.29013190859596e-52 No results within 2500 bp window ::F735-2NF::F729-2NF::M920-5NF::M624-3NF::F850-5NF::F729-4NF::M626-4NF::F648-3NF::F648-5NF::F968-2NF::F850-7NF::F624-1NF::M624-6NF::M724-6NF::M892-2NF::M724-3NF::F760-2NF::F735-5NF::F695-2NF::F796-NF::F695-3NF::F735-7NF::F729-6NF::F735-4NF::M920-4NF::F601-NF::M626-10NF::F624-4NF::M624-1NF::M892-10NF::M624-7NF::M920-1NF::F735-1NF::M920-2NF::F968-6NF::M732-4NF::F760-4NF::F802-6NF::M626-1NF::F624-3NF::F735-6NF::F729-1NF::F648-4NF::M724-2NF::M626-3NF::F968-1NF::F850-8NF::M732-6NF:: +48 chr9:25342700-25355200 5.38969757528497e-57 1.29013190859596e-52 Eepd1, SNORA70, ::M724-3NF::F968-6NF::F695-3NF::F735-4NF::F695-2NF::F695-1NF::F968-3NF::F802-5NF::M626-7NF::F968-2NF::M624-8NF::F648-2NF::M892-10NF::M626-8NF::F850-3NF::M626-1NF::F624-1NF::M892-2NF::M624-3NF::M920-5NF::M624-4NF::F624-4NF::F968-1NF::M892-3NF::F735-7NF::F760-1NF::F729-4NF::M626-10NF::F735-3NF::F968-5NF::F729-3NF::M732-4NF::F648-5NF::F994-6NF::M624-7NF::F802-4NF::F850-6NF::M732-1NF::F994-1NF::F994-2NF::M892-6NF::F994-8NF::F850-1NF::F994-7NF::F994-3NF::F994-4NF::F994-5NF::M892-7NF:: +44 chr5:22846400-22858900 8.95129666935999e-51 2.1426718837447e-46 No results within 2500 bp window ::F601-NF::F760-6NF::M624-8NF::F624-3NF::F850-1NF::M626-6NF::M892-6NF::F648-1NF::F994-4NF::F994-3NF::F968-1NF::F994-1NF::M626-10NF::F695-3NF::F994-6NF::F994-7NF::F994-8NF::M732-4NF::F695-2NF::M892-4NF::M626-8NF::F735-3NF::F994-5NF::M892-8NF::F968-5NF::F735-2NF::M624-3NF::M626-4NF::M920-3NF::M626-5NF::M892-10NF::F624-4NF::F735-4NF::M892-11NF::F802-4NF::M732-1NF::M892-3NF::F729-4NF::M626-1NF::M724-6NF::F624-1NF::F968-6NF::F648-5NF::F735-7NF:: +44 chr9:3000000-3012500 8.95129666935999e-51 2.1426718837447e-46 AC131780.8, AC131780.9, AC131780.5, AC131780.1, ::F850-2NF::M626-4NF::F735-4NF::M626-11NF::F735-2NF::M624-6NF::M724-5NF::M624-3NF::M626-6NF::F968-4NF::F695-4NF::F695-2NF::F968-3NF::M920-2NF::M724-6NF::F624-3NF::F760-4NF::F729-2NF::F735-7NF::M624-2NF::F624-1NF::M732-4NF::M724-2NF::F968-1NF::F850-8NF::M892-10NF::M626-2NF::F968-2NF::F802-6NF::M624-4NF::F648-2NF::F729-5NF::F968-6NF::M920-3NF::F850-5NF::F735-6NF::M624-7NF::F802-3NF::F735-3NF::M920-4NF::M920-1NF::M892-8NF::F648-3NF::F968-5NF:: +43 chr4:96180000-96192500 3.04152685814681e-49 7.28050284034603e-45 Cyp2j6, ::F968-4NF::F760-5NF::M892-3NF::F994-2NF::F624-4NF::F994-4NF::M626-10NF::F850-3NF::M892-1NF::F994-1NF::F735-7NF::F994-6NF::F994-7NF::M626-1NF::F968-3NF::F968-1NF::M624-8NF::F850-2NF::M892-7NF::F994-5NF::M626-4NF::F735-4NF::F624-1NF::M624-4NF::F968-2NF::F850-1NF::F760-6NF::M892-10NF::F735-2NF::F648-1NF::F802-4NF::M626-2NF::M624-3NF::F735-1NF::F994-3NF::M724-4NF::F648-5NF::F624-3NF::F796-NF::F968-6NF::F850-8NF::M892-8NF::M624-2NF:: +43 chr1:81516800-81529300 3.04152685814681e-49 7.28050284034603e-45 No results within 2500 bp window ::M724-2NF::M624-2NF::F760-4NF::M732-5NF::F648-5NF::F802-3NF::F796-NF::F695-2NF::M626-6NF::M892-3NF::M624-7NF::M624-6NF::F735-2NF::F850-3NF::F760-6NF::M892-1NF::F735-4NF::F735-3NF::F994-7NF::M892-10NF::F994-4NF::F729-4NF::M892-7NF::F850-6NF::F760-5NF::F802-4NF::M724-6NF::F994-6NF::M626-8NF::F994-3NF::F994-8NF::F850-7NF::F994-1NF::M626-2NF::M624-8NF::F648-2NF::F648-3NF::F994-5NF::F850-1NF::F968-1NF::M892-8NF::F968-3NF::F968-5NF:: +43 chr17:35136100-35148600 3.04152685814681e-49 7.28050284034603e-45 Vars, ::F760-4NF::M892-11NF::F968-4NF::M626-6NF::F695-3NF::F729-1NF::F802-5NF::M626-7NF::F648-1NF::F624-3NF::M626-2NF::F729-3NF::M624-5NF::F735-1NF::F850-4NF::M626-11NF::M624-2NF::F729-2NF::F760-1NF::F695-4NF::M892-9NF::M724-4NF::F648-2NF::M724-6NF::M892-2NF::M724-3NF::M724-1NF::M892-7NF::M732-2NF::M624-4NF::M626-9NF::M624-1NF::F729-5NF::F850-5NF::F735-4NF::F695-2NF::M626-1NF::F729-4NF::M624-6NF::F624-1NF::M626-4NF::M892-6NF::F760-2NF:: +43 chr9:35107800-35120300 3.04152685814681e-49 7.28050284034603e-45 No results within 2500 bp window ::F624-1NF::M920-2NF::F735-4NF::F735-7NF::M624-4NF::F802-4NF::M724-1NF::M624-3NF::M624-6NF::M624-7NF::F648-2NF::M732-3NF::F850-8NF::F648-4NF::M892-8NF::F802-5NF::F802-6NF::M626-10NF::M732-4NF::F850-3NF::M624-8NF::F735-2NF::F729-2NF::M732-2NF::M724-4NF::F968-1NF::M892-10NF::F735-6NF::M626-11NF::M626-8NF::F760-6NF::F648-5NF::F968-6NF::M892-3NF::M724-2NF::F695-2NF::M624-2NF::M626-6NF::F968-2NF::F760-5NF::M724-6NF::M626-2NF::F624-5NF:: +43 chr9:52992800-53005300 3.04152685814681e-49 7.28050284034603e-45 Ddx10, ::M626-11NF::F802-5NF::F802-6NF::F735-2NF::F760-2NF::F760-1NF::F994-1NF::F760-6NF::M892-3NF::F968-1NF::F648-2NF::M732-1NF::F968-2NF::F735-6NF::F624-3NF::M626-10NF::F994-4NF::F850-7NF::F994-5NF::F850-1NF::F802-4NF::F994-3NF::F994-2NF::F695-2NF::F624-4NF::F850-6NF::F648-4NF::F648-5NF::F729-4NF::M626-9NF::M892-8NF::M624-1NF::M626-1NF::F968-5NF::M626-6NF::M624-2NF::F994-6NF::F850-3NF::F850-2NF::M724-6NF::F802-3NF::F735-4NF::F994-7NF:: +52 chr11:3052400-3077400 2.87733878110872e-48 6.88748584033995e-44 Sfi1, RP23-191E3.2, ::F850-6NF::M920-2NF::M624-7NF::F735-6NF::M626-11NF::F760-5NF::M624-2NF::M624-8NF::M724-6NF::F624-1NF::F735-4NF::F735-2NF::F695-2NF::F850-8NF::F994-4NF::M626-1NF::F850-1NF::F735-7NF::F648-1NF::F624-4NF::M626-7NF::F968-6NF::F735-3NF::M626-8NF::F968-2NF::M624-6NF::F968-1NF::M892-8NF::M892-10NF::M624-5NF::M892-7NF::F648-2NF::M624-3NF::M724-4NF::M626-5NF::M892-4NF::M724-3NF::F624-3NF::F760-2NF::F624-5NF::F802-6NF::M732-2NF::M626-4NF::F850-3NF::M892-3NF::F796-NF::F648-5NF::F695-3NF::M920-4NF::F735-1NF::F760-1NF::F760-4NF:: +40 chr3:158263500-158276000 1.03717572491073e-44 2.48268753271882e-40 No results within 2500 bp window ::M624-8NF::M732-6NF::M626-4NF::F968-1NF::F648-2NF::F796-NF::F648-4NF::F648-5NF::F695-2NF::F735-7NF::F802-6NF::M626-2NF::M626-7NF::F850-1NF::F624-3NF::F850-8NF::M624-2NF::F802-5NF::M892-10NF::F760-4NF::M624-3NF::M724-4NF::F648-1NF::M626-11NF::M624-1NF::M724-3NF::F695-4NF::M626-6NF::F850-3NF::M624-4NF::F968-6NF::M624-6NF::M626-8NF::F695-3NF::F968-3NF::F735-6NF::M892-8NF::F735-2NF::F735-4NF::F760-2NF:: +34 chr11:3037500-3050000 6.07926363805008e-36 1.45519333704005e-31 Sfi1, RP23-191E3.1, RP23-191E3.2, ::M626-11NF::F850-3NF::M624-8NF::F735-4NF::M892-3NF::F648-5NF::M624-2NF::M624-3NF::F695-2NF::F735-7NF::M724-4NF::M920-1NF::F850-8NF::F760-2NF::F968-6NF::F850-6NF::M626-7NF::F735-3NF::M892-2NF::F624-3NF::M626-2NF::M626-9NF::M626-6NF::M892-10NF::F735-6NF::F648-2NF::F624-1NF::F850-2NF::F760-4NF::F735-2NF::M724-3NF::F968-2NF::M920-2NF::F968-3NF:: +33 chr6:69880000-69892500 1.59618388958204e-34 3.82078537649252e-30 AC154006.7, ::M892-9NF::F994-2NF::F994-3NF::M892-10NF::M732-1NF::M920-1NF::F994-4NF::M892-7NF::F695-1NF::M624-8NF::F850-6NF::M624-5NF::F994-1NF::M920-2NF::F850-3NF::F729-5NF::F735-6NF::F695-3NF::F994-8NF::M624-4NF::F994-6NF::F735-4NF::F735-2NF::F695-4NF::F850-1NF::F968-1NF::F994-7NF::F850-2NF::F729-3NF::F735-3NF::F968-6NF::F735-7NF::M626-6NF:: + +NFQUAD-P_0.01library +number pos pvalue bonferroni gene_name library_name +4 chr5:28496400-28508900 7.93012966614384e-17 3.17205186645753e-15 En2, ::F877-1NF::F877-6NF::F877-3NF::F877-2NF:: + +NFQUAD-P_0.001library +number pos pvalue bonferroni gene_name library_name + +NFQUAD-P_0.0001library +number pos pvalue bonferroni gene_name library_name + +NFQUAD-P_0library +number pos pvalue bonferroni gene_name library_name +6 chr5:28496400-28508900 9.10132854722052e-14 3.51129255351768e-10 En2, ::F877-5NF::F877-4NF::F877-6NF::F877-3NF::F877-1NF::F877-2NF:: +6 chr2:163468400-163480900 9.10132854722052e-14 3.51129255351768e-10 AL591488.2, 0610039K10Rik, Serinc3, ::F877-3NF::F877-5NF::F877-6NF::F877-4NF::F877-1NF::F877-2NF:: +5 chr2:98502700-98515200 2.71055515749522e-11 1.04573217976166e-07 AL837506.1, AL837506.2, ::F877-5NF::F877-3NF::F877-4NF::F877-2NF::F877-1NF:: +4 chr13:31719100-31731600 6.72713991122729e-09 2.59533057775149e-05 Foxf2, RP23-322J11.2, ::F877-4NF::F877-1NF::F877-3NF::F877-5NF:: +4 chr9:3000200-3025200 1.05487493120192e-07 0.000406970748457699 AC131780.8, AC131780.9, AC131780.1, AC131780.11, AC131780.3, AC131780.7, AC131780.2, AC131780.5, AC131780.4, ::F877-1NF::F877-4NF::F877-5NF::F877-3NF:: +5 chr11:3000500-3100500 7.71368473443027e-07 0.0029759395705432 Pisd-ps1, Sfi1, RP23-191E3.1, RP23-191E3.2, RP23-191E3.18, Fau-ps2, Eif4enif1, Drg1, ::F877-3NF::F877-5NF::F877-4NF::F877-7NF::F877-6NF:: +3 chr6:103599100-103611600 1.335649968534e-06 0.00515293757860419 Chl1, ::F877-3NF::F877-4NF::F877-5NF:: +3 chr2:57580700-57593200 1.335649968534e-06 0.00515293757860419 No results within 2500 bp window ::F877-5NF::F877-3NF::F877-6NF:: +3 chr17:35137700-35150200 1.335649968534e-06 0.00515293757860419 Vars, ::F877-1NF::F877-6NF::F877-3NF:: +3 chr11:94176300-94188800 1.335649968534e-06 0.00515293757860419 Ankrd40, Luc7l3, ::F877-5NF::F877-6NF::F877-4NF:: +3 chr10:57318100-57330600 1.335649968534e-06 0.00515293757860419 No results within 2500 bp window ::F877-3NF::F877-5NF::F877-4NF:: +3 chrX:39250500-39263000 1.335649968534e-06 0.00515293757860419 Thoc2, ::F877-2NF::F877-5NF::F877-6NF:: \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/config.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,70 @@ +use DBI; + +# +# Database stuff +# + + $dbh; # database handler + $db_name = 'largaespada_NGS_insertion_test'; +#my $db_username = 'insertion_larga'; +#my $db_password = 'uwtc.Pzc92'; + $db_username = 'sarvera'; + $db_password = 'fn101bcc'; + + $db_host = '127.0.0.1;mysql_local_infile=1'; + $db_type = 'mysql'; + $data_source = "DBI:$db_type:database=$db_name;host=$db_host"; + +# +# global values +# +# allows multiple active instances to be running in the db... +$proj = 'merge_science'; +$library_percent ='0.0001'; + +$CIS_total_pvalue = '0.05'; +$CIS_library_pvalue = '0.05'; +$CIS_region_pvalue = '0.05'; + +$cocis_threshold ='0.001'; + +$dbh = DBI->connect($data_source, $db_username, $db_password, +{ RaiseError => 1, AutoCommit => 0 }); + +sub resolve_barcodes { +#2.1 map the barcodes to the sequences..must change (sequence, #) to length of barcode +1 based on barcode sequence length!. +#Currently set up for 6,10,12 base barcodes. +####for 6mer barcodes... +#$sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,7) as decoded_sequence from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); +####for 10mer barcodes... +$sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,11) as decoded_sequence from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); +#for 12mer barcodes... +#$sth = $dbh->prepare("create table illumina_decoded_$proj select library, id, substring(sequence,13) as decoded_sequence from barcode_$proj,illumina_raw_$proj where sequence like concat(seq,'%')"); + +$sth->execute; + + } + +sub resolve_IRDR { +#2.3 +#different options available this section needs to be optomized for each dataset +#for lung 454 data +$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,32) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like '_____TGTATGTAAACTTCCGACTTCAACTG%'"); + +$sth->execute; +$sth = $dbh->prepare("insert into illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,31) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like '_____TGTATGTAACTTCCGACTTCAACTG%'"); + + + +#$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,31) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like 'TTAAGTGTATGTAACTTCCGACTTCAACTG%'"); + +#for illumina data +#$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,27) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like 'TGTATGTAAACTTCCGACTTCAACTG%'"); + +#for illumina_2 data +#$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,30) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like '___TGTATGTAAACTTCCGACTTCAACTG%'"); + +#for MULV virus +#$sth = $dbh->prepare("create table illumina_without_IRDR_$proj select library,id,substring(decoded_sequence,26) as insertion_sequence, 'good' as type from illumina_decoded_$proj where decoded_sequence like 'CCAAACCTACAGGTGGGGTCTTTCA%'"); +$sth->execute; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/convert_nr_2_annot.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,62 @@ +#This script annotates genomic positions to genes for ingenuity analyses. +#Aaron Sarver November 15, 2010 +#version #1.0 + +$in =$ARGV[0]; +$out = $ARGV[1]; + +@lib_list=(); +%seen=(); + +@uniq = (); +$libstring = ''; + + + +#open SOURCE, "< Med-nr-7-0.01.txt"; +open SOURCE, "< $in"; +open OUT, "> CIS/input.txt"; +open FIN, "> $out"; +while (defined($line = <SOURCE>)) { +$count++; +chomp $line; +@field= split(/\t/, $line); +$start = $field[1]-50; +$stop = $field[1]+50; + +print OUT "$field[0]\t$start\t$stop\n"; +} +close OUT; + +system('perl lib/feature_finder.pl -i CIS/input.txt -icol 1:2:3:6:13 -f lib/mm9.bed -o CIS/input2.txt'); + + +open SOURCE, "< CIS/input2.txt"; +while (defined($line = <SOURCE>)) { +$count++; +chomp $line; +@field= split(/\t/, $line); +#print "$field[0]\n"; +@genes= split(/,\s/,$field[3]); +foreach $gene (@genes) { +#print "$gene\n"; +push (@lib_list,$gene); +} +} + + +foreach $item (@lib_list) { +unless ($seen{$item}) { +$seen{$item}= 1; +push(@uniq,$item) +} + +} + +#open OUT, "> ingenuity_nr.txt"; +foreach $item(@uniq) { + +print FIN "$item\t10\n"; + +} +close FIN;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/feature_finder.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,241 @@ +#!