Revision 71d28e6f

b/dbTable.sql
18 18 
insert into dbTable values("hg18", "Human hg18", "human", 'white', false);
19 19 
insert into dbTable values("danRer7", "Zebrafish danRer7", "zebrafish", 'white', true);
20 20 
insert into dbTable values("mm9", "Mouse mm9", "mouse", 'white', true);
21 
insert into dbTable values("mm10", "Mouse mm10", "mouse", 'white', false);
21 22 
insert into dbTable values("rn4", "Rat rn4", "rat", 'white', true);
22 23 
insert into dbTable values("dm3", "Fruit fly dm3", "fruit fly", 'white', true);
23 24 
insert into dbTable values("tair10", "Arabidopsis tair10", "arabidopsis", 'white', true);
24 25 
insert into dbTable values("AGPv2", "Maize AGPv2", "maize", 'white', true);
25 26 
insert into dbTable values("spombe201203", "S. pombe 2012-03", "spombe", 'white', true);
26 
insert into dbTable values("temporal_day", "Temporal data at day precision", "temporal_day", 'white', true);
27 
insert into dbTable values("Am1", "Am1.0", "arabidopsis", 'white', true);
27 
-- insert into dbTable values("temporal_day", "Temporal data at day precision", "temporal_day", 'white', true);
28 
-- insert into dbTable values("Am1", "Am1.0", "arabidopsis", 'white', true);
b/hg18/decorInfo
1 1 
refGene	RefSeq genes	\N	2	0	1	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=
2 2 
gc5Base	GC percent	\N	5	14	0	\N
3 
rmsk_ensemble	RepeatMasker Ensemble	\N	4	12	0	\N
b/hg18/makeDb.sql
30 30 
"IMR90_chromhmm_fromhg19,wgEncodeBroadHmmGm12878HMM,wgEncodeBroadHmmH1hescHMM,wgEncodeBroadHmmHepg2HMM,wgEncodeBroadHmmHmecHMM,wgEncodeBroadHmmHsmmHMM,wgEncodeBroadHmmHuvecHMM,wgEncodeBroadHmmK562HMM,wgEncodeBroadHmmNhekHMM,wgEncodeBroadHmmNhlfHMM",
31 31 
"Assay,Sample,Institution",
32 32 
"CYP4Z1\\nCYP2A7\\nCYP2A6\\nCYP3A4\\nCYP1A1\\nCYP4V2\\nCYP51A1\\nCYP2C19\\nCYP26B1\\nCYP11B2\\nCYP24A1\\nCYP4B1\\nCYP2C8",
33 
"",
33 
"13,http://epgg-test.wustl.edu/cc.gz",
34 34 
"chr7,27029129,chr7,27318965",
35 35 
"encode",
36 
"refGene,gc5Base",
36 
"refGene,rmsk_ensemble",
37 37 
"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM",
38 38 
\N,\N,
39 39 
true,
......
204 204 

  		





  205
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drop table if exists publichub;


  		





  206
  206
  
    
create table publichub (


  		





  
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  id varchar(255) not null primary key,


  		





  207
  208
  
    
  name varchar(255) not null,


  		





  208
  209
  
    
  logo text null,


  		





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  210
  
    
  url text not null,


  		












  

    
      b/hg18/publichub
    
  






  1
  
  
    
Multiple Myeloma cell line with JQ1 treatment	http://bradner.dfci.harvard.edu/images/generegulationchemistry.jpg	http://vizhub.wustl.edu/dli/enhancer.txt	<a href=http://bradner.dfci.harvard.edu/ target=_blank>James E. Bradner at Harvard Medical School</a>	This collection of genome-wide sequencing results is from multiple myeloma 1S cell line under JQ1 treatment. The experiments systematically characterized response to JQ1 treatment from many aspects: histone protein modifications, oncogene transcription regulator binding of DNA, and gene transcription. Data are available as sequencing reads aligned to the reference genome.


  		





  
  1
  
    
mm1s	Multiple Myeloma cell line with JQ1 treatment	http://bradner.dfci.harvard.edu/images/generegulationchemistry.jpg	http://vizhub.wustl.edu/public/hg18/mm1s/hub	<a href=http://bradner.dfci.harvard.edu/ target=_blank>James E. Bradner at Harvard Medical School</a>	This collection of genome-wide sequencing results is from multiple myeloma 1S cell line under JQ1 treatment. The experiments systematically characterized response to JQ1 treatment from many aspects: histone protein modifications, oncogene transcription regulator binding of DNA, and gene transcription. Data are available as sequencing reads aligned to the reference genome.


  		












  

    
      b/hg18/track2Categorical
    
  






  8
  8
  
    
wgEncodeBroadHmmNhekHMM	10:['Transcriptional elongation','#00b050'], 11:['Weak transcribed','#99ff66'], 12:['Polycomb-repressed','#7f7f7f'], 13:['Heterochromatin, low signal','#f5f5f5'], 14:['Repetitive/CNV','#f5f5f5'], 15:['Repetitive/CNV','#f5f5f5'], 1:['Active promoter','#ff0000'], 2:['Weak promoter','#ff6969'], 3:['Inactive/poised promoter','#cf0bc6'], 4:['Strong enhancer','#faca00'], 5:['Strong enhancer','#faca00'], 6:['Weak enhancer','#fffc04'], 7:['Weak enhancer','#fffc04'], 8:['Insulator','#0abefe'], 9:['Transcriptional transition','#00b050']


  		





  9
  9
  
    
wgEncodeBroadHmmNhlfHMM	10:['Transcriptional elongation','#00b050'], 11:['Weak transcribed','#99ff66'], 12:['Polycomb-repressed','#7f7f7f'], 13:['Heterochromatin, low signal','#f5f5f5'], 14:['Repetitive/CNV','#f5f5f5'], 15:['Repetitive/CNV','#f5f5f5'], 1:['Active promoter','#ff0000'], 2:['Weak promoter','#ff6969'], 3:['Inactive/poised promoter','#cf0bc6'], 4:['Strong enhancer','#faca00'], 5:['Strong enhancer','#faca00'], 6:['Weak enhancer','#fffc04'], 7:['Weak enhancer','#fffc04'], 8:['Insulator','#0abefe'], 9:['Transcriptional transition','#00b050']


  		





  10
  10
  
    
IMR90_chromhmm_fromhg19	24:['Quiescent_3','#ffffff'], 25:['H3K9ac_low','#e6e6fa'], 20:['Heterochromatin_at_repeats','#afeeee'], 21:['Heterochromatin','#e0ffff'], 22:['Quiescent_1','#ffffff'], 23:['Quiescent_2','#ffffff'], 1:['TSS_poised','#e9967a'], 3:['TSS_active','#ff0000'], 2:['TSS_flanking_more_upstream','#dc143c'], 5:['TSS_flanking_downstream','#b22222'], 4:['TSS_weak','#ff4500'], 7:['Transcription','#00ff00'], 6:['TSS_flanking_more_downstream','#b22222'], 9:['Enhancer-like_Genic','#ff8c00'], 8:['Transcription_weak','#9acd32'], 11:['Enhancer_weak_1','#ffa500'], 10:['Enhancer-like_Genic_(short_genes)','#ff8c00'], 13:['Enhancer_active','#ffa500'], 12:['Enhancer_weak_2','#ffa500'], 15:['Enhancer_poised','#ffff00'], 14:['Enhancer_active_with_weakK4me1_strong_K27ac','#ffa500'], 17:['Repressed_polycomb','#c0c0c0'], 16:['Repressed_polycomb_weak','#dcdcdc'], 19:['Zinc_finger_genes_H3K36me3_K9me3','#4682b4'], 18:['H3K9me3_K27me3','#5f9ea0']


  		





  
  11
  
    
rmsk_ensemble	1:['SINE - short interspersed nuclear elements','#cc0000'], 2:['LINE - long interspersed nuclear element','#FF6600'], 3:['LTR - long terminal repeat element','#006600'], 4:['DNA transposon','#4A72E8'], 5:['Simple repeat, micro-satellite','#AB833B'], 7:['Low complexity repeat','#663333'], 6:['Satellite repeat','#660000'], 9:['Other repeats','#488E8E'],8:['RNA repeat','#cc33ff'], 10:['Unknown','#5C5C5C']


  		












  

    
      b/hg19/makeDb.sql
    
  






  290
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  institution text not null,


  		





  291
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  description text not null


  		





  292
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);


  		





  293
  
  
    
load data local infile "publichub" into table publichub;


  		





  
  293
  
    
-- load data local infile "publichub" into table publichub;


  		





  294
  294
  
    
/*


  		





  295
  295
  
    
DROP TABLE IF EXISTS `rmsk`;


  		





  296
  296
  
    
CREATE TABLE `rmsk` (


  		












  

    
      b/hg19/publichub
    
  






  1
  
  
    
methylCRF prediction of Roadmap methylomes	http://cgs.wustl.edu/~dli/labwebsite_dev/img/wang_logo.png	http://vizhub.wustl.edu/dli/methylcrf.hub	<a href=http://wang.wustl.edu/ target=_blank>Wang Lab at Washington University in St. Louis</a>	Using <a href=http://methylcrf.wustl.edu/ target=_blank>methylCRF</a> to predict single CpG methylation profiles by combining MeDIP-seq and MRE-seq data from Roadmap Project.


  		





  
  1
  
    
mcrf	Complete DNA methylomes generated by methylCRF	http://cgs.wustl.edu/~dli/labwebsite_dev/img/wang_logo.png	http://vizhub.wustl.edu/dli/methylcrf.hub	<a href=http://wang.wustl.edu/ target=_blank>Wang Lab at Washington University in St. Louis</a>	The methylCRF software is used to compute DNA methylation at single-CpG resolution by integrating MeDIP-Seq and MRE-Seq assay results. We applied methylCRF on <a href=http://www.roadmapepigenomics.org/complete_epigenomes/ target=_blank>Roadmap Complete Epigenomes</a> and generated Complete Methylomes for 45 human samples.


  		












  

    
      b/mm10/cytoband
    
  






  
  1
  
    
	chr1	0	8840440	qA1	2


  		





  
  2
  
    
	chr1	8840440	12278390	qA2	1


  		





  
  3
  
    
	chr1	12278390	20136559	qA3	3


  		





  
  4
  
    
	chr1	20136559	22101102	qA4	1


  		





  
  5
  
    
	chr1	22101102	30941543	qA5	2


  		





  
  6
  
    
	chr1	30941543	43219933	qB	1


  		





  
  7
  
    
	chr1	43219933	54516052	qC1.1	4


  		





  
  8
  
    
	chr1	54516052	55989459	qC1.2	1


  		





  
  9
  
    
	chr1	55989459	59427408	qC1.3	5


  		





  
  10
  
    
	chr1	59427408	65321035	qC2	1


  		





  
  11
  
    
	chr1	65321035	74652612	qC3	3


  		





  
  12
  
    
	chr1	74652612	80055103	qC4	1


  		





  
  13
  
    
	chr1	80055103	87422137	qC5	3


  		





  
  14
  
    
	chr1	87422137	99700527	qD	1


  		





  
  15
  
    
	chr1	99700527	102647341	qE1.1	3


  		





  
  16
  
    
	chr1	102647341	103629612	qE1.2	1


  		





  
  17
  
    
	chr1	103629612	112470053	qE2.1	2


  		





  
  18
  
    
	chr1	112470053	113943460	qE2.2	1


  		





  
  19
  
    
	chr1	113943460	125730715	qE2.3	2


  		





  
  20
  
    
	chr1	125730715	128677528	qE3	1


  		





  
  21
  
    
	chr1	128677528	139482511	qE4	4


  		





  
  22
  
    
	chr1	139482511	147340681	qF	1


  		





  
  23
  
    
	chr1	147340681	151760902	qG1	2


  		





  
  24
  
    
	chr1	151760902	152743173	qG2	1


  		





  
  25
  
    
	chr1	152743173	157163393	qG3	2


  		





  
  26
  
    
	chr1	157163393	160110207	qH1	1


  		





  
  27
  
    
	chr1	160110207	164039292	qH2.1	3


  		





  
  28
  
    
	chr1	164039292	165512699	qH2.2	1


  		





  
  29
  
    
	chr1	165512699	169932919	qH2.3	3


  		





  
  30
  
    
	chr1	169932919	175826546	qH3	1


  		





  
  31
  
    
	chr1	175826546	181720174	qH4	3


  		





  
  32
  
    
	chr1	181720174	188104936	qH5	1


  		





  
  33
  
    
	chr1	188104936	195471971	qH6	3


  		





  
  34
  
    
	chr10	0	12822904	qA1	2


  		





  
  35
  
    
	chr10	12822904	17754791	qA2	1


  		





  
  36
  
    
	chr10	17754791	23673055	qA3	3


  		





  
  37
  
    
	chr10	23673055	33536828	qA4	1


  		





  
  38
  
    
	chr10	33536828	41427846	qB1	2


  		





  
  39
  
    
	chr10	41427846	48332487	qB2	1


  		





  
  40
  
    
	chr10	48332487	56223506	qB3	2


  		





  
  41
  
    
	chr10	56223506	64114524	qB4	1


  		





  
  42
  
    
	chr10	64114524	68060034	qB5.1	2


  		





  
  43
  
    
	chr10	68060034	68553222	qB5.2	1


  		





  
  44
  
    
	chr10	68553222	74964675	qB5.3	2


  		





  
  45
  
    
	chr10	74964675	89267146	qC1	1


  		





  
  46
  
    
	chr10	89267146	96171787	qC2	3


  		





  
  47
  
    
	chr10	96171787	99130919	qC3	1


  		





  
  48
  
    
	chr10	99130919	111953824	qD1	2


  		





  
  49
  
    
	chr10	111953824	124776729	qD2	1


  		





  
  50
  
    
	chr10	124776729	130694993	qD3	3


  		





  
  51
  
    
	chr11	0	13046989	qA1	2


  		





  
  52
  
    
	chr11	13046989	17240664	qA2	1


  		





  
  53
  
    
	chr11	17240664	21900303	qA3.1	2


  		





  
  54
  
    
	chr11	21900303	25628014	qA3.2	1


  		





  
  55
  
    
	chr11	25628014	30287653	qA3.3	2


  		





  
  56
  
    
	chr11	30287653	36345184	qA4	1


  		





  
  57
  
    
	chr11	36345184	43334643	qA5	2


  		





  
  58
  
    
	chr11	43334643	47994282	qB1.1	1


  		





  
  59
  
    
	chr11	47994282	49858137	qB1.2	3


  		





  
  60
  
    
	chr11	49858137	60109343	qB1.3	1


  		





  
  61
  
    
	chr11	60109343	62905127	qB2	3


  		





  
  62
  
    
	chr11	62905127	70826513	qB3	1


  		





  
  63
  
    
	chr11	70826513	74088260	qB4	3


  		





  
  64
  
    
	chr11	74088260	82009647	qB5	1


  		





  
  65
  
    
	chr11	82009647	90396997	qC	2


  		





  
  66
  
    
	chr11	90396997	102512059	qD	1


  		





  
  67
  
    
	chr11	102512059	110433445	qE1	4


  		





  
  68
  
    
	chr11	110433445	122082543	qE2	1


  		





  
  69
  
    
	chr12	0	17601321	qA1.1	2


  		





  
  70
  
    
	chr12	17601321	21121586	qA1.2	1


  		





  
  71
  
    
	chr12	21121586	25961949	qA1.3	4


  		





  
  72
  
    
	chr12	25961949	31682379	qA2	1


  		





  
  73
  
    
	chr12	31682379	39162941	qA3	3


  		





  
  74
  
    
	chr12	39162941	44003304	qB1	1


  		





  
  75
  
    
	chr12	44003304	44883370	qB2	3


  		





  
  76
  
    
	chr12	44883370	51923899	qB3	1


  		





  
  77
  
    
	chr12	51923899	66004957	qC1	2


  		





  
  78
  
    
	chr12	66004957	71285353	qC2	1


  		





  
  79
  
    
	chr12	71285353	80966080	qC3	2


  		





  
  80
  
    
	chr12	80966080	85366411	qD1	1


  		





  
  81
  
    
	chr12	85366411	88446642	qD2	3


  		





  
  82
  
    
	chr12	88446642	95487171	qD3	1


  		





  
  83
  
    
	chr12	95487171	106047964	qE	2


  		





  
  84
  
    
	chr12	106047964	114408592	qF1	1


  		





  
  85
  
    
	chr12	114408592	120129022	qF2	4


  		





  
  86
  
    
	chr13	0	16286533	qA1	2


  		





  
  87
  
    
	chr13	16286533	21221846	qA2	1


  		





  
  88
  
    
	chr13	21221846	29611878	qA3.1	4


  		





  
  89
  
    
	chr13	29611878	33066597	qA3.2	1


  		





  
  90
  
    
	chr13	33066597	41456629	qA3.3	3


  		





  
  91
  
    
	chr13	41456629	44417817	qA4	1


  		





  
  92
  
    
	chr13	44417817	52807849	qA5	3


  		





  
  93
  
    
	chr13	52807849	59223756	qB1	1


  		





  
  94
  
    
	chr13	59223756	61691413	qB2	3


  		





  
  95
  
    
	chr13	61691413	69587914	qB3	1


  		





  
  96
  
    
	chr13	69587914	78471477	qC1	3


  		





  
  97
  
    
	chr13	78471477	80939134	qC2	1


  		





  
  98
  
    
	chr13	80939134	94758011	qC3	2


  		





  
  99
  
    
	chr13	94758011	106602762	qD1	1


  		





  
  100
  
    
	chr13	106602762	110551012	qD2.1	3


  		





  
  101
  
    
	chr13	110551012	116473388	qD2.2	1


  		





  
  102
  
    
	chr13	116473388	120421639	qD2.3	3


  		





  
  103
  
    
	chr14	0	14988269	qA1	2


  		





  
  104
  
    
	chr14	14988269	19484750	qA2	1


  		





  
  105
  
    
	chr14	19484750	29976538	qA3	3


  		





  
  106
  
    
	chr14	29976538	43465980	qB	1


  		





  
  107
  
    
	chr14	43465980	51959333	qC1	2


  		





  
  108
  
    
	chr14	51959333	54956987	qC2	1


  		





  
  109
  
    
	chr14	54956987	59953077	qC3	4


  		





  
  110
  
    
	chr14	59953077	68946038	qD1	1


  		





  
  111
  
    
	chr14	68946038	72942910	qD2	3


  		





  
  112
  
    
	chr14	72942910	84933525	qD3	1


  		





  
  113
  
    
	chr14	84933525	88930397	qE1	4


  		





  
  114
  
    
	chr14	88930397	98922577	qE2.1	2


  		





  
  115
  
    
	chr14	98922577	99921795	qE2.2	1


  		





  
  116
  
    
	chr14	99921795	107415929	qE2.3	2


  		





  
  117
  
    
	chr14	107415929	110913192	qE3	1


  		





  
  118
  
    
	chr14	110913192	120905372	qE4	2


  		





  
  119
  
    
	chr14	120905372	124902244	qE5	1


  		





  
  120
  
    
	chr15	0	16500320	qA1	2


  		





  
  121
  
    
	chr15	16500320	24292137	qA2	1


  		





  
  122
  
    
	chr15	24292137	29792244	qB1	3


  		





  
  123
  
    
	chr15	29792244	32083955	qB2	1


  		





  
  124
  
    
	chr15	32083955	43084169	qB3.1	2


  		





  
  125
  
    
	chr15	43084169	44917538	qB3.2	1


  		





  
  126
  
    
	chr15	44917538	49959302	qB3.3	4


  		





  
  127
  
    
	chr15	49959302	53626040	qC	1


  		





  
  128
  
    
	chr15	53626040	66459622	qD1	2


  		





  
  129
  
    
	chr15	66459622	68751333	qD2	1


  		





  
  130
  
    
	chr15	68751333	77459835	qD3	4


  		