/project/bioperl/perl-5.10.1-sles11/bin/perl -w +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2010, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# Jesse Erdmann +# +# POD documentation +#------------------------------------------------------------------------------ +=pod BEGIN + +=head1 NAME + + feature_finder.pl - find features nearest to another set of features within a given window. + +=head1 SYNOPSIS + + feature_finder.pl [-help] [-intervals interval_file] [-icol interval_column_config] + [-features feature_file] [-fcol feature_column_config] + [-results ALL|CLOSEST] [-direction BOTH|EITHER|UPSTREAM|DOWNSTREAM] + [-window win_size] [-output output_file] [-html html_output_file] + [-db db_name] [-cturl custom_track_url] [-include_capture] + [-promoter PROMOTER_BP] + +=head1 OPTIONS + +=over 6 + +=item B<-help> + + Print a usage summary + +=item B<-intervals interval_file> + + Specify the file containing the intervals to find the nearest features for, + default settings require a BED compatible file + +=item B<-features feature_file> + + Specify the file containing the features that will be mapped against, default + setting require a BED compatible file + +=item B<-results ALL|CLOSEST> + + The type of results to be reported. ALL will return all features within the + specified window size from each interval in the file including any overlapping + features. CLOSEST will return the closest feature within the window include + overlapping features. The special case ENCOMPASSING FEATURE AND + INTERNAL FEATURE override the closest distance. The first encountered + ENCOMPASSING FEATURE will be returned in CLOSEST mode. If no ENCOMPASSING + FEATURES exist, the first encountered INTERNAL FEATURE will be returned. If + neither exists, the closest distance is used. The closest distance is determined + by the shortest distance between either end of the interval and the feature + (e.g. start-start, start-end, end-start, end-end). + + The distance may also be ENCOMPASSING FEATURE or INTERNAL FEATURE. An + encompassing feature is one which starts before an interval and ends + after the interval. An internal feature is opposite where the feature + is entirely within the interval. + + DEFAULT:ALL + +=item B<-direction BOTH|EITHER|UPSTREAM|DOWNSTREAM> + + Direction is only used when CLOSEST is specified as the result type. BOTH + will return both the closest upstream and downstream feature in the window. + EITHER will return the closest regardless of whether it is upstream or + downstream. DOWNSTREAM will return the closest feature with a midpoint to + the right of midpoint of a + strand interval or the left of a - strand + interval. UPSTREAM is just the opposite. + + DEFAULT:BOTH + +=item B<-window win_size> + + Window size is the number of base pairs that will be considered upstream + and downstream of an interval in which to find features. This also affects + the performance of indexing and searching. Minimal testing suggests + 50000 bp to be roughly the optimal size, at least for Mus Musculus mm9/ncbim37. + + MINIMUM:2500 DEFAULT:2500 + +=item B<-output output_file> + + The file to report results to. The output format is a tab delimited file + starting with the original line from the interval file followed by a list + of matching features. Features are reported in the form of their name + followed by the distance away in bp ascending from shortest distance to + longest. e.g: + + MY_INTERVAL_INFO ENS000001(20 bp distant) ENS000002 (350 bp distant) ... + + The distance may also be ENCOMPASSING FEATURE or INTERNAL FEATURE. An + encompassing feature is one which starts before an interval and ends + after the interval. An internal feature is opposite where the feature + is entirely within the interval. + + DEFAULT:OFF + +=item B<-include_capture> + + Including capture information adds three columns to the output from + feature_finder. These are the start and end location to capture all + features found within the given window and the total distance in bp + required to capture the entire set. + +=item B<-promoter PROMOTOR_BP> + + The start and end of the capture region will be modified to include + the specified amount of the promoter region depending on the orientation + of the feature. '+' strand features modify the start position while '-' + strand features modify the end position. + + DEFAULT:0 + +=item B<-icols interval_chrom_column:start:end:label:strand> + + If the interval file is not in BED format, but still tab delimited -icols + can be used to specify which columns in the file contain specific + information. Column numbering begins with 1. + + DEFAULT:1:2:3:4:6 + +=item B<-fcols feature_chrom_column:start:end:label:strand> + + If the interval file is not in BED format, but still tab delimited -fcols + can be used to specify which columns in the file contain specific + information. Column numbering begins with 1. + + DEFAULT:1:2:3:4:6 + +=item B<-html> + + The output will be an HTML file with links to the features in the and + the interval at the UCSC browser. + +=item B<-db db_name> + + Set the database for the organism to be used in the UCSC genome browser. + Only used if an HTML output is specified. + + DEFAULT:mm9 + +=item B<-cturl custom_track_url> + + Define the URL to be used by the UCSC Genome Browser to load the custom + tracks for display purposes. If left blank the URLs will show the windows + defined by the input intervals, however the intervals themselves will not + appear. Only used if an HTML output is specified. + +=back + +=head1 BUGS + +=head1 REFERENCES + +=head1 VERSION + + 0.1 + +=cut + +#### END of POD documentation. +#----------------------------------------------------------------------------- + +use strict; +use Getopt::Long; +use Pod::Usage; +use List::Util qw[min max]; + +my $path = $0; +$path =~ s/\/\w*\.pl$//g; +require "$path/feature_finder_methods.pl"; + +my $intervals; +my $features; +my $req_res_type = "All"; # "Closest" +my $direction = "Both"; # "Upstream", "Downstream", "Both", "Either" +my $out; +my $window = 2500; +my %feature_hash; +my $help_flag; +my $interval_cols = "1:2:3:4:6"; +my $feature_cols = "1:2:3:4:6"; +my $html; +my $db = "mm9"; +my $cturl; +my $debug = 0; +my $include_capture = 0; +my $promoter = 0; + +my %options = ( + "direction|d=s" => \$direction, + "intervals|i=s" => \$intervals, + "features|f=s" => \$features, + "results|r=s" => \$req_res_type, + "output|o=s" => \$out, + "window|w=s" => \$window, + "icols=s" => \$interval_cols, + "fcols=s" => \$feature_cols, + "help|h" => \$help_flag, + "html" => \$html, + "db=s" => \$db, + "cturl=s" => \$cturl, + "include_capture|ic" => \$include_capture, + "promoter|p=i" => \$promoter, + "debug" => \$debug + ); + +GetOptions(%options) or pod2usage(2); +pod2usage(1) if $help_flag; + +pod2usage({ message => "The window specified with -window must be at least 2500.\n", exitval => 2}) if ($window < 2500); +#pod2usage({ message => "Result type specified with -result must be either $all or $close.\n", exitval => 2}) if (uc $req_res_type ne $all && uc $req_res_type ne $close); +pod2usage({ message => "Direction sepecified with -direction must be one of BOTH, EITHER, UPSTREAM or DOWNSTREAM.\n", exitval => 2}) if (uc $direction ne "BOTH" && uc $direction ne "EITHER" && uc $direction ne "UPSTREAM" && uc $direction ne "DOWNSTREAM"); + +my @icols = split(":", $interval_cols); +pod2usage({ message => "Must specify 5 columns with -icol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#icols != 4); +my $ichrom = $icols[0]-1; +my $istart = $icols[1]-1; +my $iend = $icols[2]-1; +my $ilabel = $icols[3]-1; +my $istrand = $icols[4]-1; + +my @fcols = split(":", $feature_cols); +pod2usage({ message => "Must specify 5 columns with -fcol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#fcols != 4); +my $fchrom = $fcols[0]-1; +my $fstart = $fcols[1]-1; +my $fend = $fcols[2]-1; +my $flabel = $fcols[3]-1; +my $fstrand = $fcols[4]-1; + + +my $feature_hash_ref = &feature_index(\$features, \$window, \$fchrom, \$fstart, \$fend, \$debug); +&process_intervals(\$intervals, \$out, $feature_hash_ref, \$req_res_type, \$direction, \$window, \$html, \$cturl, \$db, \$interval_cols, \$feature_cols, \$debug, \$display_distance, \$include_capture, \$promoter); +exit(0); + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/feature_finder_methods.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,376 @@ +use strict; +use List::Util qw[min max]; + +my $all = "ALL"; +my $close = "CLOSEST"; +my $first_idx = 0; +my $left = -1; +my $right = 1; +my $both = 0; +my $keys = "KEYS"; +my $NOT_FOUND = -3; +my $NOT_FOUND_STR = "NOT FOUND"; +my $ENCOMPASSING = -2; +#my $ENCOMPASSING_STR = ""; +my $ENCOMPASSING_STR = "ENCOMPASSING FEATURE"; +my $INTERNAL = -1; +#my $INTERNAL_STR = ""; +my $INTERNAL_STR = "INTERNAL FEATURE"; + +return 1; + +sub feature_index { + my ($feature_file, $window, $fchrom_col, $fstart_col, $fend_col, $debug) = @_; + open(FEATURES, "<${$feature_file}") || die "Unable to open features file, ${$feature_file}: $!\n"; + my %feature_hash = (); + my $num_indexed = 0; + while (<FEATURES>) { + if (${$debug}) { + if (($num_indexed % 1000) == 0) { + my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time); + print sprintf("%02d-%02d %02d:%02d:%02d Features Indexed: %9s\n", ($mon+1), $day, $hour, $min, $sec, $num_indexed); + } + } + chomp; + $num_indexed++; + my @split_line = split("\t"); + if (!@split_line) { next; } + my $interim_hash1 = int($split_line[${$fstart_col}]/${$window}); + my $interim_hash2 = int($split_line[${$fend_col}]/${$window}); + for (my $interim_hash = min($interim_hash1, $interim_hash2); $interim_hash <= max($interim_hash1, $interim_hash2); $interim_hash++) { + push @{$feature_hash{$split_line[${$fchrom_col}]}->{$interim_hash}->{$split_line[${$fstart_col}]}}, \@split_line; + } + } + close(FEATURES); + if (${$debug}) { print "$num_indexed indexed\n"; } + + my $min_keys_in_window; + my $max_keys_in_window; + my $num_idxs = 0; + my $total_keys = 0; + foreach my $chrom (keys %feature_hash) { + foreach my $interim_hash (keys %{$feature_hash{$chrom}}) { + $num_idxs++; + my @sorted_keys = sort {$a <=> $b} keys %{$feature_hash{$chrom}->{$interim_hash}}; + my $interim_key = join("_", ($interim_hash, $keys)); + my $num_keys = $#sorted_keys+1; + #print OUT "interim_hash:$interim_hash interim_key:$interim_key num_keys:$num_keys @sorted_keys\n"; + $feature_hash{$chrom}->{$interim_key} = \@sorted_keys; + $total_keys += $#sorted_keys + 1; + if (!defined($min_keys_in_window) || ($#sorted_keys+1) < $min_keys_in_window) { $min_keys_in_window = ($#sorted_keys+1); } + if (!defined($max_keys_in_window) || ($#sorted_keys+1) > $max_keys_in_window) { $max_keys_in_window = ($#sorted_keys+1); } + } + } + if (${$debug}) { + my $avg_keys = $total_keys/$num_idxs; + print "Smallest # of keys in window: $min_keys_in_window, Largest: $max_keys_in_window $total_keys in $num_idxs windows for an average of $avg_keys\n"; + } + + return \%feature_hash; +} + +sub process_intervals { + my ($intervals_file, $out_file, $feature_hash_ref, $req_res_type_ref, $direction_ref, $window_ref, $html_ref, $cturl_ref, $db_ref, $icols_ref, $fcols_ref, $debug_ref, $dd_ref, $capture, $promoter) = @_; + if (${$debug_ref}) { print sprintf("process_intervals(intervals:%s, out:%s, direction:%s, window:%s, icols_ref:%s)\n", ${$intervals_file}, ${$out_file}, ${$direction_ref}, ${$window_ref}, ${$icols_ref}); } + open(INTERVALS, "<${$intervals_file}") || die "Unable to open intervals file, ${$intervals_file}: $!\n"; + open(my $out_h, ">${$out_file}") || die "Unable to open output file, ${$out_file}: $!\n"; + + #if (${$debug_ref}) { print sprintf("%s features in index.\n", keys %{$feature_hash_ref}); } + + my @icols = split(":", ${$icols_ref}); + #pod2usage({ message => "Must specify 5 columns with -icol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#icols != 4); + my $ichrom = $icols[0]-1; + my $istart = $icols[1]-1; + my $iend = $icols[2]-1; + my $ilabel = $icols[3]-1; + my $istrand = $icols[4]-1; + + my @fcols = split(":", ${$fcols_ref}); + #pod2usage({ message => "Must specify 5 columns with -fcol, chrom:start:end:label:strand.\n", exitval => 2}) if ($#fcols != 4); + my $fchrom = $fcols[0]-1; + my $fstart = $fcols[1]-1; + my $fend = $fcols[2]-1; + my $flabel = $fcols[3]-1; + my $fstrand = $fcols[4]-1; + + my $cturl; + my $print = \&print_res; + if (${$html_ref}) { + $print = \&print_res_html; + print $out_h "<HTML>\n<HEAD>\n\t<TITLE>Feature Finder Annotation</TITLE>\n</HEAD>\n<BODY>\n<TABLE>\n"; + if (defined(${$cturl_ref})) { + ${$cturl} =~ s/X26/\%26/g; + } + } + + my $count = 0; + foreach (<INTERVALS>) { + if (${$debug_ref}) { + if (($count % 1000) == 0) { + my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time); + print sprintf("%02d-%02d %02d:%02d:%02d Intervals Processed: %9s\n", ($mon+1), $day, $hour, $min, $sec, $count); + } + $count++; + } + chomp; + my @split_line = split("\t"); + if (!