  
  131
  
    
	chr15	77459835	83876627	qE1	1


  		





  
  132
  
    
	chr15	83876627	87085022	qE2	3


  		





  
  133
  
    
	chr15	87085022	95793524	qE3	1


  		





  
  134
  
    
	chr15	95793524	101293631	qF1	4


  		





  
  135
  
    
	chr15	101293631	102210316	qF2	1


  		





  
  136
  
    
	chr15	102210316	104043685	qF3	3


  		





  
  137
  
    
	chr16	0	15432649	qA1	2


  		





  
  138
  
    
	chr16	15432649	16367961	qA2	1


  		





  
  139
  
    
	chr16	16367961	20576865	qA3	3


  		





  
  140
  
    
	chr16	20576865	26188738	qB1	1


  		





  
  141
  
    
	chr16	26188738	32268266	qB2	3


  		





  
  142
  
    
	chr16	32268266	38347795	qB3	1


  		





  
  143
  
    
	chr16	38347795	44894979	qB4	3


  		





  
  144
  
    
	chr16	44894979	53780444	qB5	1


  		





  
  145
  
    
	chr16	53780444	57989348	qC1.1	4


  		





  
  146
  
    
	chr16	57989348	58924660	qC1.2	1


  		





  
  147
  
    
	chr16	58924660	66874813	qC1.3	4


  		





  
  148
  
    
	chr16	66874813	70616061	qC2	1


  		





  
  149
  
    
	chr16	70616061	79033870	qC3.1	2


  		





  
  150
  
    
	chr16	79033870	79501526	qC3.2	1


  		





  
  151
  
    
	chr16	79501526	91660583	qC3.3	2


  		





  
  152
  
    
	chr16	91660583	98207768	qC4	1


  		





  
  153
  
    
	chr17	0	13943085	qA1	2


  		





  
  154
  
    
	chr17	13943085	16121692	qA2	1


  		





  
  155
  
    
	chr17	16121692	17428857	qA3.1	3


  		





  
  156
  
    
	chr17	17428857	21786071	qA3.2	1


  		





  
  157
  
    
	chr17	21786071	31371942	qA3.3	4


  		





  
  158
  
    
	chr17	31371942	40086371	qB1	1


  		





  
  159
  
    
	chr17	40086371	41393535	qB2	3


  		





  
  160
  
    
	chr17	41393535	45750749	qB3	1


  		





  
  161
  
    
	chr17	45750749	55772342	qC	4


  		





  
  162
  
    
	chr17	55772342	60129556	qD	1


  		





  
  163
  
    
	chr17	60129556	67972542	qE1.1	2


  		





  
  164
  
    
	chr17	67972542	68843985	qE1.2	1


  		





  
  165
  
    
	chr17	68843985	73201199	qE1.3	2


  		





  
  166
  
    
	chr17	73201199	78429856	qE2	1


  		





  
  167
  
    
	chr17	78429856	82787071	qE3	3


  		





  
  168
  
    
	chr17	82787071	88887171	qE4	1


  		





  
  169
  
    
	chr17	88887171	94987271	qE5	3


  		





  
  170
  
    
	chr18	0	19406146	qA1	2


  		





  
  171
  
    
	chr18	19406146	29531091	qA2	1


  		





  
  172
  
    
	chr18	29531091	35437310	qB1	4


  		





  
  173
  
    
	chr18	35437310	37124801	qB2	1


  		





  
  174
  
    
	chr18	37124801	45562255	qB3	2


  		





  
  175
  
    
	chr18	45562255	49780983	qC	1


  		





  
  176
  
    
	chr18	49780983	53999710	qD1	2


  		





  
  177
  
    
	chr18	53999710	54421583	qD2	1


  		





  
  178
  
    
	chr18	54421583	60749674	qD3	2


  		





  
  179
  
    
	chr18	60749674	67921511	qE1	1


  		





  
  180
  
    
	chr18	67921511	75093347	qE2	3


  		





  
  181
  
    
	chr18	75093347	83530802	qE3	1


  		





  
  182
  
    
	chr18	83530802	90702639	qE4	3


  		





  
  183
  
    
	chr19	0	16680094	qA	2


  		





  
  184
  
    
	chr19	16680094	25630388	qB	1


  		





  
  185
  
    
	chr19	25630388	34987514	qC1	4


  		





  
  186
  
    
	chr19	34987514	38242166	qC2	1


  		





  
  187
  
    
	chr19	38242166	47599292	qC3	4


  		





  
  188
  
    
	chr19	47599292	51667608	qD1	1


  		





  
  189
  
    
	chr19	51667608	58990576	qD2	3


  		





  
  190
  
    
	chr19	58990576	61431566	qD3	1


  		





  
  191
  
    
	chr1_GL456210_random	0	169725		1


  		





  
  192
  
    
	chr1_GL456211_random	0	241735		1


  		





  
  193
  
    
	chr1_GL456212_random	0	153618		1


  		





  
  194
  
    
	chr1_GL456213_random	0	39340		1


  		





  
  195
  
    
	chr1_GL456221_random	0	206961		1


  		





  
  196
  
    
	chr2	0	14080919	qA1	2


  		





  
  197
  
    
	chr2	14080919	16427739	qA2	1


  		





  
  198
  
    
	chr2	16427739	29100566	qA3	3


  		





  
  199
  
    
	chr2	29100566	48344489	qB	1


  		





  
  200
  
    
	chr2	48344489	60547953	qC1.1	2


  		





  
  201
  
    
	chr2	60547953	61017317	qC1.2	1


  		





  
  202
  
    
	chr2	61017317	68527140	qC1.3	2


  		





  
  203
  
    
	chr2	68527140	71812688	qC2	1


  		





  
  204
  
    
	chr2	71812688	81199968	qC3	4


  		





  
  205
  
    
	chr2	81199968	88709792	qD	1


  		





  
  206
  
    
	chr2	88709792	101382619	qE1	2


  		





  
  207
  
    
	chr2	101382619	105137531	qE2	1


  		





  
  208
  
    
	chr2	105137531	113116719	qE3	3


  		





  
  209
  
    
	chr2	113116719	115932902	qE4	1


  		





  
  210
  
    
	chr2	115932902	123912090	qE5	4


  		





  
  211
  
    
	chr2	123912090	131891278	qF1	1


  		





  
  212
  
    
	chr2	131891278	134707462	qF2	3


  		





  
  213
  
    
	chr2	134707462	141278557	qF3	1


  		





  
  214
  
    
	chr2	141278557	146910925	qG1	2


  		





  
  215
  
    
	chr2	146910925	147849653	qG2	1


  		





  
  216
  
    
	chr2	147849653	152543293	qG3	2


  		





  
  217
  
    
	chr2	152543293	159114389	qH1	1


  		





  
  218
  
    
	chr2	159114389	163338664	qH2	3


  		





  
  219
  
    
	chr2	163338664	173664672	qH3	1


  		





  
  220
  
    
	chr2	173664672	182113224	qH4	3


  		





  
  221
  
    
	chr3	0	18541182	qA1	2


  		





  
  222
  
    
	chr3	18541182	20492885	qA2	1


  		





  
  223
  
    
	chr3	20492885	35618587	qA3	4


  		





  
  224
  
    
	chr3	35618587	46840881	qB	1


  		





  
  225
  
    
	chr3	46840881	56599399	qC	2


  		





  
  226
  
    
	chr3	56599399	60990731	qD	1


  		





  
  227
  
    
	chr3	60990731	69773397	qE1	3


  		





  
  228
  
    
	chr3	69773397	72700952	qE2	1


  		





  
  229
  
    
	chr3	72700952	83923246	qE3	2


  		





  
  230
  
    
	chr3	83923246	93193838	qF1	1


  		





  
  231
  
    
	chr3	93193838	97585170	qF2.1	3


  		





  
  232
  
    
	chr3	97585170	106367836	qF2.2	1


  		





  
  233
  
    
	chr3	106367836	108319539	qF2.3	3


  		





  
  234
  
    
	chr3	108319539	115150501	qF3	1


  		





  
  235
  
    
	chr3	115150501	126860721	qG1	2


  		





  
  236
  
    
	chr3	126860721	128812425	qG2	1


  		





  
  237
  
    
	chr3	128812425	138570942	qG3	4


  		





  
  238
  
    
	chr3	138570942	143938126	qH1	1


  		





  
  239
  
    
	chr3	143938126	148329459	qH2	3


  		





  
  240
  
    
	chr3	148329459	154184569	qH3	1


  		





  
  241
  
    
	chr3	154184569	160039680	qH4	3


  		





  
  242
  
    
	chr4	0	14882673	qA1	2


  		





  
  243
  
    
	chr4	14882673	17763191	qA2	1


  		





  
  244
  
    
	chr4	17763191	28325088	qA3	2


  		





  
  245
  
    
	chr4	28325088	30245433	qA4	1


  		





  
  246
  
    
	chr4	30245433	43687848	qA5	4


  		





  
  247
  
    
	chr4	43687848	51849314	qB1	1


  		





  
  248
  
    
	chr4	51849314	55209918	qB2	3


  		





  
  249
  
    
	chr4	55209918	63371384	qB3	1


  		





  
  250
  
    
	chr4	63371384	69612505	qC1	3


  		





  
  251
  
    
	chr4	69612505	72012936	qC2	1


  		





  
  252
  
    
	chr4	72012936	84015092	qC3	2


  		





  
  253
  
    
	chr4	84015092	89776127	qC4	1


  		





  
  254
  
    
	chr4	89776127	97457507	qC5	4


  		





  
  255
  
    
	chr4	97457507	105618973	qC6	1


  		





  
  256
  
    
	chr4	105618973	110899922	qC7	4


  		





  
  257
  
    
	chr4	110899922	117621130	qD1	1


  		





  
  258
  
    
	chr4	117621130	120501647	qD2.1	3


  		





  
  259
  
    
	chr4	120501647	131063544	qD2.2	1


  		





  
  260
  
    
	chr4	131063544	133944062	qD2.3	3


  		





  
  261
  
    
	chr4	133944062	141625442	qD3	1


  		





  
  262
  
    
	chr4	141625442	147866563	qE1	2


  		





  
  263
  
    
	chr4	147866563	156508116	qE2	1


  		





  
  264
  
    
	chr4_GL456216_random	0	66673		1


  		





  
  265
  
    
	chr4_GL456350_random	0	227966		1


  		





  
  266
  
    
	chr4_JH584292_random	0	14945		1


  		





  
  267
  
    
	chr4_JH584293_random	0	207968		1


  		





  
  268
  
    
	chr4_JH584294_random	0	191905		1


  		





  
  269
  
    
	chr4_JH584295_random	0	1976		1


  		





  
  270
  
    
	chr5	0	14895174	qA1	2


  		





  
  271
  
    
	chr5	14895174	16336643	qA2	1


  		





  
  272
  
    
	chr5	16336643	25465943	qA3	4


  		





  
  273
  
    
	chr5	25465943	33634265	qB1	1


  		





  
  274
  
    
	chr5	33634265	35556223	qB2	3


  		





  
  275
  
    
	chr5	35556223	50451398	qB3	1


  		





  
  276
  
    
	chr5	50451398	58619719	qC1	3


  		





  
  277
  
    
	chr5	58619719	61022167	qC2	1


  		





  
  278
  
    
	chr5	61022167	71592936	qC3.1	2


  		





  
  279
  
    
	chr5	71592936	73514894	qC3.2	1


  		





  
  280
  
    
	chr5	73514894	77839300	qC3.3	4


  		





  
  281
  
    
	chr5	77839300	81683216	qD	1


  		





  
  282
  
    
	chr5	81683216	91293006	qE1	2


  		





  
  283
  
    
	chr5	91293006	93695453	qE2	1


  		





  
  284
  
    
	chr5	93695453	99461327	qE3	3


  		





  
  285
  
    
	chr5	99461327	101863775	qE4	1


  		





  
  286
  
    
	chr5	101863775	107629649	qE5	3


  		





  
  287
  
    
	chr5	107629649	124927271	qF	1


  		





  
  288
  
    
	chr5	124927271	126849229	qG1.1	3


  		





  
  289
  
    
	chr5	126849229	127810208	qG1.2	1


  		





  
  290
  
    
	chr5	127810208	130693145	qG1.3	3


  		





  
  291
  
    
	chr5	130693145	146068809	qG2	1


  		





  
  292
  
    
	chr5	146068809	151834684	qG3	3


  		





  
  293
  
    
	chr5_GL456354_random	0	195993		1


  		





  
  294
  
    
	chr5_JH584296_random	0	199368		1


  		





  
  295
  
    
	chr5_JH584297_random	0	205776		1


  		





  
  296
  
    
	chr5_JH584298_random	0	184189		1


  		





  
  297
  
    
	chr5_JH584299_random	0	953012		1


  		





  
  298
  
    
	chr6	0	16637394	qA1	2


  		





  
  299
  
    
	chr6	16637394	21530745	qA2	1


  		





  
  300
  
    
	chr6	21530745	27402766	qA3.1	2


  		





  
  301
  
    
	chr6	27402766	28381436	qA3.2	1


  		





  
  302
  
    
	chr6	28381436	34253458	qA3.3	2


  		





  
  303
  
    
	chr6	34253458	41593485	qB1	1


  		





  
  304
  
    
	chr6	41593485	44529495	qB2.1	4


  		





  
  305
  
    
	chr6	44529495	45997501	qB2.2	1


  		





  
  306
  
    
	chr6	45997501	50890852	qB2.3	4


  		





  
  307
  
    
	chr6	50890852	62634895	qB3	1


  		





  
  308
  
    
	chr6	62634895	74378937	qC1	2


  		





  
  309
  
    
	chr6	74378937	76825613	qC2	1


  		





  
  310
  
    
	chr6	76825613	86122980	qC3	4


  		





  
  311
  
    
	chr6	86122980	94441677	qD1	1


  		





  
  312
  
    
	chr6	94441677	95909683	qD2	3


  		





  
  313
  
    
	chr6	95909683	103249709	qD3	1


  		





  
  314
  
    
	chr6	103249709	108632396	qE1	2


  		





  
  315
  
    
	chr6	108632396	109611066	qE2	1


  		





  
  316
  
    
	chr6	109611066	116951093	qE3	2


  		





  
  317
  
    
	chr6	116951093	122823114	qF1	1


  		





  
  318
  
    
	chr6	122823114	125269790	qF2	3


  		





  
  319
  
    
	chr6	125269790	132120481	qF3	1


  		





  
  320
  
    
	chr6	132120481	139460508	qG1	4


  		





  
  321
  
    
	chr6	139460508	142885854	qG2	1


  		





  
  322
  
    
	chr6	142885854	149736546	qG3	3


  		





  
  323
  
    
	chr7	0	15202939	qA1	2


  		





  
  324
  
    
	chr7	15202939	18243527	qA2	1


  		





  
  325
  
    
	chr7	18243527	28378821	qA3	3


  		





  
  326
  
    
	chr7	28378821	34459997	qB1	1


  		





  
  327
  
    
	chr7	34459997	37500585	qB2	3


  		





  
  328
  
    
	chr7	37500585	47635878	qB3	1


  		





  
  329
  
    
	chr7	47635878	54223819	qB4	3


  		





  
  330
  
    
	chr7	54223819	60811759	qB5	1


  		





  
  331
  
    
	chr7	60811759	71453817	qC	2


  		





  
  332
  
    
	chr7	71453817	77028229	qD1	1


  		





  
  333
  
    
	chr7	77028229	80575581	qD2	4


  		





  
  334
  
    
	chr7	80575581	90204110	qD3	1


  		





  
  335
  
    
	chr7	90204110	99832639	qE1	2


  		





  
  336
  
    
	chr7	99832639	102366462	qE2	1


  		





  
  337
  
    
	chr7	102366462	111488226	qE3	3


  		





  
  338
  
    
	chr7	111488226	118582931	qF1	1


  		





  
  339
  
    
	chr7	118582931	123143813	qF2	3


  		





  
  340
  
    
	chr7	123143813	137333224	qF3	1


  		





  
  341
  
    
	chr7	137333224	140880577	qF4	3


  		





  
  342
  
    
	chr7	140880577	145441459	qF5	1


  		





  
  343
  
    
	chr7_GL456219_random	0	175968		1


  		





  
  344
  
    
	chr8	0	15940729	qA1.1	2


  		





  
  345
  
    
	chr8	15940729	16878419	qA1.2	1


  		





  
  346
  
    
	chr8	16878419	20160333	qA1.3	3


  		





  
  347
  
    
	chr8	20160333	29537233	qA2	1


  		





  
  348
  
    
	chr8	29537233	33756838	qA3	3


  		





  
  349
  
    
	chr8	33756838	44071427	qA4	1


  		





  
  350
  
    
	chr8	44071427	48291032	qB1.1	4


  		





  
  351
  
    
	chr8	48291032	50166412	qB1.2	1


  		





  
  352
  
    
	chr8	50166412	55792551	qB1.3	4


  		





  
  353
  
    
	chr8	55792551	59543311	qB2	1


  		





  
  354
  
    
	chr8	59543311	67044831	qB3.1	2


  		





  
  355
  
    
	chr8	67044831	67982521	qB3.2	1


  		





  
  356
  
    
	chr8	67982521	74546350	qB3.3	2


  		





  
  357
  
    
	chr8	74546350	80172490	qC1	1


  		





  
  358
  
    
	chr8	80172490	84860940	qC2	3


  		





  
  359
  
    
	chr8	84860940	90018235	qC3	1


  		





  
  360
  
    
	chr8	90018235	91424770	qC4	3


  		





  
  361
  
    
	chr8	91424770	95644374	qC5	1


  		





  
  362
  
    
	chr8	95644374	103145894	qD1	2


  		





  
  363
  
    
	chr8	103145894	104083584	qD2	1


  		





  
  364
  
    
	chr8	104083584	110647414	qD3	3


  		





  
  365
  
    
	chr8	110647414	123775073	qE1	1


  		





  
  366
  
    
	chr8	123775073	129401213	qE2	3


  		





  
  367
  
    
	chr9	0	14412120	qA1	2


  		





  
  368
  
    
	chr9	14412120	19526099	qA2	1


  		





  
  369
  
    
	chr9	19526099	24175170	qA3	3


  		





  
  370
  
    
	chr9	24175170	38122384	qA4	1


  		





  
  371
  
    
	chr9	38122384	44166177	qA5.1	4


  		





  
  372
  
    
	chr9	44166177	46490712	qA5.2	1


  		





  
  373
  
    
	chr9	46490712	54859040	qA5.3	4


  		





  
  374
  
    
	chr9	54859040	63227369	qB	1


  		





  
  375
  
    
	chr9	63227369	69736069	qC	3


  		





  
  376
  
    
	chr9	69736069	77639490	qD	1


  		





  
  377
  
    
	chr9	77639490	82753468	qE1	3


  		





  
  378
  
    
	chr9	82753468	84613097	qE2	1


  		





  
  379
  
    
	chr9	84613097	91121796	qE3.1	2


  		





  
  380
  
    
	chr9	91121796	91586703	qE3.2	1


  		





  
  381
  
    
	chr9	91586703	100884846	qE3.3	2


  		





  
  382
  
    
	chr9	100884846	101814660	qE4	4


  		





  
  383
  
    
	chr9	101814660	108323360	qF1	1


  		





  
  384
  
    
	chr9	108323360	111112803	qF2	3


  		





  
  385
  
    
	chr9	111112803	119946038	qF3	1


  		





  
  386
  
    
	chr9	119946038	124595110	qF4	3


  		





  
  387
  
    
	chrM	0	16299		1


  		





  
  388
  
    
	chrUn_GL456239	0	40056		1


  		





  
  389
  
    
	chrUn_GL456359	0	22974		1


  		





  
  390
  
    
	chrUn_GL456360	0	31704		1


  		





  
  391
  
    
	chrUn_GL456366	0	47073		1


  		