@split_line) { next; } + if (!defined(${$feature_hash_ref}{$split_line[$ichrom]})) { + #if (${$debug_ref}) { print "."; } + next; + } + my $win_start = min($split_line[$istart], $split_line[$iend]) - ${$window_ref}; + if ($win_start < 0) { $win_start = 0; } + my $start_idx = int($win_start/${$window_ref}) -1; + if ($start_idx < 0) { $start_idx = 0; } + my $win_end = max($split_line[$istart], $split_line[$iend]) + ${$window_ref}; + my $end_idx = int($win_end/${$window_ref}) +1; + + if (uc ${$req_res_type_ref} eq $all) { + &$print(\$out_h, \@split_line, \$istart, \$iend, &compare(\$out_h, $feature_hash_ref, \$all, \@split_line, \$split_line[$ichrom], \$win_start, \$win_end, \$start_idx, \$end_idx, \$both, \$ichrom, \$istart, \$iend, \$ilabel, \$istrand, \$fchrom, \$fstart, \$fend, \$flabel, $debug_ref), \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom, \$istart, \$iend); + } + else { + my %left_res = (); + my %right_res = (); + #if (${$debug_ref}) { print sprintf("STRAND:%s\tDIRECTION:%s\n", $split_line[$istrand], ${$direction_ref}); } + if ($split_line[$istrand] ne "+" && $split_line[$istrand] ne "-") { warn sprintf("Found \"%s\" as the strand of %s:%s-%s %s, please verify icols match your input data\n", $split_line[$istrand], $split_line[$ichrom], $split_line[$istart], $split_line[$iend], $split_line[$ilabel]); } + if (($split_line[$istrand] eq "+" && uc ${$direction_ref} ne "DOWNSTREAM") || ($split_line[$istrand] eq "-" && uc ${$direction_ref} ne "UPSTREAM")) { + %left_res = %{&compare(\$out_h, $feature_hash_ref, \$close, \@split_line, \$split_line[$ichrom], \$win_start, \$win_end, \$start_idx, \$end_idx, \$left, \$ichrom, \$istart, \$iend, \$ilabel, \$istrand, \$fchrom, \$fstart, \$fend, \$flabel, $debug_ref)}; + } + if (($split_line[$istrand] eq "-" && uc ${$direction_ref} ne "DOWNSTREAM") || ($split_line[$istrand] eq "+" && uc ${$direction_ref} ne "UPSTREAM")) { + %right_res = %{&compare(\$out_h, $feature_hash_ref, \$close, \@split_line, \$split_line[$ichrom], \$win_start, \$win_end, \$start_idx, \$end_idx, \$right, \$ichrom, \$istart, \$iend, \$ilabel, \$istrand, \$fchrom, \$fstart, \$fend, \$flabel, $debug_ref)}; + } + if (keys %left_res == 0) { + &$print(\$out_h, \@split_line, \$istart, \$iend, \%right_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom); + } + elsif (keys %right_res == 0) { + &$print(\$out_h, \@split_line, \$istart, \$iend, \%left_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom); + } + else { + my @left_keys = keys %left_res; + my @right_keys = keys %right_res; + if (uc ${$direction_ref} eq "BOTH") { + @left_res{keys %right_res} = values %right_res; + &$print(\$out_h, \@split_line, \$istart, \$iend, \%left_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom); + } + else { + if ($left_keys[0] <= $right_keys[0]) { + &$print(\$out_h, \@split_line, \$istart, \$iend, \%left_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom); + } + elsif ($right_keys[0] < $left_keys[0]) { + &$print(\$out_h, \@split_line, \$istart, \$iend, \%right_res, \$flabel, \$fstart, \$fend, \$fstrand, $window_ref, $promoter, $capture, $dd_ref, $db_ref, $cturl_ref, \$ichrom); + } + } + } + } + } + close(INTERVALS); + if (${$html_ref}) { + print $out_h "</TABLE>\n</BODY>\n</HTML>\n"; + } + close($out_h); + +} + +sub compare { + my ($out_h_ref, $feature_hash_ref, $res_type, $interval_array_ref, $chrom, $window_start, $window_end, $start_idx, $end_idx, $direction, $ichrom, $istart, $iend, $ilabel, $istrand, $fchrom, $fstart, $fend, $flabel, $debug) = @_; + #if (${$debug}) { print sprintf("compare(result type:%s, chrom:%s, win start:%s, win end:%s, direction:%s, ichrom_col:%s, fchrom_col:%s, ilabel_col:%s, flabel_col:%s, debug:%s)\n", ${$res_type}, ${$chrom}, ${$window_start}, ${$window_end}, ${$direction}, ${$ichrom}, ${$fchrom}, ${$ilabel}, ${$flabel}, ${$debug}); } + my %result = (); + my %reshash = (); + my $feature_start; + my $feature_end; + my $interval_start; + my $interval_end; + my $interval_idx; + my $best_distance = $NOT_FOUND; + for ($interval_idx = ${$start_idx}; $interval_idx <= ${$end_idx}; $interval_idx++) { + my $interval_key = join("_", ($interval_idx, $keys)); + if (!defined(${$feature_hash_ref}{${$chrom}}->{$interval_key})) { + next; + } + + my @feature_keys = @{${$feature_hash_ref}{${$chrom}}->{$interval_key}}; + my $interval_midp = (($interval_array_ref->[${$istart}] + $interval_array_ref->[${$iend}])/2); + foreach my $feature_idx (@feature_keys) { + foreach my $feature (@{${$feature_hash_ref}{${$chrom}}->{$interval_idx}->{$feature_idx}}) { + $feature_start = min($feature->[${$fstart}], $feature->[${$fend}]); + $feature_end = max($feature->[${$fstart}], $feature->[${$fend}]); + $interval_start = min($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]); + $interval_end = max($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]); + my $reskey = join(":", ($interval_array_ref->[${$ichrom}], ${$window_start}, ${$window_end}, $interval_array_ref->[${$ilabel}], $feature->[${$fchrom}], $feature_start, $feature_end, $feature->[${$flabel}])); + my $distance; + if ($feature_start <= $interval_start && $feature_end >= $interval_end) { $distance = $ENCOMPASSING; } + elsif ($interval_start < $feature_start && $interval_end > $feature_end) { $distance = $INTERNAL; } + else { + $distance = min(abs($interval_array_ref->[${$istart}] - $feature_start), abs($interval_array_ref->[${$istart}] - $feature_end), abs($interval_array_ref->[${$iend}] - $feature_start), abs($interval_array_ref->[${$iend}] - $feature_end)); + #if (${$debug}) { print "FEATURE:$feature->[${$flabel}]\tDISTANCE:$distance\n"; } + } + my $dir_str = ""; + my $feature_midp = ($feature_start + $feature_end)/2; + if ($interval_midp >= $feature_midp) { + if ($interval_array_ref->[${$istrand}] eq "+") { $dir_str = "UPSTREAM"; } + else { $dir_str = "DOWNSTREAM" } + } + else { + if ($interval_array_ref->[${$istrand}] eq "-") { $dir_str = "UPSTREAM"; } + else { $dir_str = "DOWNSTREAM" } + } + + if (${$res_type} eq $close) { + if (${$direction} == $left) { + if ($interval_midp < $feature_midp) { next; } + } + elsif (${$direction} == $right) { + if ($interval_midp >= $feature_midp) { next; } + } + + #print ${$out_h_ref} "distance:$distance best_distance:$best_distance\n"; + if ($best_distance > $NOT_FOUND) { + if ($distance < $best_distance) { + delete $result{$best_distance}; + if (!defined($reshash{$reskey})) { + $reshash{$reskey} = $feature; + push @{$result{$distance}{$feature->[${$flabel}]}}, $feature, $dir_str; + #$result{$distance}{$feature->[${$flabel}]} = $dir_str; + $best_distance = $distance; + } + } + } + else { + if (!defined($reshash{$reskey})) { + $reshash{$reskey} = $feature; + push @{$result{$distance}{$feature->[${$flabel}]}}, $feature, $dir_str; + #$result{$distance}{$feature->[${$flabel}]} = $dir_str; + $best_distance= $distance; + } + } + } + else { + # if the interval start - the window is less than the end of the feature and the interval end + the window is greater than the start of the feature it's included + if (${$window_start} <= $feature_end && ${$window_end} >= $feature_start) { + if (!defined($reshash{$reskey})) { + $reshash{$reskey} = $feature; + push @{$result{$distance}{$feature->[${$flabel}]}}, $feature, $dir_str; + #$result{$distance}{$feature->[${$flabel}]} = $dir_str; + } + } + } + } + } + } + return \%result; +} + +sub print_res { + my ($out_h_ref, $interval_array_ref, $istart, $iend, $result_hash_ref, $flabel, $fstart, $fend, $fstrand, $window, $promoter_len, $capture, $dd_ref) = @_; + print ${$out_h_ref} join("\t", @{$interval_array_ref}); + my @sorted_keys = sort {$a <=> $b} keys %{$result_hash_ref}; + if (defined($sorted_keys[0])) { + print ${$out_h_ref} sprintf("\t"); + my $left_end = $interval_array_ref->[${$istart}]; + my $right_end = $interval_array_ref->[${$iend}]; + my $fstart_pos; + my $fend_pos; + foreach my $next_key (@sorted_keys) { + foreach my $res (keys %{$result_hash_ref->{$next_key}}) { + #my @feature_keys = keys %{$res}; + if (defined($capture) && ${$capture}) { + if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '+') { + $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}] - ${$promoter_len}; + } else { + $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}]; + } + if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '-') { + $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}] + ${$promoter_len}; + } else { + $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}]; + } + if ($fstart_pos < $left_end) { $left_end = $fstart_pos; } + if ($fend_pos > $right_end) { $right_end = $fend_pos; } + } + if (!${$dd_ref}) { + print ${$out_h_ref} sprintf("%s, ", $res); + } else { + if ($next_key == $ENCOMPASSING) { + print ${$out_h_ref} sprintf("%s (%s), ", $res, $ENCOMPASSING_STR); + } + elsif ($next_key == $INTERNAL) { + print ${$out_h_ref} sprintf("%s (%s), ", $res, $INTERNAL_STR); + } + else { + print ${$out_h_ref} sprintf("%s (%s bp %s), ", $res, $next_key, @{$result_hash_ref->{$next_key}->{$res}}[1]); + } + } + } + } + if (defined($capture) && ${$capture}) { + print ${$out_h_ref} sprintf("\t%s\t%s\t%s", $left_end, $right_end, $right_end - $left_end); + } + } + else { + print ${$out_h_ref} sprintf("\tNo results within ${$window} bp window"); + } + print ${$out_h_ref} sprintf("\n"); +} + +sub print_res_html { + my ($out_h_ref, $interval_array_ref, $istart, $iend, $result_hash_ref, $flabel, $fstart, $fend, $fstrand, $window, $promoter_len, $capture, $dd_ref, $db, $cturl, $ichrom) = @_; + print ${$out_h_ref} sprintf("<TR>\n\t<TD>"); + my $win_start = min($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]) - $window; + my $win_end = max($interval_array_ref->[${$istart}], $interval_array_ref->[${$iend}]) + $window; + print ${$out_h_ref} sprintf("<A HREF=\"http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s:%s-%s&display_app=ucsc&authz_method=display_at", $db, $interval_array_ref->[${$ichrom}], $win_start, $win_end); + my $left_end = $interval_array_ref->[${$istart}]; + my $right_end = $interval_array_ref->[${$iend}]; + my $fstart_pos; + my $fend_pos; + if (defined($cturl)) { + #print ${$out_h_ref} sprintf ("&hgt.customText=%s/display_as?id=%s&display_app=ucsc&authz_method=display_at", $server_url, $out_dbkey); + print ${$out_h_ref} sprintf("&hgt.customText=%s", $cturl); + } + print ${$out_h_ref} sprintf("\">UCSC Visualization</A></TD><TD>"); + #custom track stuff something like : &hgt.customText=%s/display_as?id=%s&display_app=ucsc&authz_method=display_at, $server_url, $out_dbkey + print ${$out_h_ref} join("</TD><TD>", @{$interval_array_ref}); + my @sorted_keys = sort {$a <=> $b} keys %{$result_hash_ref}; + if (defined($sorted_keys[0])) { + foreach my $next_key (@sorted_keys) { + foreach my $res (keys %{$result_hash_ref->{$next_key}}) { + if (${$capture}) { + if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '+') { + $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}] - ${$promoter_len}; + } else { + $fstart_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstart}]; + } + if (@{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fstrand}] eq '-') { + $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}] + ${$promoter_len}; + } else { + $fend_pos = @{$result_hash_ref->{$next_key}->{$res}}[0]->[${$fend}]; + } + if ($fstart_pos < $left_end) { $left_end = $fstart_pos; } + if ($fend_pos > $right_end) { $right_end = $fend_pos; } + } + + if (!${$dd_ref}) { + print ${$out_h_ref} sprintf("<TD>%s</TD>", $res); + } else { + if ($next_key == $ENCOMPASSING) { + print ${$out_h_ref} sprintf("<TD>%s (%s)</TD>", $res, $ENCOMPASSING_STR); + } + elsif ($next_key == $INTERNAL) { + print ${$out_h_ref} sprintf("<TD>%s (%s)</TD>", $res, $INTERNAL_STR); + } + else { + print ${$out_h_ref} sprintf("<TD>%s (%s bp %s)</TD>", $res, $next_key, @{$result_hash_ref->{$next_key}->{$res}}[0]); + } + } + } + } + + if (${$capture}) { + print ${$out_h_ref} sprintf("<TD>%s</TD><TD>%s</TD><TD>%s</TD>", $left_end, $right_end, $right_end - $left_end); + } + } + else { + print ${$out_h_ref} sprintf("<TD>No results within $window bp window</TD>"); + } + print ${$out_h_ref} sprintf("</TD>\n</TR>\n"); +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/insert_vis.R Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,31 @@ +args <- commandArgs(trailingOnly = TRUE) +libdata <- read.table(args[2], header=TRUE, sep=",", row.names="Library") +pdf(args[4]) +boxplot (libdata[, 2:8], main="Library Sequences", ylab="Raw Count", xlab="Sequence Type", names=c(1:7)) +legend("topright", c("1:Barcoded sequences", "2:Sequences with mutagen", "3:Mappable sequences", "4:Unique, mappable sequences", "5:Sequences mapped to reference", "6:Unique sequences mapped to reference", "7:Non redundant insertions"), cex=0.7) + +regiondata <- read.table(args[3], header=TRUE, sep=",", row.names="Library") +sortedregiondata <- regiondata[order(regiondata[,1], decreasing=TRUE),] +sortedregionmatrix <- data.matrix(sortedregiondata) +barplot(height=t(sortedregionmatrix[c(1:10,(nrow(sortedregionmatrix)-9):nrow(sortedregionmatrix)),1:2]), ylab="Raw Count", beside=TRUE, col=c("blue", "red"), main="Mappable Sequences by Library (Top 10 vs. Bottom 10)", las=2, cex.names=0.7) +legend("topright", c("Mappable sequences", "Sequences with a mapping"), fill=c("blue", "red"), cex=0.7) +abline(v=30.5, lty=2) +axis(1, lab=F, at=(c(0:19)*3)+2) + +matrixcalcs <- cbind(sortedregionmatrix, sortedregionmatrix[,2]/sortedregionmatrix[,1]) +sortedregionmatrix <- matrixcalcs[order(matrixcalcs[,7], decreasing=TRUE), ] +barplot(height=t(sortedregionmatrix[c(1:10,(nrow(sortedregionmatrix)-9):nrow(sortedregionmatrix)),1:2]), ylab="Raw Count", beside=TRUE, main="Successful Mappings by Library (Top 10 vs. Bottom 10)", las=2, cex.names=0.7, col=c("blue", "red")) +legend("topright", c("Mappable sequences", "Sequences with a mapping"), fill=c("blue", "red"), cex=0.7) +abline(v=30.5, lty=2) +axis(1, lab=F, at=(c(0:19)*3)+2) + +matrixcalcs <- cbind(matrixcalcs, matrixcalcs[,6]/matrixcalcs[,1]) +sortedregionmatrix <- matrixcalcs[order(matrixcalcs[,8], decreasing=TRUE), ] +barplot(height=t(sortedregionmatrix[c(1:10,(nrow(sortedregionmatrix)-9):nrow(sortedregionmatrix)),c(1,6)]), ylab="Raw Count", beside=TRUE, main="Redundancy of Mapped Regions by Library (Top 10 vs. Bottom 10)", las=2, cex.names=0.7, col=c("blue", "red")) +legend("topright", c("Mappable sequences", "Distinct regions mapped"), fill=c("blue", "red"), cex=0.7) +abline(v=30.5, lty=2) +axis(1, lab=F, at=(c(0:19)*3)+2) + +dev.off() + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/list2tab.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,93 @@ +#!/usr/bin/perl +# The Missing Textutils, Ondrej Bojar, obo@cuni.cz +# http://www.cuni.cz/~obo/textutils +# +# 'list2tab' builds a 2D table out of key-key-value triples. +# +# $Id: list2tab,v 1.4 2006/07/07 15:01:53 bojar Exp $ +# + +$rows = shift; +$cols = shift; +$data = shift; +$blankvalue = shift; +@rows = split /,/, $rows; +@cols = split /,/, $cols; +@data = split /,/, $data; + +$blankvalue = "-" if $blankvalue eq ""; + +if (!$rows || !$cols || !$data) { + my $help = <<EOH; +Sample usage: + ./list2tab.pl 1,2 5,6 3,4 [default_value] < datafile > tablefile +The output table will have lines labelled with values seen in columns 1 and 2, +columns labelled with values from columns 5,6 and the values in the interior of the table will come from columns 3,4. + +Sample input: +GIN Praha 5 +IOL Praha 20 +GIN Brno 10 +IOL Nova Paka 2 + +Output produced by: "list2tab 2 1 3 none" + + GIN IOL +Brno 10 none +Nova Paka none 2 +Praha 5 20 +EOH + print STDERR $help; + exit $1; +} + + +while (<>) { + chomp; + @line = split /\t/; + $key = $val = $datum = ""; + foreach $row (@rows) { + $key .= $line[$row-1]."\t"; + } + chop $key; + foreach $col (@cols) { + $val .= $line[$col-1]."\t"; + } + chop $val; + foreach $dat (@data) { + $datum .= $line[$dat-1]."\t"; + } + chop $datum; + $datum =~ s/^ *//; + $datum =~ s/ *$//; + + $table{"$key\t$val"} = $datum; +#print STDERR "Tabulka >>$key\t$val<<.....$datum\n"; + $keys{$key} = 1; + push @svals, $val if (!