  
  392
  
    
	chrUn_GL456367	0	42057		1


  		





  
  393
  
    
	chrUn_GL456368	0	20208		1


  		





  
  394
  
    
	chrUn_GL456370	0	26764		1


  		





  
  395
  
    
	chrUn_GL456372	0	28664		1


  		





  
  396
  
    
	chrUn_GL456378	0	31602		1


  		





  
  397
  
    
	chrUn_GL456379	0	72385		1


  		





  
  398
  
    
	chrUn_GL456381	0	25871		1


  		





  
  399
  
    
	chrUn_GL456382	0	23158		1


  		





  
  400
  
    
	chrUn_GL456383	0	38659		1


  		





  
  401
  
    
	chrUn_GL456385	0	35240		1


  		





  
  402
  
    
	chrUn_GL456387	0	24685		1


  		





  
  403
  
    
	chrUn_GL456389	0	28772		1


  		





  
  404
  
    
	chrUn_GL456390	0	24668		1


  		





  
  405
  
    
	chrUn_GL456392	0	23629		1


  		





  
  406
  
    
	chrUn_GL456393	0	55711		1


  		





  
  407
  
    
	chrUn_GL456394	0	24323		1


  		





  
  408
  
    
	chrUn_GL456396	0	21240		1


  		





  
  409
  
    
	chrUn_JH584304	0	114452		1


  		





  
  410
  
    
	chrX	0	15772338	qA1.1	2


  		





  
  411
  
    
	chrX	15772338	18236766	qA1.2	1


  		





  
  412
  
    
	chrX	18236766	21194080	qA1.3	3


  		





  
  413
  
    
	chrX	21194080	28094478	qA2	1


  		





  
  414
  
    
	chrX	28094478	33516219	qA3.1	4


  		





  
  415
  
    
	chrX	33516219	34501991	qA3.2	1


  		





  
  416
  
    
	chrX	34501991	39923732	qA3.3	4


  		





  
  417
  
    
	chrX	39923732	47809902	qA4	1


  		





  
  418
  
    
	chrX	47809902	56188957	qA5	4


  		





  
  419
  
    
	chrX	56188957	63089355	qA6	1


  		





  
  420
  
    
	chrX	63089355	69496867	qA7.1	4


  		





  
  421
  
    
	chrX	69496867	70975524	qA7.2	1


  		





  
  422
  
    
	chrX	70975524	77383037	qA7.3	4


  		





  
  423
  
    
	chrX	77383037	82311893	qB	1


  		





  
  424
  
    
	chrX	82311893	91183833	qC1	2


  		





  
  425
  
    
	chrX	91183833	92169604	qC2	1


  		





  
  426
  
    
	chrX	92169604	101041545	qC3	2


  		





  
  427
  
    
	chrX	101041545	109913486	qD	1


  		





  
  428
  
    
	chrX	109913486	120264083	qE1	2


  		





  
  429
  
    
	chrX	120264083	121249854	qE2	1


  		





  
  430
  
    
	chrX	121249854	135050651	qE3	2


  		





  
  431
  
    
	chrX	135050651	141458163	qF1	1


  		





  
  432
  
    
	chrX	141458163	148851447	qF2	3


  		





  
  433
  
    
	chrX	148851447	156244731	qF3	1


  		





  
  434
  
    
	chrX	156244731	163638015	qF4	3


  		





  
  435
  
    
	chrX	163638015	171031299	qF5	1


  		





  
  436
  
    
	chrX_GL456233_random	0	336933		1


  		





  
  437
  
    
	chrY	0	20642557	qA1	2


  		





  
  438
  
    
	chrY	20642557	32684048	qA2	4


  		





  
  439
  
    
	chrY	32684048	45298944	qB	3


  		





  
  440
  
    
	chrY	45298944	54473414	qC1	2


  		





  
  441
  
    
	chrY	54473414	61927671	qC2	3


  		





  
  442
  
    
	chrY	61927671	72248949	qC3	2


  		





  
  443
  
    
	chrY	72248949	83143632	qD	3


  		





  
  444
  
    
	chrY	83143632	91744698	qE	4


  		





  
  445
  
    
	chrY_JH584300_random	0	182347		1


  		





  
  446
  
    
	chrY_JH584301_random	0	259875		1


  		





  
  447
  
    
	chrY_JH584302_random	0	155838		1


  		





  
  448
  
    
	chrY_JH584303_random	0	158099		1


  		












  

    
      b/mm10/dataset
    
  






  
  1
  
    
mock	images/mock.png	Mock data set	\N	Just a mock data set...


  		












  

    
      b/mm10/decorInfo
    
  






  
  1
  
    
knownGene	UCSC genes	\N	2	0	1	http://genome.ucsc.edu/cgi-bin/hgGene?db=mm9&hgg_type=knownGene&hgg_gene=


  		





  
  2
  
    
knownGenepromoter	promoters (UCSC genes)	knownGene	2	0	0	\N


  		





  
  3
  
    
knownGeneutr3	3' UTRs (UCSC genes)	knownGene	2	0	0	\N


  		





  
  4
  
    
knownGeneutr5	5' UTRs (UCSC genes)	knownGene	2	0	0	\N


  		





  
  5
  
    
knownGeneexons	exons (UCSC genes)	knownGene	2	0	0	\N


  		





  
  6
  
    
knownGeneintrons	introns (UCSC genes)	knownGene	2	0	0	\N


  		





  
  7
  
    
refGene	RefSeq genes	\N	2	0	1	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=


  		





  
  8
  
    
refGenepromoter	promoters (RefSeq genes)	refGene	2	0	0	\N


  		





  
  9
  
    
refGeneutr3	3' UTRs (RefSeq genes)	refGene	2	0	0	\N


  		





  
  10
  
    
refGeneutr5	5' UTRs (RefSeq genes)	refGene	2	0	0	\N


  		





  
  11
  
    
refGeneexons	exons (RefSeq genes)	refGene	2	0	0	\N


  		





  
  12
  
    
refGeneintrons	introns (RefSeq genes)	refGene	2	0	0	\N


  		





  
  13
  
    
ensGene	Ensembl genes	\N	2	0	1	http://www.ensembl.org/Mus_musculus/geneview?gene=


  		





  
  14
  
    
ensGenepromoter	promoters (Ensembl genes)	ensGene	2	0	0	\N


  		





  
  15
  
    
ensGeneutr3	3' UTRs (Ensembl genes)	ensGene	2	0	0	\N


  		





  
  16
  
    
ensGeneutr5	5' UTRs (Ensembl genes)	ensGene	2	0	0	\N


  		





  
  17
  
    
ensGeneexons	exons (Ensembl genes)	ensGene	2	0	0	\N


  		





  
  18
  
    
ensGeneintrons	introns (Ensembl genes)	ensGene	2	0	0	\N


  		





  
  19
  
    
rmsk_ensemble	RepeatMasker Ensemble	\N	4	12	0	\N


  		





  
  20
  
    
RNA	RNA	\N	4	0	0	\N


  		





  
  21
  
    
DNA	DNA transposon	\N	4	0	0	\N


  		





  
  22
  
    
SINE	SINE	\N	4	0	0	\N


  		





  
  23
  
    
LINE	LINE	\N	4	0	0	\N


  		





  
  24
  
    
LTR	LTR	\N	4	0	0	\N


  		





  
  25
  
    
Low_complexity	low complexity	\N	4	0	0	\N


  		





  
  26
  
    
Satellite	satellite	\N	4	0	0	\N


  		





  
  27
  
    
Simple_repeat	simple repeat	\N	4	0	0	\N


  		





  
  28
  
    
Other	other repeats	\N	4	0	0	\N


  		





  
  29
  
    
Unknown	unknown	\N	4	0	0	\N


  		





  
  30
  
    
phastCons	PhastCons	\N	6	14	0	\N


  		





  
  31
  
    
phastCons60wayEuarchontoGlire	euarchontoglires PhastCons	\N	6	14	0	\N


  		





  
  32
  
    
phastCons60wayGlire	glires PhastCons	\N	6	14	0	\N


  		





  
  33
  
    
phastCons60wayPlacental	placental PhastCons	\N	6	14	0	\N


  		





  
  34
  
    
phyloP60wayEuarchontoglire	euarchontoglires PhyloP	\N	6	14	0	\N


  		





  
  35
  
    
phyloP60wayGlire	glires PhyloP	\N	6	14	0	\N


  		





  
  36
  
    
phyloP60wayPlacental	placental PhyloP	\N	6	14	0	\N


  		





  
  37
  
    
phyloP60way	PhyloP	\N	6	14	0	\N


  		





  
  38
  
    
cpgIsland	CpG Island	\N	5	0	0	\N


  		





  
  39
  
    
gc5Base	GC percent	\N	5	14	0	\N


  		












  

    
      b/mm10/makeDb.sql
    
  






  
  1
  
    
-- -------------------


  		





  
  2
  
    
--                  --


  		





  
  3
  
    
--  mm10


  		





  
  4
  
    
--                  --


  		





  
  5
  
    
-- -------------------


  		





  
  6
  
    
drop table if exists config;


  		





  
  7
  
    
create table config (


  		





  
  8
  
    
  bbiPath text not null,


  		





  
  9
  
    
  seqPath text null,


  		





  
  10
  
    
  defaultTracks text null,


  		





  
  11
  
    
  defaultMdcategory varchar(255) not null,


  		





  
  12
  
    
  defaultGenelist text not null,


  		





  
  13
  
    
  defaultCustomtracks text not null,


  		





  
  14
  
    
  defaultPosition varchar(255) not null,


  		





  
  15
  
    
  defaultDataset varchar(255) not null,


  		





  
  16
  
    
  defaultDecor text null,


  		





  
  17
  
    
  defaultScaffold text not null,


  		





  
  18
  
    
  ideogram_wiggle1 varchar(255) null,


  		





  
  19
  
    
  ideogram_wiggle2 varchar(255) null,


  		





  
  20
  
    
  hasGene boolean not null,


  		





  
  21
  
    
  allowJuxtaposition boolean not null,


  		





  
  22
  
    
  keggSpeciesCode varchar(255) null,


  		





  
  23
  
    
  information text not null,


  		





  
  24
  
    
  runmode tinyint not null,


  		





  
  25
  
    
  initmatplot boolean not null


  		





  
  26
  
    
);


  		





  
  27
  
    
insert into config values(


  		





  
  28
  
    
"/srv/epgg/data/data/subtleKnife/mm10/",


  		





  
  29
  
    
"/srv/epgg/data/data/subtleKnife/seq/mm10.gz",


  		





  
  30
  
    
\N,


  		





  
  31
  
    
"Sample",


  		





  
  32
  
    
"CYP4Z1\\nCYP2A7\\nCYP2A6\\nCYP3A4\\nCYP1A1\\nCYP4V2\\nCYP51A1\\nCYP2C19\\nCYP26B1\\nCYP11B2\\nCYP24A1\\nCYP4B1\\nCYP2C8",


  		





  
  33
  
    
"3,http://vizhub.wustl.edu/hubSample/mm9/wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdSig.gz,1,http://vizhub.wustl.edu/hubSample/mm9/bed.gz,5,http://vizhub.wustl.edu/hubSample/mm9/wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdAlnRep2.gz,100,http://vizhub.wustl.edu/hubSample/mm9/hub.txt",


  		





  
  34
  
    
"chr6,52003572,chr6,52426257",


  		





  
  35
  
    
"mock",


  		





  
  36
  
    
"knownGene,rmsk_ensemble",


  		





  
  37
  
    
"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY,chrM",


  		





  
  38
  
    
\N,\N,


  		





  
  39
  
    
true,


  		





  
  40
  
    
true,


  		





  
  41
  
    
"mmu",


  		





  
  42
  
    
"Assembly version|mm10|Sequence source|<a href=http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/ target=_blank>UCSC browser</a>|Date parsed|July 31, 2013|Chromosomes|22|Misc|44|Total bases|2,730,871,774|Logo art|<a href=http://free-extras.com/images/mouse-8552.htm target=_blank>link</a>",


  		





  
  43
  
    
0,


  		





  
  44
  
    
false


  		





  
  45
  
    
);


  		





  
  46
  
    

  		





  
  47
  
    

  		





  
  48
  
    
-- grouping types on genomic features


  		





  
  49
  
    
-- table name defined in macro: TBN_GF_GRP


  		





  
  50
  
    
drop table if exists gfGrouping;


  		





  
  51
  
    
create table gfGrouping (


  		





  
  52
  
    
  id TINYINT not null primary key,


  		





  
  53
  
    
  name char(50) not null


  		





  
  54
  
    
);


  		





  
  55
  
    
insert into gfGrouping values (2, "Genes");


  		





  
  56
  
    
-- insert into gfGrouping values (3, "non-coding RNA");


  		





  
  57
  
    
insert into gfGrouping values (4, "RepeatMasker");


  		





  
  58
  
    
insert into gfGrouping values (6, "Sequence conservation");


  		





  
  59
  
    
insert into gfGrouping values (5, "Others");


  		





  
  60
  
    

  		





  
  61
  
    

  		





  
  62
  
    

  		





  
  63
  
    
drop table if exists decorInfo;


  		





  
  64
  
    
create table decorInfo (


  		





  
  65
  
    
  name char(50) not null primary key,


  		





  
  66
  
    
  printname char(100) not null,


  		





  
  67
  
    
  parent char(50) null,


  		





  
  68
  
    
  grp tinyint not null,


  		





  
  69
  
    
  fileType tinyint not null,


  		





  
  70
  
    
  hasStruct tinyint null,


  		





  
  71
  
    
  queryUrl varchar(255) null


  		





  
  72
  
    
);


  		





  
  73
  
    
load data local infile 'decorInfo' into table decorInfo;


  		





  
  74
  
    

  		





  
  75
  
    
drop table if exists track2Label;


  		





  
  76
  
    
create table track2Label (


  		





  
  77
  
    
  name varchar(255) not null primary key,


  		





  
  78
  
    
  label text null


  		





  
  79
  
    
);


  		





  
  80
  
    
load data local infile 'track2Label' into table track2Label;


  		





  
  81
  
    

  		





  
  82
  
    
drop table if exists track2ProcessInfo;


  		





  
  83
  
    
create table track2ProcessInfo (


  		





  
  84
  
    
  name varchar(255) not null primary key,


  		





  
  85
  
    
  detail text null


  		





  
  86
  
    
);


  		





  
  87
  
    
load data local infile 'track2ProcessInfo' into table track2ProcessInfo;


  		





  
  88
  
    

  		





  
  89
  
    
drop table if exists track2BamInfo;


  		





  
  90
  
    
create table track2BamInfo (


  		





  
  91
  
    
  name varchar(255) not null,


  		





  
  92
  
    
  bamfile varchar(255) not null,


  		





  
  93
  
    
  bamfilelabel varchar(255) not null


  		





  
  94
  
    
);


  		





  
  95
  
    
load data local infile "track2BamInfo" into table track2BamInfo;


  		





  
  96
  
    

  		





  
  97
  
    
drop table if exists track2Detail;


  		





  
  98
  
    
create table track2Detail (


  		





  
  99
  
    
  name varchar(255) not null primary key,


  		





  
  100
  
    
  detail text null


  		





  
  101
  
    
);


  		





  
  102
  
    
load data local infile 'track2Detail' into table track2Detail;


  		





  
  103
  
    
load data local infile 'track2Detail_decor' into table track2Detail;


  		





  
  104
  
    

  		





  
  105
  
    
drop table if exists track2GEO;


  		





  
  106
  
    
create table track2GEO (


  		





  
  107
  
    
  name varchar(255) not null primary key,


  		





  
  108
  
    
  geo char(20) not null


  		





  
  109
  
    
);


  		





  
  110
  
    
load data local infile 'track2GEO' into table track2GEO;


  		





  
  111
  
    

  		





  
  112
  
    
drop table if exists track2Categorical;


  		





  
  113
  
    
create table track2Categorical (


  		





  
  114
  
    
  name varchar(255) not null primary key,


  		





  
  115
  
    
  info text not null


  		





  
  116
  
    
);


  		





  
  117
  
    
load data local infile 'track2Categorical' into table track2Categorical;


  		





  
  118
  
    

  		





  
  119
  
    

  		





  
  120
  
    
drop table if exists track2VersionInfo;


  		





  
  121
  
    
create table track2VersionInfo (


  		





  
  122
  
    
  name varchar(255) not null primary key,


  		





  
  123
  
    
  info varchar(255) not null


  		





  
  124
  
    
);


  		





  
  125
  
    
load data local infile 'track2VersionInfo' into table track2VersionInfo;


  		





  
  126
  
    

  		





  
  127
  
    

  		





  
  128
  
    
drop table if exists track2Annotation;


  		





  
  129
  
    
create table track2Annotation (


  		





  
  130
  
    
  name varchar(255) not null primary key,


  		





  
  131
  
    
  attridx varchar(255) not null


  		





  
  132
  
    
);


  		





  
  133
  
    
load data local infile "track2Annotation" into table track2Annotation;


  		





  
  134
  
    

  		





  
  135
  
    
drop table if exists track2Ft;


  		





  
  136
  
    
create table track2Ft (


  		





  
  137
  
    
  name varchar(255) not null primary key,


  		





  
  138
  
    
  ft tinyint not null


  		





  
  139
  
    
);


  		





  
  140
  
    
load data local infile "track2Ft" into table track2Ft;


  		





  
  141
  
    

  		





  
  142
  
    
drop table if exists track2Style;


  		





  
  143
  
    
create table track2Style (


  		





  
  144
  
    
  name varchar(255) not null primary key,


  		





  
  145
  
    
  style text not null


  		





  
  146
  
    
);


  		





  
  147
  
    
load data local infile "track2Style" into table track2Style;


  		





  
  148
  
    

  		





  
  149
  
    
drop table if exists track2Regions;


  		





  
  150
  
    
create table track2Regions (


  		





  
  151
  
    
  name varchar(255) not null primary key,


  		





  
  152
  
    
    regionname varchar(255) not null,


  		





  
  153
  
    
	  regions text not null


  		





  
  154
  
    
	   );


  		





  
  155
  
    

  		





  
  156
  
    

  		





  
  157
  
    
drop table if exists metadataVocabulary;


  		





  
  158
  
    
create table metadataVocabulary (


  		





  
  159
  
    
  child varchar(255) not null,


  		





  
  160
  
    
  parent varchar(255) not null


  		





  
  161
  
    
);


  		





  
  162
  
    
load data local infile "metadataVocabulary" into table metadataVocabulary;


  		





  
  163
  
    

  		





  
  164
  
    
drop table if exists trackAttr2idx;


  		





  
  165
  
    
create table trackAttr2idx (


  		





  
  166
  
    
  idx varchar(255) not null primary key,


  		





  
  167
  
    
  attr varchar(255) not null,


  		





  
  168
  
    
  note varchar(255) null,


  		





  
  169
  
    
  description text null


  		





  
  170
  
    
);


  		





  
  171
  
    
load data local infile "trackAttr2idx" into table trackAttr2idx;


  		





  
  172
  
    

  		





  
  173
  
    

  		





  
  174
  
    
drop table if exists tempURL;


  		





  
  175
  
    
create table tempURL (


  		





  
  176
  
    
  session varchar(100) not null,


  		





  
  177
  
    
  offset INT unsigned not null,


  		





  
  178
  
    
  urlpiece text not null


  		





  
  179
  
    
);


  		





  
  180
  
    

  		





  
  181
  
    

  		





  
  182
  
    
drop table if exists dataset;


  		





  
  183
  
    
create table dataset (


  		





  
  184
  
    
  tablename varchar(255) not null,


  		





  
  185
  
    
  logo varchar(255) null,


  		





  
  186
  
    
  name varchar(255) not null,


  		





  
  187
  
    
  url varchar(255) null,


  		





  
  188
  
    
  description text not null


  		





  
  189
  
    
);


  		