$vals{$val}); + $vals{$val} = 1; +} + +@skeys = sort {uc($a) cmp uc($b)} keys %keys; +#@svals = sort {uc($a) cmp uc($b)} keys %vals; + +#print STDERR "Klice: ".join(",",@skeys)."\n"; +#print STDERR "Hodnoty: ".join(",",@svals)."\n"; + + +print "\t" x $#rows; + +foreach $col (@svals) { + print "\t$col"; +} +print "\n"; + +foreach $row (@skeys) { + print "$row"; + foreach $col (@svals) { + $pos = "$row\t$col"; + print "\t$table{$pos}" if defined $table{$pos}; + print "\t$blankvalue" if ! defined $table{$pos}; + } + print "\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/list_projects.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,91 @@ +#/bin/perl +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2010 - 2011, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# Jesse Erdmann +# +# POD documentation +#------------------------------------------------------------------------------ +=pod BEGIN + +=head1 NAME + + list_projects.pl - TAPDANCE utility to list projects in the database + + TAPDANCE functionality. + +=head1 SYNOPSIS + + list_projects.pl [-help] + + See http://sf.net/p/tapdancebio for full documentation + +=head1 OPTIONS + +=over 6 + +=item B<-help> + + Print this usage summary. + +=item B<-user username> + + Filter projects based on the user that created the project. + +=item B<-tag tags> + + Any number of tags may be specified to filter projects where at least + one of the tags has been specified as a metadata element for a library + within the project. + +=back + +=cut + +#### END of POD documentation. +#----------------------------------------------------------------------------- +use strict; +use Getopt::Long; +use Pod::Usage; + +my $path = $0; +$path =~ s/\/\w*\.pl$//g; +require "$path/tapdance_base_config.pl"; +require "$path/project_man.pl"; +require "$path/util.pl"; + +my $user = "cmd_line"; +my ($out_file, $help_flag); +my @tags = (); +my $query_type = "all"; +my $db_config; +my %options = ( + "user|u=s" => \$user, + "tag=s" => \@tags, + "query_type=s" => \$query_type, + "db_config=s" => \$db_config, + "help" => \$help_flag +); + +GetOptions(%options) or pod2usage(2); +pod2usage(1) if $help_flag; + +if (defined($db_config)) { + my $db_cnf_path = $path . "/" . $db_config; + require "$db_cnf_path"; +} + +$user = &sanitize_project($user); + +my $projects_ref = &get_project_list($user, $query_type, @tags); +foreach my $project (@{$projects_ref}) { + my $full_name = $project; + $project =~ s/$user//; + print "$full_name\t$project\n"; +} + +exit;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/matrix2fisher.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,139 @@ +#!/usr/bin/perl +# This script takes a matrix as input and generates an R script to look for +# simularity between rows. +# +# 'tab2list' is a complement to list2tab. It reads a 2-dimensional table and +# produces a list in the form: row label - column label - value. +# +use Getopt::Long; + +$keycols = 1; +$usage = 0; +@cis; +%hash; +open OUT, "> FISH/Fisher_pre.txt"; +open OUT2, "> FISH/Fisher_pre_named.txt"; +GetOptions("keycols=i" => \$keycols, "usage" => \$usage, "help"=>\$usage); + +if ($usage) { + print STDERR "usage: tab2list < infile > outfile + Options: + --keycols=X ... How many cols from left are to be kept (default: 1)\n"; + exit 0; +} + +$keycols--; + +$_ = <>; +chomp; +@headline = split /\t/, $_; +@anim = @headline; +shift(@anim); +while (<>) { + chomp; + @line = split /\t/, $_; + $head = ""; + foreach my $i (0 .. $keycols) { + $head .= "$line[$i]\t"; + } + chop $head; +push (@cis,$head); + + foreach my $i ($keycols+1 .. $#line) { + # print "$head\t$headline[$i]\t$line[$i]\n"; + $value=$head."|".$headline[$i]; + $hash{$value}=$line[$i]; + +} +} +foreach (@cis){ +#print "$_"; +} + +print "\n"; +foreach (@anim){ +#print "$_"; +} + +print "\n"; +foreach (keys %hash) { +# print "The key $_ $hash{$_}\n"; +} + +%seen; +$first=0; +$second=0; +$third=0; +$fourth=0; + +foreach $x(@cis){ +foreach $y(@cis){ +$first=0; +$second=0; +$third=0; +$fourth=0; +if ($x eq $y){ +next;} +$z = $x."|".$y; +if (exists $seen{$z}){ +next;} +$seen{$z}= '1'; +$z2 = $y."|".$x; +$seen{$z2}= '1'; +foreach $a(@anim) { +$b =$x."|".$a; +$c =$y."|".$a; +if (($hash{$b}==0) and ($hash{$c}==0)){ +$fourth = $fourth + 1; +} +elsif (($hash{$b}==0) and ($hash{$c}==1)){ +$third = $third + 1; +} +elsif (($hash{$b}==1) and ($hash{$c}==0)){ +$second = $second + 1; +} +elsif (($hash{$b}==1) and ($hash{$c}==1)){ +$first = $first + 1; +} +#print "$a|$x|$y\n"; +#print "$hash{$b}|$hash{$c}\n"; +} +print OUT "object__object\t$first\t$second\t$third\t$fourth\n"; +print OUT2 "$x"."__"."$y\t$first\t$second\t$third\t$fourth\n"; +} +} +close OUT; +close OUT2; +open SOURCE, "< FISH/Fisher_pre.txt"; +open OUT, "> FISH/Fisher.R"; +while (defined($line = <SOURCE>)) { +chomp $line; + @field= split(/\t/, $line); +print OUT "$field[0] <- matrix(c($field[1],$field[2],$field[3],$field[4]), nr=2, dimnames=list(c(\"cis\", \"nocis\"), c(\"pheno\", \"notpheno\")))\n$field[0]\nfisher.test($field[0]".",alternative = \"greater\")\n"; +} +#system "module load R"; +#system "R < FISH/Fisher.R --vanilla > FISH/fisher_dump.txt"; +open (my $fisher_dump, ">", "FISH/fisher_dump.txt") || die "Unable to open FISH/fisher_dump.txt. $!\n"; +open (my $out, "Rscript --vanilla FISH/Fisher.R | "); +while (<$out>) { + print $fisher_dump $_; +} +close($out); +close($fisher_dump); +close OUT; + +open SOURCE, "< FISH/fisher_dump.txt"; +open OUT, "> FISH/R_result.txt"; +while (defined($line = <SOURCE>)) { + chomp ($line); + @field= split(/\t/, $line); + if ($field[0] =~ m/data/){ + print OUT "$field[0]\t"; + } + if ($field[0] =~ m/p-value/){ + print OUT "$field[0]\n"; + } + } +close OUT; +print "cooperation analyses complete"; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/mm9.bed Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,36543 @@ +chr5 28496400 28510400 BADEN2 + + +chr2 98367843 98602471 BADrepeat + + +chr9 3000200 3050087 BADrepeat + + +chr9 35112796 35125296 BADrepeat + + +chr11 3004575 3137194 BADrepeat + + +chrY 278235 2899983 BADrepeat + + +chr9 3000135 3012635 BADrepeat + + +chr1 3044314 3044814 AC157543.3 + + +chr1 3092097 3092206 U6 + + +chr1 3195982 3661579 Xkr4 - - +chr1 3456668 3503634 1.3000001-3776472.1 + + +chr1 3668961 3669024 U7 - - +chr1 3670236 3671871 Gm10568 + + +chr1 3773818 3773879 U7 - - +chr1 4334224 4350473 Rp1 - - +chr1 4481009 4487435 Sox17 - - +chr1 4519098 4519204 U6 + + +chr1 4713358 4713460 U6 - - +chr1 4763287 4775820 Mrpl15 - - +chr1 4797869 4876851 Lypla1 + + +chr1 4847884 4887983 Tcea1 + + +chr1 4870130 4870732 AC102311.1 - - +chr1 4899657 5060366 Rgs20 - - +chr1 4960938 4966901 AC102242.1 + + +chr1 5073233 5152526 Atp6v1h + + +chr1 5578574 5596212 Oprk1 + + +chr1 5906385 5907374 Npbwr1 - - +chr1 6196278 6266729 Rb1cc1 + + +chr1 6203374 6204671 AC139064.2 - - +chr1 6204693 6205373 4732440D04Rik - - +chr1 6349537 6384812 AC139064.1 + + +chr1 6477312 6851021 St18 + + +chr1 7079231 7163707 Pcmtd1 + + +chr1 7167820 7168140 Gm9826 + + +chr1 7255884 7256013 SNORA17 + + +chr1 7339487 7387950 AC103380.1 - - +chr1 7488080 7488381 AC163387.1 + + +chr1 8351556 9289959 Sntg1 - - +chr1 8458507 8458906 AC102786.2 - - +chr1 8578696 8578805 AC102703.1 - - +chr1 8782004 8782243 AC163389.1 - - +chr1 8806219 8806328 AC163389.1 + + +chr1 8846009 8846348 AC118192.1 - - +chr1 8953077 8953702 AC122738.1 - - +chr1 9448751 9448853 U6 + + +chr1 9535539 9537531 Rrs1 + + +chr1 9538029 9568051 Adhfe1 + + +chr1 9550913 9621256 AC103620.4 - - +chr1 9564629 9565730 AC103620.1 + + +chr1 9591280 9617224 3110035E14Rik + + +chr1 9657496 9690290 Mybl1 - - +chr1 9708703 9738463 Vcpip1 - - +chr1 9737729 9782003 AC158928.2 + + +chr1 9788234 9889929 Sgk3 + + +chr1 9792275 9792634 AC158928.3 - - +chr1 9824579 9824683 U6 - - +chr1 9898719 9932166 6030422M02Rik + + +chr1 9932106 9934199 AC102570.1 - - +chr1 9932544 9932630 SNORD87 - - +chr1 9951005 9951205 Gm10567 - - +chr1 9958705 9999217 Lrrc67 - - +chr1 9972468 9982447 AC102570.3 + + +chr1 9999895 9999998 U6 - - +chr1 10014683 10028208 Cops5 - - +chr1 10028299 10126849 Cspp1 + + +chr1 10127652 10222751 Arfgef1 - - +chr1 10156620 10156859 7SK + + +chr1 10314801 10710026 Cpa6 - - +chr1 10544179 10545634 AC102469.1 - - +chr1 10545635 10545741 U6 - - +chr1 10685204 10685695 AC102426.1 + + +chr1 10911751 10911841 SNORA66 + + +chr1 10983546 11288582 Prex2 + + +chr1 11124192 11124319 SNORA40 - - +chr1 11404186 11965982 A830018L16Rik + + +chr1 11404193 11527788 AC102654.1 + + +chr1 12365017 12365123 U6 + + +chr1 12708610 12850458 Sulf1 + + +chr1 12856630 12981258 Slco5a1 - - +chr1 13052235 13052429 AC118477.1 + + +chr1 13103509 13117244 Prdm14 - - +chr1 13129186 13364164 Ncoa2 - - +chr1 13324579 13324690 U6 - - +chr1 13554783 13579945 Tram1 - - +chr1 13614926 13650627 Lactb2 - - +chr1 13658852 13691804 Xkr9 + + +chr1 13764415 13764545 SNORA17 - - +chr1 13922459 13922766 7SK + + +chr1 14159035 14300281 Eya1 - - +chr1 14743427 14746047 Msc - - +chr1 14745535 14748454 Gm9947 + + +chr1 14829950 14830237 Smt3h2-ps4 - - +chr1 14855153 14856046 AC121789.1 + + +chr1 14862729 14908943 Trpa1 - - +chr1 15009121 15009240 SNORA17 - - +chr1 15057114 15057692 AC123942.2 + + +chr1 15258880 15259878 AC166075.1 - - +chr1 15676016 15676127 SNORA17 - - +chr1 15747913 15748044 SNORA17 + + +chr1 15795739 15833509 Terf1 + + +chr1 15843943 15882803 Gm106 - - +chr1 15869611 15869913 7SK + + +chr1 16056060 16083406 4930444P10Rik - - +chr1 16091376 16094743 Rpl7 - - +chr1 16095855 16123815 Rdh10 + + +chr1 16218755 16510193 Stau2 - - +chr1 16243673 16258002 AC167117.2 + + +chr1 16559863 16609570 Ube2w - - +chr1 16632849 16646946 Tceb1 - - +chr1 16647633 16652359 AC157362.1 + + +chr1 16655272 16668356 Tmem70 + + +chr1 16678514 16699686 Ly96 + + +chr1 16986750 16987054 AC135017.1 - - +chr1 16987445 17087970 Jph1 - - +chr1 17135443 17154352 Gdap1 + + +chr1 17510082 17510192 SNORA17 + + +chr1 17591985 17617901 Pi15 + + +chr1 17666108 17717727 AC104917.1 - - +chr1 17717126 17756425 Crispld1 + + +chr1 18105272 18135983 Crisp4 - - +chr1 18200134 18213645 Defb44 - - +chr1 18226554 18227524 Defb18 - - +chr1 18241061 18255219 Defb41 - - +chr1 18250605 18255161 AC168116.1 - - +chr1 18959843 18959914 SNORA17 - - +chr1 19053380 19094921 AC098736.3 - - +chr1 19093103 19156427 Tcfap2d + + +chr1 19143391 19144047 Hmgb2 - - +chr1 19198995 19228815 Tcfap2b + + +chr1 19503936 19504000 SNORD29 - - +chr1 19911391 19911480 AC163028.1 - - +chr1 20047860 20608145 Pkhd1 - - +chr1 20371174 20382381 AC101789.2 + + +chr1 20434339 20434641 AC101789.1 - - +chr1 20434892 20434993 U6 - - +chr1 20669091 20669163 mmu-mir-206 + + +chr1 20672850 20672968 mmu-mir-133b + + +chr1 20720986 20724577 Il17a + + +chr1 20767232 20774351 Il17f - - 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23279108 23279178 mmu-mir-30a + + +chr1 23298540 23298623 mmu-mir-30c-2 + + +chr1 23373263 23390014 Ogfrl1 - - +chr1 23768592 23855997 B3gat2 + + +chr1 23851685 23929156 Smap1 - - +chr1 24002778 24012495 1110058L19Rik - - +chr1 24018522 24093413 Fam135a - - +chr1 24184449 24259523 Col9a1 + + +chr1 24268729 24594311 Col19a1 - - +chr1 24555680 24555816 SNORA64 - - +chr1 24619243 24619539 AC116997.1 - - +chr1 24621347 24621490 Gm10925 - - +chr1 24685383 24823144 Lmbrd1 + + +chr1 25124321 25886552 Bai3 - - +chr1 25280575 25281018 AC122187.1 + + +chr1 25336290 25336396 U6 - - +chr1 25507916 25508019 U6 + + +chr1 25887502 25888723 Gm9884 + + +chr1 26623678 26623783 SNORA17 + + +chr1 26738659 26744305 4931408C20Rik - - +chr1 27015948 27016066 5S_rRNA - - +chr1 27099346 27286771 AC102363.1 + + +chr1 27130448 27130557 AC153790.1 + + +chr1 28637343 28637613 AC122186.1 - - +chr1 28832989 28837097 Gm597 - - +chr1 28857083 28859566 AC121566.1 - - +chr1 28994880 28995185 AC122020.1 + + +chr1 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RP23-408K4.5 + + +chrX 162937744 162956499 Tceanc - - +chrX 162960939 163023652 Egfl6 - - +chrX 163056034 163059474 RP23-364L1.1 - - +chrX 163099957 163127744 RP23-364L1.2 + + +chrX 163292122 163292985 RP23-421J13.1 + + +chrX 163295601 163302381 RP23-421J13.2 - - +chrX 163373401 163373847 RP23-247O14.1 + + +chrX 163466821 163466929 AL671993.1 - - +chrX 163466834 163467368 RP23-428E5.1 - - +chrX 163501126 163508312 RP23-428E5.2 - - +chrX 163526025 163540022 RP23-428E5.3 - - +chrX 163602029 163609210 RP23-428E5.4 + + +chrX 163645025 163647247 Tmsb4x - - +chrX 163680626 163702261 Tlr8 - - +chrX 163742861 163768490 Tlr7 - - +chrX 163784254 163820681 Prps2 - - +chrX 163799387 163802353 RP23-139P21.5 + + +chrX 163802112 163802229 SNORA70 - - +chrX 163883921 163884463 RP23-217I22.1 - - +chrX 163909241 165015163 Frmpd4 - - +chrX 164214193 164215488 RP23-174C4.1 + + +chrX 164340247 164340356 5S_rRNA + + +chrX 164425437 164426156 RP23-42G2.1 + + +chrX 164512386 164512854 RP23-42G2.2 + + +chrX 164804396 164804790 RP23-92L12.1 + + +chrX 164983941 164984273 RP23-260K2.2 + + +chrX 165019823 165019934 U6 - - +chrX 165092049 165111830 Msl3 - - +chrX 165212789 165213188 RP23-24O15.1 - - +chrX 165233031 165742367 Arhgap6 + + +chrX 165475606 165544468 X.165403154-166679264.1 - - +chrX 165614046 165625141 Amelx - - +chrX 165688125 165758304 Hccs - - +chrX 165758554 165806122 RP23-37L2.2 + + +chrX 165806121 165808072 RP23-37L2.3 + + +chrX 165885762 165913845 RP23-421I14.1 + + +chrX 166123131 166428730 Mid1 + + +chrX 166133713 166133831 SNORA51 - - +chrX 166214189 166217567 4933400A11Rik - - +chrX 166412975 166416849 RP23-154O12.1 - - +chrX 166416979 166423164 RP23-154O12.2 - - +chrX 166423733 166424871 WI1-2389C6.2 - - +chrX 166515832 166516203 CH25-423E5.1 - - +chrX 166638587 166638958 CH25-592M6.1 - - +chrY 61650 133852 Zfy1 - - +chrY 155092 180667 Ube1y1 + + +chrY 234231 280254 Kdm5d + + +chrY 328073 328191 5S_rRNA - - +chrY 346986 365290 Eif2s3y + + +chrY 433304 582202 Uty - - +chrY 598038 623020 Ddx3y - - +chrY 635400 796225 Usp9y - - +chrY 644716 644820 U6 - - +chrY 1362123 1426357 Zfy2 - - +chrY 1918381 1919568 Sry - - +chrY 2086609 2097407 Rbmy1a1 + + +chrY 2118068 2129384 AC132601.1 + + +chrY 2160043 2168098 AC130839.1 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/project_man.