  
  190
  
    
-- load data local infile "dataset" into table dataset;


  		





  
  191
  
    

  		





  
  192
  
    
drop table if exists mock;


  		





  
  193
  
    
create table mock (


  		





  
  194
  
    
  tkname varchar(255) not null


  		





  
  195
  
    
);


  		





  
  196
  
    
load data local infile "mock" into table mock;


  		





  
  197
  
    

  		





  
  198
  
    

  		





  
  199
  
    
drop table if exists scaffoldInfo;


  		





  
  200
  
    
create table scaffoldInfo (


  		





  
  201
  
    
  parent varchar(255) not null,


  		





  
  202
  
    
  child varchar(255) not null,


  		





  
  203
  
    
  childLength int unsigned not null


  		





  
  204
  
    
);


  		





  
  205
  
    
load data local infile "scaffoldInfo" into table scaffoldInfo;


  		





  
  206
  
    

  		





  
  207
  
    

  		





  
  208
  
    
drop table if exists cytoband;


  		





  
  209
  
    
create table cytoband (


  		





  
  210
  
    
  id int null auto_increment primary key,


  		





  
  211
  
    
  chrom char(20) not null,


  		





  
  212
  
    
  start int not null,


  		





  
  213
  
    
  stop int not null,


  		





  
  214
  
    
  name char(20) not null,


  		





  
  215
  
    
  colorIdx int not null


  		





  
  216
  
    
);


  		





  
  217
  
    
load data local infile "cytoband" into table cytoband;


  		





  
  218
  
    

  		





  
  219
  
    
/*


  		





  
  220
  
    
DROP TABLE IF EXISTS `rmsk`;


  		





  
  221
  
    
CREATE TABLE `rmsk` (


  		





  
  222
  
    
  `bin` smallint(5) unsigned NOT NULL default '0',


  		





  
  223
  
    
  `swScore` int(10) unsigned NOT NULL default '0',


  		





  
  224
  
    
  `milliDiv` int(10) unsigned NOT NULL default '0',


  		





  
  225
  
    
  `milliDel` int(10) unsigned NOT NULL default '0',


  		





  
  226
  
    
  `milliIns` int(10) unsigned NOT NULL default '0',


  		





  
  227
  
    
  `genoName` varchar(255) NOT NULL default '',


  		





  
  228
  
    
  `genoStart` int(10) unsigned NOT NULL default '0',


  		





  
  229
  
    
  `genoEnd` int(10) unsigned NOT NULL default '0',


  		





  
  230
  
    
  `genoLeft` int(11) NOT NULL default '0',


  		





  
  231
  
    
  `strand` char(1) NOT NULL default '',


  		





  
  232
  
    
  `repName` varchar(255) NOT NULL default '',


  		





  
  233
  
    
  `repClass` varchar(255) NOT NULL default '',


  		





  
  234
  
    
  `repFamily` varchar(255) NOT NULL default '',


  		





  
  235
  
    
  `repStart` int(11) NOT NULL default '0',


  		





  
  236
  
    
  `repEnd` int(11) NOT NULL default '0',


  		





  
  237
  
    
  `repLeft` int(11) NOT NULL default '0',


  		





  
  238
  
    
  `id` char(1) NOT NULL default '',


  		





  
  239
  
    
  KEY `genoName` (`genoName`(14),`bin`)


  		





  
  240
  
    
);


  		





  
  241
  
    
load data local infile 'rmsk.txt' into table rmsk;


  		





  
  242
  
    
*/


  		












  

    
      b/mm10/metadataVocabulary
    
  






  
  1
  
    
mock term	Sample


  		





  
  2
  
    
11	mock term


  		





  
  3
  
    
12	mock term


  		





  
  4
  
    
13	mock term


  		





  
  5
  
    
14	mock term


  		





  
  6
  
    
15	mock term


  		





  
  7
  
    
16	mock term


  		





  
  8
  
    
17	mock term


  		





  
  9
  
    
18	mock term


  		





  
  10
  
    
19	mock term


  		





  
  11
  
    
20	mock term


  		





  
  12
  
    
21	mock term


  		





  
  13
  
    
22	mock term


  		





  
  14
  
    
23	mock term


  		





  
  15
  
    
24	mock term


  		





  
  16
  
    
25	mock term


  		





  
  17
  
    
26	mock term


  		





  
  18
  
    
27	mock term


  		





  
  19
  
    
28	mock term


  		





  
  20
  
    
29	mock term


  		





  
  21
  
    
30	mock term


  		












  

    
      b/mm10/mock
    
  






  
  1
  
    
mock1


  		





  
  2
  
    
mock2


  		





  
  3
  
    
mock3


  		





  
  4
  
    
mock4


  		





  
  5
  
    
mock5


  		





  
  6
  
    
mock6


  		





  
  7
  
    
mock7


  		





  
  8
  
    
mock8


  		





  
  9
  
    
mock9


  		





  
  10
  
    
mock10


  		





  
  11
  
    
mock11


  		





  
  12
  
    
mock12


  		





  
  13
  
    
mock13


  		





  
  14
  
    
mock14


  		





  
  15
  
    
mock15


  		





  
  16
  
    
mock16


  		





  
  17
  
    
mock17


  		





  
  18
  
    
mock18


  		





  
  19
  
    
mock19


  		





  
  20
  
    
mock20


  		












  

    
      b/mm10/scaffoldInfo
    
  






  
  1
  
    
ROOT	chromosome	0


  		





  
  2
  
    
ROOT	other	0


  		





  
  3
  
    
chromosome	chr1	195471971


  		





  
  4
  
    
chromosome	chr10	130694993


  		





  
  5
  
    
chromosome	chr11	122082543


  		





  
  6
  
    
chromosome	chr12	120129022


  		





  
  7
  
    
chromosome	chr13	120421639


  		





  
  8
  
    
chromosome	chr14	124902244


  		





  
  9
  
    
chromosome	chr15	104043685


  		





  
  10
  
    
chromosome	chr16	98207768


  		





  
  11
  
    
chromosome	chr17	94987271


  		





  
  12
  
    
chromosome	chr18	90702639


  		





  
  13
  
    
chromosome	chr19	61431566


  		





  
  14
  
    
chromosome	chr2	182113224


  		





  
  15
  
    
chromosome	chr3	160039680


  		





  
  16
  
    
chromosome	chr4	156508116


  		





  
  17
  
    
chromosome	chr5	151834684


  		





  
  18
  
    
chromosome	chr6	149736546


  		





  
  19
  
    
chromosome	chr7	145441459


  		





  
  20
  
    
chromosome	chr8	129401213


  		





  
  21
  
    
chromosome	chr9	124595110


  		





  
  22
  
    
chromosome	chrM	16299


  		





  
  23
  
    
chromosome	chrX	171031299


  		





  
  24
  
    
chromosome	chrY	91744698


  		





  
  25
  
    
other	chr1_GL456210_random	169725


  		





  
  26
  
    
other	chr1_GL456211_random	241735


  		





  
  27
  
    
other	chr1_GL456212_random	153618


  		





  
  28
  
    
other	chr1_GL456213_random	39340


  		





  
  29
  
    
other	chr1_GL456221_random	206961


  		





  
  30
  
    
other	chr4_GL456216_random	66673


  		





  
  31
  
    
other	chr4_JH584292_random	14945


  		





  
  32
  
    
other	chr4_GL456350_random	227966


  		





  
  33
  
    
other	chr4_JH584293_random	207968


  		





  
  34
  
    
other	chr4_JH584294_random	191905


  		





  
  35
  
    
other	chr4_JH584295_random	1976


  		





  
  36
  
    
other	chr5_JH584296_random	199368


  		





  
  37
  
    
other	chr5_JH584297_random	205776


  		





  
  38
  
    
other	chr5_JH584298_random	184189


  		





  
  39
  
    
other	chr5_GL456354_random	195993


  		





  
  40
  
    
other	chr5_JH584299_random	953012


  		





  
  41
  
    
other	chr7_GL456219_random	175968


  		





  
  42
  
    
other	chrX_GL456233_random	336933


  		





  
  43
  
    
other	chrY_JH584300_random	182347


  		





  
  44
  
    
other	chrY_JH584301_random	259875


  		





  
  45
  
    
other	chrY_JH584302_random	155838


  		





  
  46
  
    
other	chrY_JH584303_random	158099


  		





  
  47
  
    
other	chrUn_GL456239	40056


  		





  
  48
  
    
other	chrUn_GL456367	42057


  		





  
  49
  
    
other	chrUn_GL456378	31602


  		





  
  50
  
    
other	chrUn_GL456381	25871


  		





  
  51
  
    
other	chrUn_GL456382	23158


  		





  
  52
  
    
other	chrUn_GL456383	38659


  		





  
  53
  
    
other	chrUn_GL456385	35240


  		





  
  54
  
    
other	chrUn_GL456390	24668


  		





  
  55
  
    
other	chrUn_GL456392	23629


  		





  
  56
  
    
other	chrUn_GL456393	55711


  		





  
  57
  
    
other	chrUn_GL456394	24323


  		





  
  58
  
    
other	chrUn_GL456359	22974


  		





  
  59
  
    
other	chrUn_GL456360	31704


  		





  
  60
  
    
other	chrUn_GL456396	21240


  		





  
  61
  
    
other	chrUn_GL456372	28664


  		





  
  62
  
    
other	chrUn_GL456387	24685


  		





  
  63
  
    
other	chrUn_GL456389	28772


  		





  
  64
  
    
other	chrUn_GL456370	26764


  		





  
  65
  
    
other	chrUn_GL456379	72385


  		





  
  66
  
    
other	chrUn_GL456366	47073


  		





  
  67
  
    
other	chrUn_GL456368	20208


  		





  
  68
  
    
other	chrUn_JH584304	114452


  		












  

    
      b/mm10/track2Annotation
    
  






  
  1
  
    
mock1	11


  		





  
  2
  
    
mock2	12


  		





  
  3
  
    
mock3	13


  		





  
  4
  
    
mock4	14


  		





  
  5
  
    
mock5	15


  		





  
  6
  
    
mock6	16


  		