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,117 @@ +#!/project/bioperl/perl-5.10.1-sles11/bin/perl -w + +## +# +# This file requires that a database connection be configured and +# connected to the scalar $dbh +# +## + +if (!defined($project_table_name)) { + $project_table_name = "TAPDANCE_project_master"; +} +return 1; + +sub project_table_check { + my $create_string = "CREATE TABLE IF NOT EXISTS " . $project_table_name . " (name VARCHAR(255) NOT NULL, insert_gen TIMESTAMP, cis_call TIMESTAMP)"; + my $sth = $dbh->prepare($create_string); + $sth->execute; +} + + +sub project_exists { + my ($proj_name) = @_; + &project_table_check(); + my $test_string = "SELECT COUNT(name) FROM " . $project_table_name . " WHERE name = '" . $proj_name . "'"; + my $sth = $dbh->prepare($test_string); + $sth->execute; + (@row) = $sth->fetchrow_array; + return $row[0] > 0; +} + +sub update_project { + &project_table_check(); + my ($proj_name, $insert_gen, $cis_call) = @_; + my $update_string = "UPDATE " . $project_table_name . " SET"; + my $prefix = " "; + if ($insert_gen) { + $update_string = $update_string . $prefix . "insert_gen = NOW()"; + $prefix = ", " + } + if ($cis_call) { + $update_string = $update_string . $prefix . "cis_call = NOW()"; + } + $update_string = $update_string . " WHERE name = '" . $proj_name . "'"; + my $sth = $dbh->prepare($update_string); + $sth->execute; +} + +sub insert_project { + &project_table_check(); + my ($proj_name, $insert_gen, $cis_call) = @_; + my $insert_string = "INSERT INTO " . $project_table_name; + my $insert_cols_string = " (name"; + my $insert_vals_string = " VALUES('" . $proj_name . "'"; + if ($insert_gen) { + $insert_cols_string = $insert_cols_string . ", insert_gen"; + $insert_vals_string = $insert_vals_string . ", NOW()"; + } + if ($cis_call) { + $insert_cols_string = $insert_cols_string . ", cis_call"; + $insert_vals_string = $insert_vals_string . ", NOW()"; + } + $insert_cols_string = $insert_cols_string . ") "; + $insert_vals_string = $insert_vals_string . ") "; + $insert_string = $insert_string . $insert_cols_string . $insert_vals_string; + my $sth = $dbh->prepare($insert_string); + $sth->execute; +} + +sub delete_project { + &project_table_check(); + my ($proj_name) = @_; + my $delete_string = "DELETE FROM " . $project_table_name . " WHERE name = '" . $proj_name . "'"; + my $sth = $dbh->prepare($delete_string); + $sth->execute; +} + +sub set_project_status { + my ($proj_name, $insert_gen, $cis_call) = @_; + if (&project_exists($proj_name)) { + &update_project($proj_name, $insert_gen, $cis_call); + } else { + &insert_project($proj_name, $insert_gen, $cis_call); + } +} + +sub get_project_list { + my ($user_name, $query_type, @tags) = @_; + &project_table_check(); + my $select_string = "SELECT name FROM " . $project_table_name . " WHERE name LIKE '" . $user_name . "%'"; + my $sth = $dbh->prepare($select_string); + $sth->execute(); + my @projects = (); + while ((@row) = $sth->fetchrow_array) { + if ($query_type eq "all") { + push @projects, $row[0]; + } else { + my $conjunctive; + #if ($query_type eq "union") { + #$conjunctive = "AND"; + #} elsif ($query_type eq "join") { + $conjunctive = "OR"; + #} + $select_string = "SELECT COUNT(*) from metadata_$row[0] where descriptor LIKE '%"; + $select_string = $select_string . join("%' " . $conjunctive . " descriptor LIKE '%", @tags) . "%'"; + #print $select_string . "\n"; + my $sth2 = $dbh->prepare($select_string); + $sth2->execute; + while ((@row2) = $sth2->fetchrow_array) { + if ($row2[0] > 0) { + push @projects, $row[0]; + } + } + } + } + return \@projects; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/project_test.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,37 @@ +#/bin/perl + +require 'config.pl'; +require 'project_man.pl'; + +&set_project_status("jesse_test1", 1, 0); +&set_project_status("jesse_test2", 1, 1); +&set_project_status("jesse_test3", 1, 0); +&set_project_status("jesse_test1", 0, 1); +&set_project_status("aaron_test1", 1, 1); + + +my $projects_ref = &get_project_list(""); +print "All:\n"; +foreach my $project (@{$projects_ref}) { + print "\t$project\n"; +} + +$projects_ref = &get_project_list("aaron_"); +print "\nAaron:\n"; +foreach my $project (@{$projects_ref}) { + print "\t$project\n"; +} + +$projects_ref = &get_project_list("jesse_"); +print "\nJesse:\n"; +foreach my $project (@{$projects_ref}) { + print "\t$project\n"; +} + +&delete_project("aaron_test1"); +$projects_ref = &get_project_list(""); +print "\nAll (aaron deleted):\n"; +foreach my $project (@{$projects_ref}) { + print "\t$project\n"; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/shuffle.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,34 @@ +@list = (1,2,3,4); +foreach $val(@list){ +print "$val"; +} +print "\n"; +shuffle(\@list); +foreach $val(@list){ +print "$val"; +} + +open SOURCE, "< cis4cluster.txt"; +open OUT, "> shuffled.txt"; +while (defined($line = <SOURCE>)) { +chomp $line; + @field= split(/\t/, $line); +$name = shift(@field); +shuffle(\@field); +print OUT "$name"; +foreach $val(@field) { +print OUT "\t$val"; +} +print OUT "\n"; +} + +sub shuffle { + my $array = shift; + my $i; + for ($i = @$array; --$i; ) { + my $j = int rand ($i+1); + next if $i == $j; + @$array[$i,$j] = @$array[$j,$i]; + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/tapdance_base_config.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,88 @@ +use DBI; + +##### +# Database configuration +##### +# +# Specify the username to connect to the database as +#$db_username="MY_DB_USERNAME"; +# +# Specify the password for the DB user +#$db_password="MY_DB_PASSWORD"; +# +# The software running the application +# Currently supported: +# * MySQL (Several database operations use MySQL specific SQL) +#$db_type='mysql'; +# +# The machine name or IP address to connect to the database on +#$db_host="127.0.0.1"; +# +# The port that the database is listening to on the host +#$db_port='3306'; +# +# The database to use for TAPDANCE +#$db_name="MY_TAPDANCE_DB"; +#$db_name="MY_DB"; +# +# Collapse db config to a single connection string +#$data_source = "dbi:$db_type:dbname=$db_name:$db_host;mysql_local_infile=1:$db_port"; +# +# Connect to the daatbase, running 'perl ./tabdance_base_config.pl +# can be used to verfiy the database configuration +#$dbh = DBI->connect($data_source, $db_username, $db_password, { RaiseError => 1, AutoCommit => 0 }); +# +# The name of the table to collect top level project information +$project_table_name = "TAPDANCE_project_master"; + +##### +# Required project dependant config variables +##### +# Project Name +#$proj = 'ProjName'; + +# Environment Directory or the top level directory for the project +# Contents will be as follows +# * CIS (directory containing intermediary files generated during CIS calculation) +# * config.pl (this file) +# * data (data inputs) +# * barcode2lib.txt (barcode to library name mapping, phase 1) +# * seq.tab (tabular sequence data, phase 1) +# * FISH (directory containing intermediary files generated during Fisher exact tests) +# * lib (executable code and some resources used by code) +# * mapping (directory containing intermediary files generated during mapping to the reference genome) +# * results (directory containing final outputs) +#$envDir = 'DirectoryName'; + +##### +# Config variables for insertion analysis +##### +# Specify the alignment + +# Specify the bowtie command to use, useful if you want to use a specific bowtie version not on the path +# or would like special options. For example, to quiet bowtie output. Defaults to 'bowtie' on user $PATH +$bowtie_exe='bowtie --quiet'; + +# Specify the genome idnex to use, should be a full path excluding the file extension or just the name of +# the genome index if the index is in the indexes folder of the bowtie installation. Defaults to 'mm9' +#$bowtie_idx = '/project/ccbioinf/Software/bowtie_indexes/mus_musculus_ncbi37'; +$bowtie_idx='mm9'; + +# Specify the IRDR string to use, see common options below, defaults to a Sleeping Beauty mutagen +# '__GTATGTAAACTTCCGACTTCAACTG' +$mutagens="__GTATGTAAACTTCCGACTTCAACTG"; + +##### +# Config variables for CIS calling +##### +# The interval file of features to annotate CIS calls with +$annotation_file="lib/mm9.bed"; +# +$library_percent ='0.0001'; +# +$CIS_total_pvalue = '0.05'; +$CIS_library_pvalue = '0.05'; +$CIS_region_pvalue = '0.05'; +# +$cocis_threshold ='0.001'; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/util.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,125 @@ +#!/project/bioperl/perl-5.10.1-sles11/bin/perl -w + +my $dos_end = chr(13); + +my %chrom_map = ( + "gi|149288852|ref|NC_000067.5|NC_000067" => "chr1", + "gi|149288869|ref|NC_000076.5|NC_000076" => "chr10", + "gi|149288871|ref|NC_000077.5|NC_000077" => "chr11", + "gi|149292731|ref|NC_000078.5|NC_000078" => "chr12", + "gi|149292733|ref|NC_000079.5|NC_000079" => "chr13", + "gi|149292735|ref|NC_000080.5|NC_000080" => "chr14", + "gi|149301884|ref|NC_000081.5|NC_000081" => "chr15", + "gi|149304713|ref|NC_000082.5|NC_000082" => "chr16", + "gi|149313536|ref|NC_000083.5|NC_000083" => "chr17", + "gi|149321426|ref|NC_000084.5|NC_000084" => "chr18", + "gi|149323268|ref|NC_000085.5|NC_000085" => "chr19", + "gi|149338249|ref|NC_000068.6|NC_000068" => "chr2", + "gi|149352351|ref|NC_000069.5|NC_000069" => "chr3", + "gi|149354223|ref|NC_000070.5|NC_000070" => "chr4", + "gi|149354224|ref|NC_000071.5|NC_000071" => "chr5", + "gi|149361431|ref|NC_000072.5|NC_000072" => "chr6", + "gi|149361432|ref|NC_000073.5|NC_000073" => "chr7", + "gi|149361523|ref|NC_000074.5|NC_000074" => "chr8", + "gi|149361524|ref|NC_000075.5|NC_000075" => "chr9", + "gi|149361525|ref|NC_000086.6|NC_000086" => "chrX", + "gi|149361526|ref|NC_000087.6|NC_000087" => "chrY" +); + +return 1; + +sub get_chrom_map { + return \%chrom_map; +} + +sub sanitize_project { + my ($project) = @_; + $project =~ s/@/_/g; + $project =~ s/\./_/g; + $project =~ s/\s/_/g; + return $project; +} + +sub process_fasta { + my $fn = shift @_; + my $process = shift @_; + my $curr_seq_id = ""; + my $curr_seq = ""; + my $entries = 0; + push (my @opts, @_); + open (FILE, "<${$fn}") || die "Unable to open ${$fn}, $!\n"; + while (<FILE>) { + chomp; + $_ =~ s/$dos_end//g; + if ($_=~/^>/) { + if (length($curr_seq_id) > 0 && length($curr_seq) > 0) { + #print join("\t", ("Joined:", $curr_seq_id, $curr_seq, @opts, "\n")); + &$process(\$curr_seq_id, \$curr_seq, \@opts); + $entries++; + } + if (($entries % 100000) == 0) { + my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time); + print sprintf("%02d-%02d %02d:%02d:%02d Entries Processed: %9s\n", $mon+1, $day, $hour, $min, $sec, $entries); + } + $curr_seq_id = $_; + $curr_seq_id =~ s/>//g; + $curr_seq = ""; + } + elsif (length($_) > 0) { $curr_seq = join("", ($curr_seq, $_)); } + } + if (length($curr_seq_id) > 0 && length($curr_seq) > 0) { + &$process(\$curr_seq_id, \$curr_seq, \@opts); + $entries++; + #$entries = 1; #for performance, returning 1 as true indicating there is at least one entry processed + } + close (FILE); + return $entries; +} + +sub process_fastq { + my $fn = shift @_; + my $process = shift @_; + my $curr_seq_id = ""; + my $curr_str = ""; + my $curr_seq = ""; + my $entries = 0; + push (my @opts, @_); + open (FILE, "<${$fn}") || die "Unable to open ${$fn}, $!\n"; + while (<FILE>) { + chomp; + $_ =~ s/$dos_end//g; + if ($_=~/^@/) { + if (length($curr_seq_id) > 0 && length($curr_seq) > 0 && length($curr_str) > 0) { + #print join("\t", ("Joined:", $curr_seq_id, $curr_seq, @opts, "\n")); + &$process(\$curr_seq_id, \$curr_seq, \$curr_str, \@opts); + $entries++; + } + if (($entries % 100000) == 0) { + my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time); + print sprintf("%02d-%02d %02d:%02d:%02d Entries Processed: %9s\n", $mon+1, $day, $hour, $min, $sec, $entries); + } + $curr_seq_id = $_; + $curr_seq_id =~ s/@//g; + $curr_seq = ""; + $curr_str = ""; + } + elsif ($_=~/^\+/) { + $curr_seq = $curr_str; + $curr_str = $_; + $curr_str =~ s/\+//g; + if ($curr_seq_id ne $curr_str) { + warn "Invalid FASTQ file, sequence id and quality score id mismatch: $curr_seq_id, $curr_str\n"; + return -1; + } + $curr_str = ""; + } + elsif (length($_) > 0) { $curr_str = join("", ($curr_str, $_)); } + } + if (length($curr_seq_id) > 0 && length($curr_seq) > 0 && length($curr_str) > 0) { + &$process(\$curr_seq_id, \$curr_seq, \$curr_str, \@opts); + $entries++; + #$entries = 1; #for performance, returning 1 as true indicating there is at least one entry processed + } + close (FILE); + return $entries; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/visualize.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,72 @@ +require 'config.pl'; +open OUT, "> FISH/library_cis_list.txt"; +open OUT2, ">FISH/multi_test.txt"; + +$query1 = "select count(name) from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100"; +$sth = $dbh->prepare("$query1"); + +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { +$cis_number = $row[0]; +} + +$query2="select name,gene_name, library_name from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100"; + +$sth = $dbh->prepare("$query2"); +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { +#print $row[2]; +@chunks = split(/::/m, $row[2]); +foreach $lib(@chunks) { +if ($lib ne '') { +print OUT "$row[0]::$row[1]\t$lib\t1\n"; +} +} +} +close OUT; + +$sth = $dbh->prepare("select count(distinct descriptor) from metadata_$proj where descriptor != 'all';"); + +$sth->execute; + +while ((@row) = $sth->fetchrow_array) { +$desc_number = $row[0]; +} +$ann_cis_testing = $desc_number*$cis_number; +$cis_cis_testing = $cis_number*($cis_number-3)/2; +$ann_ann_testing = $desc_number*($desc_number-3)/2; +print OUT2 "$cis_number\t$desc_number\t$ann_cis_testing\t$cis_cis_testing\t$ann_ann_testing\n"; +close OUT2; +$sth = $dbh->prepare("select 'descriptor', descriptor, library from metadata_$proj;"); +$sth->execute; + +open OUT, "> FISH/library_descriptor_list.txt"; + +while ((@row) = $sth->fetchrow_array) { +print OUT "$row[0]::$row[1]\t$row[2]\t1\n"; +} + +close OUT; + +open (my $list, ">", "FISH/list.txt"); +open (my $cis_list, "<", "FISH/library_cis_list.txt"); +while(<$cis_list>) { + print $list $_; +} +close($cis_list); +open (my $desc_list, "<", "FISH/library_descriptor_list.txt"); +while (<$desc_list>) { + print $list $_; +} +close($desc_list); +close($list); +#system ("cat FISH/library_cis_list.txt FISH/library_descriptor_list.txt > FISH/list.txt"); +system ("perl lib/list2tab.pl 1 2 3 0 FISH/list.txt > FISH/cis4cluster.txt"); +system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_cis_list.txt > results/Assoc/Cis.txt"); +system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_descriptor_list.txt > results/Assoc/Ann.txt"); + +print "generated the matrix file cis4cluster.txt"; + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/list_projects.xml Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,45 @@ +<tool id="list_proj" name="List TAPDANCE Projects" version="1.0"> + <description>Generate a list of available projects</description> + <command interpreter="perl">lib/list_projects.pl -u $userEmail + #if $meta.meta_select.__str__() != 'all': + #for $item in $meta.tags + -tag $item.tag.__str__() + #end for + -query_type $meta.meta_select.__str__() + #end if + > $result + </command> + <inputs> + <conditional name="meta"> + <param name="meta_select" type="select" label="Filter on metadata tags?"> + <option value="all">Return all available projects</option> + <!--<option value="union">Return projects with all of the following tags</option>--> + <option value="join">Return projects with at least one of the following tags</option> + </param> + <when value="all"> + <param type="hidden" name="tags" value=""/> + </when> + <!--<when value="union"> + <repeat name="tags" title="Metadata Tags" min="1"> + <param name="tag" type="text"/> + </repeat> + </when>--> + <when value="join"> + <repeat name="tags" title="Metadata Tags" min="1"> + <param name="tag" type="text"/> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="result" label="TAPDANCE Projects"/> + </outputs> + <help> + See full help at https://sourceforge.net/p/tapdancebio/wiki/ + + `Report a Problem`_ + + .. _Report a Problem: https://sourceforge.net/p/tapdancebio/tickets/new/ + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tapdance.xml Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,235 @@ +<tool id="tapdance_runner" name="TAPDANCE" version="1.0" force_history_refresh="True"> + <description>A tool for identifying Common Insertion Sites</description> + <command interpreter="perl">tapdance_runner.pl -index $index -index_id $index.id -index_path $index.extra_files_path + #if $predef.predef_select.__str__() == 'PREDEF': + -s $predef.seqs -b $predef.bar2lib -pn $userEmail$predef.proj_name -config $predef.config + #else + ## INPUT + #if $predef.start_point.start_select.__str__() == 'sequences': + -s $predef.start_point.seqs -b $predef.start_point.bar2lib -bowtieIdx $predef.start_point.genomeIdx -pn $userEmail$predef.start_point.proj_name + #for $entry in $predef.start_point.mutagens + #if $entry.mutagen.mutagen_select.__str__() == 'CUSTOM': + -mutagen $entry.mutagen.mutagen_custom.__str__() + #else + -mutagen $entry.mutagen.mutagen_select.__str__() + #end if + #end for + #end if + #if $predef.start_point.start_select.__str__() == 'single_project': + -pn $predef.start_point.cis_project.__str__() + #end if + #if $predef.start_point.start_select.__str__() == 'multiple_projects': + -pn $userEmail$predef.start_point.proj_name -merge $predef.start_point.merge_projects.__str__() + #end if + + ## OUTPUT + #if $predef.start_point.start_select.__str__() != 'single_project': + -pb $projBed -projectBedId $projBed.id + ##-ps $projSum -projectSummaryId $projSum.id -pv $projVis -projectVisId $projVis.id + #end if + #if $predef.results.result_select.__str__() == 'cis': + -cw $cisWig -cwid $cisWig.id -cwpath $__new_file_path__ + ##-cs $cisSum -cisSumId $cisSum.id + -lib_pct $predef.results.cis_params.lib_pct -CIS_tot_p $predef.results.cis_params.CIS_tot_p -CIS_lib_p $predef.results.cis_params.CIS_lib_p -CIS_reg_p $predef.results.cis_params.CIS_reg_p -coCIS_thresh $predef.results.cis_params.coCIS_thresh + #if $predef.results.metadata.metadata_select.__str__() == 'CUSTOM': + -m $predef.results.metadata.metadata_custom.__str__() + #end if + #if $predef.results.annotation.annotation_select.__str__() == 'CUSTOM': + -m $predef.results.annotation.annotation_file.__str__() + #end if + #for $entry in $predef.results.omitChroms + -o $entry.omitChrom.__str__() + #end for + #else + -no_cis + #end if + #end if + </command> + <inputs> + <conditional name="predef"> + <param name="predef_select" type="select" label="Enter values below or use a predefined config file?"> + <option value="CUSTOM">Enter values below</option> + <option value="PREDEF">Use predefined config file</option> + </param> + <when value="PREDEF"> + <param name="proj_name" type="text" label="New Project Name" optional="false"/> + <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/> + <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/> + <param name="config" type="data" format="text" label="Predefined Config File" optional="false"/> + <conditional name="metadata"> + <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom"> + <option value="AUTOMATIC">Generate default</option> + <option value="CUSTOM">Use uploaded data</option> + </param> + <when value="AUTOMATIC"> + <param name="metadata_custom" type="hidden" value=""/> + </when> + <when value="CUSTOM"> + <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/> + </when> + </conditional> + </when> + <when value="CUSTOM"> + <conditional name="start_point"> + <param name="start_select" type="select" label="Starting Point"> + <option value="sequences">FASTQ or FASTA</option> + <option value="single_project">Existing Project</option> + <option value="multiple_projects">Merge Multiple Projects</option> + </param> + <when value="sequences"> + <param name="proj_name" type="text" label="New Project Name" optional="false"/> + <param name="seqs" type="data" format="fastq,fasta,tabular" label="Sequence File" optional="false"/> + <param name="bar2lib" type="data" format="tabular" label="Barcode to Library Map" optional="false"/> + <repeat name="mutagens" title="Mutagen(s)" min="1"> + <conditional name="mutagen"> + <param name="mutagen_select" type="select" label="Mutagen matching" help="Choose the appropriate match for this experiment"> + <option value="TGTATGTAAACTTCCGACTTCAACTG">Sleeping Beauty Example, TGTATGTAAACTTCCGACTTCAACTG</option> + <option value="CUSTOM">Other</option> + </param> + <when value="TGTATGTAAACTTCCGACTTCAACTG"> + <param name="mutagen_custom" type="hidden" value=""/> + </when> + <when value="CUSTOM"> + <param name="mutagen_custom" type="text" label="Mutagen Sequence" help="Enter the sequence to match as the mutagen, '_' may be used to match any single base. E.G. _GTATGTAAACTTCCGACTTCAACTG would match both AGTATGTAAACTTCCGACTTCAACTG and TGTATGTAAACTTCCGACTTCAACTG"/> + </when> + </conditional> + </repeat> + <param name="genomeIdx" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact help@msi.umn.edu"> + <options from_file="bowtie_indices.loc"> + <column name="value" index="3" /> + <column name="name" index="0" /> + </options> + </param> + </when> + <when value="single_project"> + <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/> + <param name="cis_project" type="select" label="Project" data_ref="proj_source"> + <options from_dataset="proj_source"> + <column name="name" index="1"/> + <column name="value" index="0"/> + </options> + </param> + </when> + <when value="multiple_projects"> + <param name="proj_name" type="text" label="New Project Name" optional="false"/> + <param name="proj_source" type="data" format="tabular" label="Available Projects File" help="If you do not have a project list file, select the project type 'Generate Project List'"/> + <param name="merge_projects" type="select" multiple="true" label="Projects to Merge" data_ref="proj_source"> + <options from_dataset="proj_source"> + <column name="name" index="1"/> + <column name="value" index="0"/> + </options> + </param> + </when> + </conditional> + <conditional name="results"> + <param name="result_select" type="select" label="Desired Results"> + <option value="cis">CIS calls</option> + <option value="inserts">Inserts Only (useful for QC)</option> + </param> + <when value="inserts"> + <param type="hidden" value="" name="inserts_only"/> + </when> + <when value="cis"> + <conditional name="metadata"> + <param name="metadata_select" type="select" label="Library Metadata" help="Automatic metadata generation or custom"> + <option value="AUTOMATIC">Generate default</option> + <option value="CUSTOM">Use uploaded data</option> + </param> + <when value="AUTOMATIC"> + <param name="metadata_custom" type="hidden" value=""/> + </when> + <when value="CUSTOM"> + <param name="metadata_custom" type="data" format="tabular" label="Metadata Input" help="Library/Tag pairs, tab delmited"/> + </when> + </conditional> + <repeat name="omitChroms" title="Chromosomes to Omit" help="The chromosome of the donor concatemer is often omitted"> + <param type="text" name="omitChrom" label="Chromosome Label" help="e.g. chr1"/> + </repeat> + <conditional name="annotation"> + <param name="annotation_select" label="Annotation Features" type="select" help="Specify an interval file containing genomic features to annotate CIS calls"> + <option value="DEFAULT">Default: mm9 refSeq genes</option> + <option value="CUSTOM">Specify interval file</option> + </param> + <when value="DEFAULT"> + <param type="hidden" name="annotation_file" value=""/> + </when> + <when value="CUSTOM"> + <param type="data" format="interval" name="annotation_file" label="Annotation Source"/> + </when> + </conditional> + <conditional name="cis_params"> + <param name="cis_params_select" type="select" label="CIS calling parameters"> + <option value="default">Use defaults</option> + <option value="custom">Specify values</option> + </param> + <when value="default"> + <param type="hidden" value="0.0001" name="lib_pct"/> + <param type="hidden" value="0.05" name="CIS_tot_p"/> + <param type="hidden" value="0.05" name="CIS_lib_p"/> + <param type="hidden" value="0.05" name="CIS_reg_p"/> + <param type="hidden" value="0.0001" name="coCIS_thresh"/> + </when> + <when value="custom"> + <param type="float" value="0.0001" name="lib_pct" label="Library Percent"/> + <param type="float" value="0.05" name="CIS_tot_p" label="CIS Total pvalue"/> + <param type="float" value="0.05" name="CIS_lib_p" label="CIS Library pvalue"/> + <param type="float" value="0.05" name="CIS_reg_p" label="CIS Region pvalue"/> + <param type="float" value="0.0001" name="coCIS_thresh" label="coCIS Threshold"/> + </when> + </conditional> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data format="html" name="index" label="TAPDANCE Results"/> + <data format="bed" name="projBed" label="Non Redundant Inserts BED" visible="false"> + <filter>( + predef['predef_select'] == 'PREDEF' or + predef['start_point']['start_select'] != 'single_project' + ) + </filter> + </data> + <!-- + <data format="txt" name="projSum" label="Summary" hidden="true"> + <filter>( + predef['predef_select'] == 'PREDEF' or + predef['start_point']['start_select'] == 'sequences' + ) + </filter> + </data> + <data format="pdf" name="projVis" label="Insert Graphs"> + <filter>(predef['predef_select'] == 'PREDEF' or predef['start_point']['start_select'] != 'single_project')</filter> + </data> + --> + <!-- due to optional start with seqs, can no longer use the seqs metadata as a source for cisWig metadata --> + <data format="wig" name="cisWig" label="CIS WIG"> + <filter>( + predef['predef_select'] == 'PREDEF' or + predef['results']['result_select'] == 'cis' + ) + </filter> + </data> + <!-- + <data format="txt" name="cisSum" label="CIS Summary"> + <filter>( + predef['predef_select'] == 'PREDEF' or + predef['results']['result_select'] == 'cis' + ) + </filter> + </data> + --> + </outputs> + <!--<code file="tapdance_index.py"> + <hook exec_after_process="exec_after_completion" /> + </code>--> + <help> + See full help at https://sourceforge.net/p/tapdancebio/wiki/ + + `Report a Problem`_ + + .. _Report a Problem: https://sourceforge.net/p/tapdancebio/tickets/new/ + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tapdance_runner.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,621 @@ +#!/project/bioperl/perl-5.10.1-sles11/bin/perl -w +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2010 - 2011, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# Jesse Erdmann +# +# POD documentation +#------------------------------------------------------------------------------ +=pod BEGIN + +=head1 NAME + + tapdance_runner.pl - TAPDANCE wrapper that provides a single interface to all + TAPDANCE functionality. + +=head1 SYNOPSIS + + tapdance_runner.pl [-help] + + See http://sf.net/p/tapdancebio for full documentation + +=head1 OPTIONS + +=over 6 + +=item B<-help> + + Print this usage summary. + +=item B<-seqFile sequence_file> + + The sequences to be processed for insertions. + +=item B<-bar2libFile barcode_to_library_mapping_file> + + A tab delimited file where each line contains the barcode and name of a + library. Additionally, columns after the second column will be treated as + metadata tags to be associated with the library. + +=item B<-baseConfig custom_config> + + OPTIONAL. If there is a custom tapdance_base_config.txt to be used in + special cases, use this parameter to specify it's use. An example where + this might be useful is the case where distinct groups of users are using + the same TAPDANCE installation, but separate mutagens. + +=item B<-config predefined_config_file> + + A configuration file may be used rather than specify options on + the command line. Any options specified in the base config file + will be overriden by values specified in this config file. + +=item B<-db_config database_configuration_file> + + Use this option if the database configuration needs to be kept separate + from other configuration information. This is most useful in Galaxy + where the end user should not have the database user credentials + exposed to them. + +=item B<-bowtieIdx reference_genome> + + The name of the bowtie index to use for aligning individual sequences. This + is only used during the first phase of TAPDANCE. It is important to note that + the index name is not a single file. For instance, the mm9 index has several + files name mm9.[0-9].ebwt and mm9.rev.[0-9].ebwt. However, the correct + value for this parameter would be /my/path/to/indexes/mm9 + +=item B<-mutagen mutagen_sequence> + + The sequence to match determining whether the mutagen of interest is present. + Any sequences not matching this sequence will not be used in the analysis + while those that do will have the mutagen trimmed prior to alignment. If, for + instance the mutagen for a particular project has a sequence of ACTG, but the + user also wanted to remove up two bases following the mutagen sequence the + wildcard character '_' can be used to specify a mutagen sequence of ACTG__. + + Any number of mutagen sequences may be specified by entering multiple -mutagen + entries on the command line. E.G. perl tapdance_runner.pl -mutagen ACGT + -mutagen TGCA. This is useful when a mutagen has more than one common captured + sequence in the data. + +=item B<-projectName project_name> + + A name for the project, up to 255 chars. + +=item B<-omittedChromosomes chromosomes_to_omit> + + It can be useful to remove the chromosome of the donor concatamer from the + calulations to remove the effects of local hopping for some projects. The + chromosomes can be specified as a comma delimited list and must match the + names used in the reference genome. E.G -omittedChromosomes chr1 + -omittedChromosomes chr2 + +=item B<-output_dir location_to_write_to> + + The location where execution will be performed + + DEFAULT:'./' + +=item B<-metadata library_metadata> + + OPTIONAL. To specify metadata on libraries outside of the barcode to library + mapping file, this parameter may be used. The file should contain the name of + the library in one column and the metadata tag to affiliate with it in the + second. Each library may have as many entries as needed. + +=item B<-lib_pct library_percent> + +=item B<-CIS_tot_p CIS_total_pvalue> + +=item B<-CIS_lib_p CIS_library_pvalue> + +=item B<-CIS_reg_p CIS_region_pvalue> + +=item B<-coCIS_thresh cocis_threshold> + +=item B<-merge merge> + + Specify projects to be merged as the new project specified with -project_name. + E.G. -merge my_first_project -merge my_second_project -project_name + my_merged_project. + +=item B<-annotation annotation_file> + + Specify the bed file to annotate CISes with. The default feature set is USCS's + mm9 refSeq genes. + +=item B<-no_cis> + + To generate a list of inserts only, specify no_cis. This is useful in cases + where a new set of data needs to be merged with a previous set of data. Use + this option as a first step to prepare the new data. Use -merge to combine + the resulting projects and call CISes on the new project. + +=item B<-seqType seqfile_format> + + OPTIONAL. If not specified, TAPDANCE will attempt to identify the input file + type on it's own. Valid options are 'tab', 'fasta' and 'fastq'. + +=item B<-debug> + + OPTIONAL. + +=back + +=cut + +#### END of POD documentation. +#----------------------------------------------------------------------------- + +use strict; +use Cwd; +use Getopt::Long; +use File::Copy; +use File::Find; +use File::Temp qw/ tempfile tempdir /; +use Pod::Usage; + +#tapdance_runner.pl -s $seqs -b $bar2lib -g $genomeIdx -pn $projName -o $omitChrom -pb $projBed -ps $projSum -cb $cisBed -cs $cisSum -bc $baseConfig + +my $dbh; +my $path = $0; +$path =~ s/\/\w*\.pl$//g; +require "$path/lib/tapdance_base_config.pl"; +require "$path/util.pl"; + +#Universal variables +my ($seqFile, $seqType, $bar2libFile, $bowtieIdx, $bwaIdx, $projName, @omitChrom, $baseConfig, @mutagens_array, $metadata, $merge, $preconfig_file, $library_percent, $CIS_total_pvalue, $CIS_library_pvalue, $CIS_region_pvalue, $cocis_threshold, $annotation_file, $db_config); +my $no_cis = 0; + +#CMD line variables +my ($debug, $output_dir, $noUnlink, $help_flag); + +#Galaxy variables +my ($index, $index_id, $index_path, $projBed, $projBedId, $projSum, $projSumId, $projVis, $projVisId, $cisWig, $cisWigId, $cisWigPath, $cisSum, $cisSumId, $tmpDir); + + +my %options = ( +#Universal Variables + "seqFile|s=s" => \$seqFile, + "seqType|st=s" => \$seqType, + "bar2libFile|b=s" => \$bar2libFile, + "bowtieIdx=s" => \$bowtieIdx, + #"bwaIdx=s" => \$bwaIdx, + "projectName|pn=s" => \$projName, + "omittedChromosomes|o=s" => \@omitChrom, + "baseConfig|bc=s" => \$baseConfig, + "metadata|m=s" => \$metadata, + "mutagen=s" => \@mutagens_array, + "lib_pct=f" => \$library_percent, + "CIS_tot_p=f" => \$CIS_total_pvalue, + "CIS_lib_p=f" => \$CIS_library_pvalue, + "CIS_reg_p=f" => \$CIS_region_pvalue, + "coCIS_thresh=f" => \$cocis_threshold, + "merge=s" => \$merge, + "annotation=s" => \$annotation_file, + "config=s" => \$preconfig_file, + "db_config=s" => \$db_config, + "no_cis" => \$no_cis, + +#CMD Line Variables + "help" => \$help_flag, + "output_dir=s" => \$output_dir, + "debug|d" => \$debug, + +#Galaxy Variables + "index=s" => \$index, + "index_id=s" => \$index_id, + "index_path=s" => \$index_path, + "projectBed|pb=s" => \$projBed, + "projectBedId=s" => \$projBedId, + "cisWig|cw=s" => \$cisWig, + "cisWigId|cwid=s" => \$cisWigId, + "cisWigPath|cwpath=s" => \$cisWigPath, + "tmp_dir|t=s" => \$tmpDir, + "no_unlink" => \$noUnlink + ); + +GetOptions(%options) or pod2usage(2); +pod2usage(1) if $help_flag; + +$projName = &sanitize_project($projName); +my $meta_gen = 0; + +my $envDirN; +if (defined($output_dir)) { + $envDirN = $output_dir; + unless (-d $output_dir) { + mkdir ($output_dir); + } +} +elsif (defined($tmpDir)) { + if ($noUnlink) { + $envDirN = tempdir(DIR => $tmpDir); + } + else { + $envDirN = tempdir(DIR => $tmpDir, UNLINK => 1); + } +} +else { + if ($noUnlink) { + $envDirN = tempdir(); + } + else { + $envDirN = tempdir(UNLINK => 1); + } +} +if ($debug) { print "EnvDir = $envDirN\n"; } + +if (!defined($baseConfig)) { $baseConfig = "$path/lib"; } +open(my $baseConfigH, "<", $baseConfig . "/tapdance_base_config.pl") || die "Unable to open $baseConfig: $!\n"; +open(my $envConfigH, ">", $envDirN . "/config.pl") || die "Unable to open environment $envDirN/config.pl: $!\n"; + +if (defined($db_config)) { + print $envConfigH "require '" . $envDirN . "/" . $db_config . "';\n"; +} + +# Copy system defaults first, overwrite as needed +while (<$baseConfigH>) { + print $envConfigH $_; +} +close($baseConfigH); + +if (defined($preconfig_file)) { + open(my $preConfigH, "<", $preconfig_file) || die "Unable to open input configuration file $preconfig_file. $!\n"; +} +else { + print $envConfigH "#Project specific custom values, will override values set above\n"; + print $envConfigH "\$proj = '$projName';\n"; + print $envConfigH "\$envDir = '$envDirN';\n"; + if (defined($library_percent)) { + print $envConfigH "\$library_percent = '$library_percent';\n"; + } + if (defined($CIS_total_pvalue)) { + print $envConfigH "\$CIS_total_pvalue = '$CIS_total_pvalue';\n"; + } + if (defined($CIS_library_pvalue)) { + print $envConfigH "\$CIS_library_pvalue = '$CIS_library_pvalue';\n"; + } + if (defined($CIS_region_pvalue)) { + print $envConfigH "\$CIS_region_pvalue = '$CIS_region_pvalue';\n"; + } + if (defined($cocis_threshold)) { + print $envConfigH "\$cocis_threshold = '$cocis_threshold';\n"; + } + if (defined($bowtieIdx && $bwaIdx)) { + print $envConfigH "\$bwa_exe = 'bwa';\n"; + print $envConfigH "\$bowtie_exe = 'bowtie --quiet';\n"; + print $envConfigH "\$bwa_idx = '$bwaIdx';\n"; + print $envConfigH "\$bowtie_idx = '$bowtieIdx';\n"; + print $envConfigH "\$aligner = 'bow_bwa';\n"; + } + elsif (defined($bowtieIdx)) { + print $envConfigH "\$bowtie_exe = 'bowtie --quiet';\n"; + print $envConfigH "\$bowtie_idx = '$bowtieIdx';\n"; + print $envConfigH "\$aligner = 'bowtie';\n"; + } + elsif (defined($bwaIdx)) { + print $envConfigH "\$bwa_exe = 'bwa';\n"; + print $envConfigH "\$bwa_idx = '$bwaIdx';\n"; + print $envConfigH "\$aligner = 'bwa';\n"; + } + + if ($#mutagens_array >= 0 && length($mutagens_array[0]) > 0) { + print $envConfigH "\$mutagens = '" . join(",", @mutagens_array) . "';\n"; + } + if (defined($annotation_file)) { + print $envConfigH "\$annotation_file ='" . $annotation_file . "';\n"; + } + if (!defined($seqType) && defined($seqFile)) { + $seqType = &determine_seq_input_type(\$seqFile, \$envConfigH); + } +} +print $envConfigH "return 1;\n"; +close($envConfigH); + +my ($output, $orig_dir); +mkdir ("$envDirN/data"); # || die "Unable to create data dir, $envDirN/data. $!\n"; +mkdir("$envDirN/lib"); # || die "Unable to create lib. $!\n"; +my @lib_source = ($path . "/lib/"); +find(\&lib_copy, @lib_source); + +my $copy_ins_files = 0; +my $indexH; +if (defined($index)) { + open ($indexH, ">", $index) || die "Unable to open $index for writing: $!\n"; + print $indexH "<HTML>\n<HEAD>\n<TITLE>$projName Results</TITLE>\n</HEAD>\n<BODY>\n<H1>$projName</H1>\n"; + if (defined($index_path)) { + unless (-d $index_path) { + mkdir($index_path); + } + } +} + +### +# Phase 1, sequences through mapping to insert list +### +if (defined($seqFile)) { + my $seqOutFn = "$envDirN/data/seqs.tab"; + &pre_process_seqs(\$seqType, \$seqFile, \$seqOutFn, \$debug); + copy("$bar2libFile", "$envDirN/data/barcode2lib.txt") || die "Unable to link barcode to library file in execution environment. $!\n"; + $orig_dir = &cwd; + if ($debug) { print "Starting dir: $orig_dir.\n"; } + chdir($envDirN); + if ($debug) { print "Current dir: " . &cwd . "\n"; } + open($output, "perl $envDirN/lib/TAPDANCE.pl |") || die "Unable to run TAPDANCE.pl. $!\n"; + if ($debug) { while (<$output>) { print "$_"; } } + close($output); + chdir($orig_dir); + if (defined($index)) { + print $indexH "<H3>Insertion Analysis</H3>\n<P>To visualize the insertions in this project use the \"Non Redundant Inserts BED\" file in the history.\n<UL>\n"; + #if (defined($projSum)) { + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_InsertsVis_hidden.pdf", "pdf", "QC graphs of inserts", 0) . "</LI>\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_InsertsSummary_hidden.txt", "txt", "Summary of all inserts", 0) . "</LI>\n"; + copy("$envDirN/results/summary_$projName.txt", $index_path . "/primary_" . $index_id . "_InsertsSummary_hidden.txt") || die "Unable to retrieve project summary, $envDirN/results/summary_$projName.txt. $!\n"; + system("Rscript --vanilla $envDirN/lib/insert_vis.R --args $envDirN/results/lib_stats_$projName.txt $envDirN/results/region_stats_$projName.txt " . $index_path . "/primary_" . $index_id . "_InsertsVis_hidden.pdf"); + #copy("$envDirN/results/summary_$projName.txt", "$projSum") || die "Unable to retrieve project summary, $envDirN/results/summary_$projName.txt. $!\n"; + print $indexH "</UL>\n</P>\n"; + } + #if (defined($projVis)) { + #system("Rscript --vanilla $envDirN/lib/insert_vis.R --args $envDirN/results/lib_stats_$projName.txt $envDirN/results/region_stats_$projName.txt $projVis"); + #} + $copy_ins_files=1; + if ($debug) { print "TAPDANCE.pl done.\n"; } +} + +### +# Phase 4, merge projects +### +if (defined($merge)) { + open(my $meta_tab, ">", "$envDirN/data/meta.tab") || die "Unable to write project merge list to $envDirN/data/meta.tab: $!\n"; + my @merge_projs = split(',', $merge); + foreach my $merge_proj (@merge_projs) { + print $meta_tab "$merge_proj\n"; + } + close($meta_tab); + $orig_dir = &cwd; + if ($debug) { print "Starting dir: $orig_dir.\n" } + chdir($envDirN); + open($output, "perl $envDirN/lib/TAP4.pl |") || die "Unable to run TAP4.pl. $!\n"; + if ($debug) { while (<$output>) { print "$_"; } } + close($output); + chdir($orig_dir); + $copy_ins_files=1; + if ($debug) { print "TAP4.pl done.\n"; } +} + +### +# Copy insert files +### +if ($copy_ins_files) { + #if (defined($projBed)) { + if (defined($index)) { + #copy("$envDirN/results/raw_$projName.BED", "$projBed") || die "Unable to retrieve project BED, $envDirN/results/raw_$projName.BED. $!\n"; + #print $indexH "<A HREF=\"primary_" . $index_id . "_InsertsBED_hidden_bed?preview=true\">A BED containing all inserts</A><BR>\n"; + copy("$envDirN/results/raw_$projName.BED", $index_path . "/primary_" . $index_id . "_InsertsBED_visible_bed") || die "Unable to retrieve project BED, $envDirN/results/raw_$projName.BED. $!\n"; + } + if ($debug) { print "Files copied.\n"; } +} + +### +# Phase 2, calculate CISes +### +if (!$no_cis) { #defined($cisWig) && defined($cisSum)) { + #Fill chromo tab for phase two + open(my $chromoTabH, ">", $envDirN . "/data/chromo.tab") || die "Unable to open chromo tab $envDirN/data/chromo.tab: $!\n"; + if (defined($metadata)) { + copy("$metadata", "$envDirN/data/metadata.tab") || die "Unable to copy provided metadata, $metadata. $!\n"; + } + foreach (@omitChrom) { print $chromoTabH "$_\n"; } + close ($chromoTabH); + if ($debug) { print "Omitted chromosomes written.\n"; } + + my ($metadataTabH, $barcodeInH); + my %metadata_attrs = (); + my @map; + if (!defined($metadata) && defined($bar2libFile)) { + open($metadataTabH, ">", $envDirN . "/data/metadata.tab") || die "Unable to open chromo tab $envDirN/data/metadata.tab: $!\n"; + open($barcodeInH, "<", "$envDirN/data/barcode2lib.txt") || die "Unable to open barcode to library mapping, $bar2libFile: $!\n"; + my ($idx, $lib_name); + while (<$barcodeInH>) { + chomp; + @map = split("\t", $_); + $map[1] =~ s/^\s+//; + $map[1] =~ s/\s+$//; + $map[1] =~ m/(.*)-[L|R]/; + $lib_name = $1; + print $metadataTabH join("\t", $lib_name, "all", "cis") . "\n"; + for ($idx = 3; $idx <= $#map; $idx++) { + $map[$idx] =~ s/^\s+//; + $map[$idx] =~ s/\s+$//; + print $metadataTabH join("\t", $lib_name, $map[$idx], "cis") . "\n"; + $metadata_attrs{$map[$idx]} = 1; + } + } + close($barcodeInH); + close($metadataTabH); + $meta_gen = 1; + if ($debug) { print "Metadata written.\n"; } + } + else { + open(my $metadata_file, "<", $envDirN . "/data/metadata.tab") || die "Unable to open meta, $!\n"; + while(<$metadata_file>) { + chomp; + @map = split("\t", $_); + if (uc $map[2] eq "CIS" && uc $map[1] ne "ALL") { + $metadata_attrs{$map[1]} = 1; + } + } + close($metadata_file); + } + + #mkdir("$envDirN/CIS"); # || die "Unable to create lib. $!\n"; + + #if ($debug) { print "Created $envDirN/CIS\n"; } + + $orig_dir = &cwd; + if ($debug) { print "Starting dir: $orig_dir.\n" } + chdir($envDirN); + open($output, "perl ./lib/TAP2.pl |") || die "Unable to run TAP2.pl. $!\n"; + if ($debug) { while (<$output>) { print "$_"; } } + close($output); + chdir($orig_dir); + if ($debug) { print "TAP2.pl run.\n"; } + + if ($debug) { print "TAP2.pl done.\n"; } + if (defined($index)) { + print $indexH "<H3>CIS calls</H3>\n<P>To Visualize the CIS Calls, use the \"CIS WIG\" history entry. Each metadata tag that generated it's own CIS calls has it's own WIG file in the history as \"CIS WIG (tag)\".\n<UL>\n"; + #if (defined($cisSum)) { + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_CISSummary_hidden.txt", "txt", "Summary of all CIS calls", 0) . "</LI>\n"; + copy("$envDirN/results/summary_CIS_$projName.txt", $index_path . "/primary_" . $index_id . "_CISSummary_hidden.txt") || die "Unable to retrieve CIS summary, $envDirN/results/cis_summary.txt. $!\n"; + #print $indexH "<A HREF=\"primary_" . $index_id . "_CISWIG_visible_wig\">WIG of all CIS calls</A><BR>\n"; + #copy($envDirN . "/results/all/plot_all-nr-" . $projName . "-" . $library_percent . ".wig", $index_path . "/primary_" . $index_id . "_CISWIG_visible_wig") || die "Unable to retrieve CIS WIG, $envDirN/results/all/plot_all-nr-$projName-$library_percent.wig. $!\n"; + copy($envDirN . "/results/all/plot_all-nr-" . $projName . "-" . $library_percent . ".wig", $cisWig) || die "Unable to retrieve CIS WIG, $envDirN/results/all/plot_all-nr-$projName-$library_percent.wig. $!\n"; + print $indexH "<UL>\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_Ann_hidden.txt", "txt", "Ann.txt", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Ann.txt", $index_path . "/primary_" . $index_id . "_Ann_hidden.txt") || die "Unable to retrieve Ann.txt. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_Cis_hidden.txt", "txt", "Cis.txt", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Cis.txt", $index_path . "/primary_" . $index_id . "_Cis_hidden.txt") || die "Unable to retrieve Cis.txt. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_AnnAnnTable_hidden.txt", "txt", "Ann_Ann_table.txt", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Ann_Ann_table.xls", $index_path . "/primary_" . $index_id . "_AnnAnnTable_hidden.txt") || die "Unable to retrieve Ann_Ann_table.xls. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_AnnAnnMatrix_hidden.txt", "txt", "Ann_ann_matrix.txt", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Ann_ann_matrix.txt", $index_path . "/primary_" . $index_id . "_AnnAnnMatrix_hidden.txt") || die "Unable to retrieve Ann_ann_matrix.txt. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_AnnCisTable_hidden.txt", "txt", "Ann_cis_table.xls", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Ann_cis_table.xls", $index_path . "/primary_" . $index_id . "_AnnCisTable_hidden.txt") || die "Unable to retrieve Ann_cis_table.xls. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_AnnCisMatrix_hidden.txt", "txt", "Ann_cis_matrix.txt", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Ann_cis_matrix.txt", $index_path . "/primary_" . $index_id . "_AnnCisMatrix_hidden.txt") || die "Unable to retrieve Ann_cis_matrix.txt. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_CisCisTable_hidden.txt", "txt", "Cis_cis_table.xls", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Cis_cis_table.xls", $index_path . "/primary_" . $index_id . "_CisCisTable_hidden.txt") || die "Unable to retrieve Cis_cis_table.xls. $!\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_CisCisMatrix_hidden.txt", "txt", "Cis_cis_matrix.txt", 0) . "</LI>\n"; + copy("$envDirN/results/Assoc/Cis_cis_matrix.txt", $index_path . "/primary_" . $index_id . "_CisCisMatrix_hidden.txt") || die "Unable to retrieve Cis_cis_matrix.txt. $!\n"; + print $indexH "</UL>\n</UL>\n</P>\n"; + #copy("$envDirN/results/summary_CIS_$projName.txt", "$cisSum") || die "Unable to retrieve CIS summary, $envDirN/results/cis_summary.txt. $!\n"; + #} + #if (defined($cisWig)) { + #copy("$envDirN/results/all/plot_all-nr-$projName-$library_percent.wig", "$cisWig") || die "Unable to retrieve CIS WIG, $envDirN/results/all/plot_all-nr-$projName-$library_percent.wig. $!\n"; + #} + #if (defined($cisWigId) && defined($cisWigPath)) { + #my $count; + my $filesize; + foreach my $tag (keys %metadata_attrs) { + #open(FILE, "< $envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig") or die "can't open $envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig: $!"; + #for ($count=0; <FILE>; $count++) { } + #if ($count > 1) { + if (-e "$envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig") { + $filesize = -s "$envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig"; + if ($filesize > 0) { + #print $indexH "<A HREF=\"primary_" . $index_id . "_" . $tag . "_visible_wig\">Summary of CIS calls for libraries with the " . $tag . " label</A><BR>\n"; + #copy("$envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig", $index_path . "/primary_" . $index_id . "_" . $tag . "_visible_wig") || die "Unable to retrieve CIS WIG, $envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig. $!\n"; + copy("$envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig", "$cisWigPath/primary_" . $cisWigId . "_" . $tag . "_visible_wig") || die "Unable to retrieve CIS WIG, $envDirN/results/$tag/plot_" . $tag . "-nr-" . $projName . "-" . $library_percent . ".wig. $!\n"; + } + } + } + } + if ($debug) { print "Files copied.\n"; } +} + +if (defined($index)) { + print $indexH "<P>To add files to your history for further processing in Galaxy, right-click the link and select \"Copy Link URL\". Open the \"Get Data\" menu in the \"Tools\" sidebar and open the \"Upload File\" link. Paste the copied URL in the \"URL/Text\" box.</P>\n."; + print $indexH "<H3>Generated configuration files</H3>\n<UL>\n"; + print $indexH "<LI>" . &link_file("primary_" . $index_id . "_ConfigPl_hidden.txt", "txt", "Project configuration", 0) . "</LI>\n"; + copy("$envDirN/config.pl", $index_path . "/primary_" . $index_id . "_ConfigPl_hidden.txt") || die "Unable to retrieve config.pl. $!\n"; + if ($meta_gen) { + print $indexH "<LI>" . &link_file("config.pl", "txt", "Project configuration", 0) . "</LI>\n"; + copy("$envDirN/config.pl", $index_path . "/primary_" . $index_id . "_ConfigPl_hidden.txt") || die "Unable to retrieve config.pl. $!\n"; + } + print $indexH "</UL>\n</BODY>\n</HTML>\n"; + close($indexH); +} + +exit(0); + +sub determine_seq_input_type { + my ($input_fn_ref, $config_fh_ref) = @_; + open(INPUT, "<", ${$input_fn_ref}) || die "Unable to open input file ${$input_fn_ref}, $!\n"; + my $first_line = <INPUT>; + close (INPUT); + if ($first_line=~/^@/) { + print ${$config_fh_ref} sprintf("\$quality = 1;\n"); + return "fastq"; + } + elsif ($first_line=~/^>/) { + print ${$config_fh_ref} sprintf("\$quality = 0;\n"); + return "fasta"; + } + else { + my @split_array = split("\t", $first_line); + if ($#split_array > 0) { + return "tab"; + } + else { + die "Unable to determine sequence input value type (fastq|fasta|tabular)\n"; + } + } +} + +sub pre_process_seqs { + my ($seq_type_ref, $in_file_ref, $out_fn_ref, $debug_ref) = @_; + #FASTQ + if (${$seq_type_ref} eq "fastq") { + if (${$debug_ref}) { print "FASTQ\n"; } + open (my $out_fh, ">", ${$out_fn_ref}) || die "Unable to open ${$out_fn_ref}, $!\n"; + &process_fastq($in_file_ref, \&fastq_entry, \$out_fh); + close($out_fh); + } + + #FASTA + elsif (${$seq_type_ref} eq "fasta") { + if (${$debug_ref}) { print "FASTA\n"; } + open (my $out_fh, ">", ${$out_fn_ref}) || die "Unable to open ${$out_fn_ref}, $!\n"; + &process_fasta($in_file_ref, \&fasta_entry, \$out_fh); + close($out_fh); + } + + #Tab, no quality info + else { + if (${$debug_ref}) { print "TABULAR\n"; } + copy (${$in_file_ref}, ${$out_fn_ref}) || die "Unable to copy seq file to execution environment. $!\n"; + #open($output, "ln -s ${$in_file_ref} ${$out_fn_ref} |") || die "Unable to link seq file in execution environment. $!\n"; + #if (${$debug_ref}) { while (<$output>) { print "$_"; } } + #close($output); + } +} + +sub fasta_entry { + my ($seq_id_ref, $seq_ref, $array_ref) = @_; + print "fasta_entry(" . join(",", ${$seq_id_ref}, ${$seq_ref}) . ")\n"; + #print ${$array_ref->[0]} join("\t", ${$seq_id_ref}, "", ${$seq_ref}) . "\n"; + #my $seq_qual = ""; + #for(my $i = 0; $i < length(${$seq_ref}); $i++) { $seq_qual = $seq_qual . 'h'; } + #print sprintf("Fasta_entry: length of sequence:%s length of quality:%s", length(${$seq_id_ref}), length($seq_qual)); + print ${$array_ref->[0]} join("\t", ${$seq_id_ref}, "", ${$seq_ref}); + ${$seq_ref} =~ s/[A,C,T,G]/I/g; + ${$seq_ref} =~ s/N/!/g; + print ${$array_ref->[0]} sprintf("\t%s\n", ${$seq_ref}); +} + +sub fastq_entry { + my ($seq_id_ref, $seq_ref, $seq_qual, $array_ref) = @_; + #print "fastq_entry(" . join(",", ${$seq_id_ref}, ${$seq_ref}, ${$seq_qual}) . ")\n"; + print ${$array_ref->[0]} join("\t", ${$seq_id_ref}, "", ${$seq_ref}, ${$seq_qual}) . "\n"; +} + +sub lib_copy { + unless(-d $File::Find::name) { + copy($File::Find::name, "$envDirN/lib") || die "Unable to copy $File::Find::name to $envDirN/lib. $!\n"; + } +} + +sub link_file { + my ($file_name, $file_type, $link_text, $download) = @_; + my $out = "<A HREF=\"" . $file_name . "\">" . $link_text . "</A>"; + if ($download) { + $out = $out . " [<A HREF=\"" . $file_name . "/display?to_ext=" . $file_type . "\">Download</A>]"; + } + return $out; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/util.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,125 @@ +#!/project/bioperl/perl-5.10.1-sles11/bin/perl -w + +my $dos_end = chr(13); + +my %chrom_map = ( + "gi|149288852|ref|NC_000067.5|NC_000067" => "chr1", + "gi|149288869|ref|NC_000076.5|NC_000076" => "chr10", + "gi|149288871|ref|NC_000077.5|NC_000077" => "chr11", + "gi|149292731|ref|NC_000078.5|NC_000078" => "chr12", + "gi|149292733|ref|NC_000079.5|NC_000079" => "chr13", + "gi|149292735|ref|NC_000080.5|NC_000080" => "chr14", + "gi|149301884|ref|NC_000081.5|NC_000081" => "chr15", + "gi|149304713|ref|NC_000082.5|NC_000082" => "chr16", + "gi|149313536|ref|NC_000083.5|NC_000083" => "chr17", + "gi|149321426|ref|NC_000084.5|NC_000084" => "chr18", + "gi|149323268|ref|NC_000085.5|NC_000085" => "chr19", + "gi|149338249|ref|NC_000068.6|NC_000068" => "chr2", + "gi|149352351|ref|NC_000069.5|NC_000069" => "chr3", + "gi|149354223|ref|NC_000070.5|NC_000070" => "chr4", + "gi|149354224|ref|NC_000071.5|NC_000071" => "chr5", + "gi|149361431|ref|NC_000072.5|NC_000072" => "chr6", + "gi|149361432|ref|NC_000073.5|NC_000073" => "chr7", + "gi|149361523|ref|NC_000074.5|NC_000074" => "chr8", + "gi|149361524|ref|NC_000075.5|NC_000075" => "chr9", + "gi|149361525|ref|NC_000086.6|NC_000086" => "chrX", + "gi|149361526|ref|NC_000087.6|NC_000087" => "chrY" +); + +return 1; + +sub get_chrom_map { + return \%chrom_map; +} + +sub sanitize_project { + my ($project) = @_; + $project =~ s/@/_/g; + $project =~ s/\./_/g; + $project =~ s/\s/_/g; + return $project; +} + +sub process_fasta { + my $fn = shift @_; + my $process = shift @_; + my $curr_seq_id = ""; + my $curr_seq = ""; + my $entries = 0; + push (my @opts, @_); + open (FILE, "<${$fn}") || die "Unable to open ${$fn}, $!\n"; + while (<FILE>) { + chomp; + $_ =~ s/$dos_end//g; + if ($_=~/^>/) { + if (length($curr_seq_id) > 0 && length($curr_seq) > 0) { + #print join("\t", ("Joined:", $curr_seq_id, $curr_seq, @opts, "\n")); + &$process(\$curr_seq_id, \$curr_seq, \@opts); + $entries++; + } + #if (($entries % 100000) == 0) { + # my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time); + # print sprintf("%02d-%02d %02d:%02d:%02d Entries Processed: %9s\n", $mon+1, $day, $hour, $min, $sec, $entries); + #} + $curr_seq_id = $_; + $curr_seq_id =~ s/>//g; + $curr_seq = ""; + } + elsif (length($_) > 0) { $curr_seq = join("", ($curr_seq, $_)); } + } + if (length($curr_seq_id) > 0 && length($curr_seq) > 0) { + &$process(\$curr_seq_id, \$curr_seq, \@opts); + $entries++; + #$entries = 1; #for performance, returning 1 as true indicating there is at least one entry processed + } + close (FILE); + return $entries; +} + +sub process_fastq { + my $fn = shift @_; + my $process = shift @_; + my $curr_seq_id = ""; + my $curr_str = ""; + my $curr_seq = ""; + my $entries = 0; + push (my @opts, @_); + open (FILE, "<${$fn}") || die "Unable to open ${$fn}, $!\n"; + while (<FILE>) { + chomp; + $_ =~ s/$dos_end//g; + if ($_=~/^@/) { + if (length($curr_seq_id) > 0 && length($curr_seq) > 0 && length($curr_str) > 0) { + #print join("\t", ("Joined:", $curr_seq_id, $curr_seq, @opts, "\n")); + &$process(\$curr_seq_id, \$curr_seq, \$curr_str, \@opts); + $entries++; + } + if (($entries % 100000) == 0) { + my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst) = localtime(time); + print sprintf("%02d-%02d %02d:%02d:%02d Entries Processed: %9s\n", $mon+1, $day, $hour, $min, $sec, $entries); + } + $curr_seq_id = $_; + $curr_seq_id =~ s/@//g; + $curr_seq = ""; + $curr_str = ""; + } + elsif ($_=~/^\+/) { + $curr_seq = $curr_str; + $curr_str = $_; + $curr_str =~ s/\+//g; + if ($curr_seq_id ne $curr_str) { + warn "Invalid FASTQ file, sequence id and quality score id mismatch: $curr_seq_id, $curr_str\n"; + return -1; + } + $curr_str = ""; + } + elsif (length($_) > 0) { $curr_str = join("", ($curr_str, $_)); } + } + if (length($curr_seq_id) > 0 && length($curr_seq) > 0 && length($curr_str) > 0) { + &$process(\$curr_seq_id, \$curr_seq, \$curr_str, \@opts); + $entries++; + #$entries = 1; #for performance, returning 1 as true indicating there is at least one entry processed + } + close (FILE); + return $entries; +}