  
  7
  
    
mock7	17


  		





  
  8
  
    
mock8	18


  		





  
  9
  
    
mock9	19


  		





  
  10
  
    
mock10	20


  		





  
  11
  
    
mock11	21


  		





  
  12
  
    
mock12	22


  		





  
  13
  
    
mock13	23


  		





  
  14
  
    
mock14	24


  		





  
  15
  
    
mock15	25


  		





  
  16
  
    
mock16	26


  		





  
  17
  
    
mock17	27


  		





  
  18
  
    
mock18	28


  		





  
  19
  
    
mock19	29


  		





  
  20
  
    
mock20	30


  		












  

    
      b/mm10/track2Categorical
    
  






  
  1
  
    
rmsk_ensemble	1:['SINE - short interspersed nuclear elements','#cc0000'], 2:['LINE - long interspersed nuclear element','#FF6600'], 3:['LTR - long terminal repeat element','#006600'], 4:['DNA transposon','#4A72E8'], 5:['Simple repeat, micro-satellite','#AB833B'], 7:['Low complexity repeat','#663333'], 6:['Satellite repeat','#660000'], 9:['Other repeats','#488E8E'],8:['RNA repeat','#cc33ff'], 10:['Unknown','#5C5C5C']


  		












  

    
      b/mm10/track2Detail
    
  






  
  1
  
    
mock20	\N


  		





  
  2
  
    
mock19	\N


  		





  
  3
  
    
mock18	\N


  		





  
  4
  
    
mock13	\N


  		





  
  5
  
    
mock12	\N


  		





  
  6
  
    
mock11	\N


  		





  
  7
  
    
mock10	\N


  		





  
  8
  
    
mock17	\N


  		





  
  9
  
    
mock16	\N


  		





  
  10
  
    
mock15	\N


  		





  
  11
  
    
mock14	\N


  		





  
  12
  
    
mock9	\N


  		





  
  13
  
    
mock8	\N


  		





  
  14
  
    
mock3	\N


  		





  
  15
  
    
mock2	\N


  		





  
  16
  
    
mock1	\N


  		





  
  17
  
    
mock7	\N


  		





  
  18
  
    
mock6	\N


  		





  
  19
  
    
mock5	\N


  		





  
  20
  
    
mock4	\N


  		












  

    
      b/mm10/track2Detail_decor
    
  






  
  1
  
    
knownGene	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz


  		





  
  2
  
    
knownGenepromoter	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz


  		





  
  3
  
    
knownGeneutr3	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz


  		





  
  4
  
    
knownGeneutr5	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz


  		





  
  5
  
    
knownGeneexons	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz


  		





  
  6
  
    
knownGeneintrons	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz


  		





  
  7
  
    
refGene	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  8
  
    
refGenepromoter	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  9
  
    
refGeneutr3	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  10
  
    
refGeneutr5	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  11
  
    
refGeneexons	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  12
  
    
refGeneintrons	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  13
  
    
ensGene	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz


  		





  
  14
  
    
ensGenepromoter	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ensGene.txt.gz


  		





  
  15
  
    
ensGeneutr3	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ensGene.txt.gz


  		





  
  16
  
    
ensGeneutr5	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ensGene.txt.gz


  		





  
  17
  
    
ensGeneexons	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ensGene.txt.gz


  		





  
  18
  
    
ensGeneintrons	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ensGene.txt.gz


  		





  
  19
  
    
rmsk_ensemble	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  20
  
    
RNA	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  21
  
    
DNA	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  22
  
    
SINE	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  23
  
    
LINE	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  24
  
    
LTR	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  25
  
    
Low_complexity	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  26
  
    
Satellite	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  27
  
    
Simple_repeat	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  28
  
    
Other	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  29
  
    
Unknown	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz


  		





  
  30
  
    
phastCons	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons.bw


  		





  
  31
  
    
phastCons60wayEuarchontoGlire	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons60wayEuarchontoGlire.bw


  		





  
  32
  
    
phastCons60wayGlire	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons60wayGlire.bw


  		





  
  33
  
    
phastCons60wayPlacental	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons60wayPlacental.bw


  		





  
  34
  
    
phyloP60wayEuarchontoglire	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phyloP60way/mm10.60way.phyloP60wayEuarchontoglire.bw


  		





  
  35
  
    
phyloP60wayGlire	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phyloP60way/mm10.60way.phyloP60wayGlire.bw


  		





  
  36
  
    
phyloP60wayPlacental	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phyloP60way/mm10.60way.phyloP60wayPlacental.bw


  		





  
  37
  
    
phyloP60way	Download date=Jul-31-2013; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/phyloP60way/mm10.60way.phyloP60way.bw


  		





  
  38
  
    
cpgIsland	Download date=Jul-31-2013; Parsed by=in house script; Download from=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/cpgIslandExt.txt.gz


  		





  
  39
  
    
gc5Base	Download date=Jul-31-2013; Parsed by=hgGcPercent in Kent utils


  		












  

    
      b/mm10/track2Ft
    
  






  
  1
  
    
mock1	2


  		





  
  2
  
    
mock2	2


  		





  
  3
  
    
mock3	2


  		





  
  4
  
    
mock4	2


  		





  
  5
  
    
mock5	2


  		





  
  6
  
    
mock6	2


  		





  
  7
  
    
mock7	2


  		





  
  8
  
    
mock8	2


  		





  
  9
  
    
mock9	2


  		





  
  10
  
    
mock10	2


  		





  
  11
  
    
mock11	2


  		





  
  12
  
    
mock12	2


  		





  
  13
  
    
mock13	2


  		





  
  14
  
    
mock14	2


  		





  
  15
  
    
mock15	2


  		





  
  16
  
    
mock16	2


  		





  
  17
  
    
mock17	2


  		





  
  18
  
    
mock18	2


  		





  
  19
  
    
mock19	2


  		





  
  20
  
    
mock20	2


  		












  

    
      b/mm10/track2Label
    
  






  
  1
  
    
mock20	mock20


  		





  
  2
  
    
mock19	mock19


  		





  
  3
  
    
mock18	mock18


  		





  
  4
  
    
mock13	mock13


  		





  
  5
  
    
mock12	mock12


  		





  
  6
  
    
mock11	mock11


  		





  
  7
  
    
mock10	mock10


  		





  
  8
  
    
mock17	mock17


  		





  
  9
  
    
mock16	mock16


  		





  
  10
  
    
mock15	mock15


  		





  
  11
  
    
mock14	mock14


  		





  
  12
  
    
mock9	mock9


  		





  
  13
  
    
mock8	mock8


  		





  
  14
  
    
mock3	mock3


  		





  
  15
  
    
mock2	mock2


  		





  
  16
  
    
mock1	mock1


  		





  
  17
  
    
mock7	mock7


  		





  
  18
  
    
mock6	mock6


  		





  
  19
  
    
mock5	mock5


  		





  
  20
  
    
mock4	mock4


  		












  

    
      b/mm10/track2Style
    
  






  
  1
  
    
cpgIsland	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  2
  
    
DNA	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  3
  
    
ensGene	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  4
  
    
ensGeneexons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  5
  
    
ensGeneintrons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  6
  
    
ensGenepromoter	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  7
  
    
ensGeneutr3	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  8
  
    
ensGeneutr5	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  9
  
    
knownGene	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  10
  
    
knownGeneexons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  11
  
    
knownGeneintrons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  12
  
    
knownGenepromoter	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  13
  
    
knownGeneutr3	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  14
  
    
knownGeneutr5	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  15
  
    
LINE	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  16
  
    
Low_complexity	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  17
  
    
LTR	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  18
  
    
Other	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  19
  
    
refGene	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  20
  
    
refGeneexons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  21
  
    
refGeneintrons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  22
  
    
refGenepromoter	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  23
  
    
refGeneutr3	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  24
  
    
refGeneutr5	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'


  		





  
  25
  
    
RNA	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  26
  
    
Satellite	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  27
  
    
Simple_repeat	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  28
  
    
SINE	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  29
  
    
Unknown	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)','isrmsk':true


  		





  
  30
  
    
phastCons	\N


  		





  
  31
  
    
phastCons60wayEuarchontoGlire	\N


  		





  
  32
  
    
phastCons60wayGlire	\N


  		





  
  33
  
    
phastCons60wayPlacental	\N


  		





  
  34
  
    
phyloP60wayEuarchontoglire	\N


  		





  
  35
  
    
phyloP60wayGlire	\N


  		





  
  36
  
    
phyloP60wayPlacental	\N


  		





  
  37
  
    
phyloP60way	\N


  		





  
  38
  
    
gc5Base	\N


  		












  

    
      b/mm10/trackAttr2idx
    
  






  
  1
  
    
11	1	mock


  		





  
  2
  
    
12	2	mock


  		





  
  3
  
    
13	3	mock


  		





  
  4
  
    
14	4	mock


  		





  
  5
  
    
15	5	mock


  		





  
  6
  
    
16	6	mock


  		





  
  7
  
    
17	7	mock


  		





  
  8
  
    
18	8	mock


  		





  
  9
  
    
19	9	mock


  		





  
  10
  
    
20	10	mock


  		





  
  11
  
    
21	11	mock


  		





  
  12
  
    
22	12	mock


  		





  
  13
  
    
23	13	mock


  		





  
  14
  
    
24	14	mock


  		





  
  15
  
    
25	15	mock


  		





  
  16
  
    
26	16	mock


  		





  
  17
  
    
27	17	mock


  		





  
  18
  
    
28	18	mock


  		





  
  19
  
    
29	19	mock


  		





  
  20
  
    
30	20	mock


  		












  

    
      b/mm9/decorInfo
    
  






  88
  88
  
    
wgEncodeCrgMapabilityAlign40mer	40mer alignability ENCODE/CRG(Guigo)	\N	7	14	0	\N


  		





  89
  89
  
    
wgEncodeCrgMapabilityAlign50mer	50mer alignability ENCODE/CRG(Guigo)	\N	7	14	0	\N


  		





  90
  90
  
    
wgEncodeCrgMapabilityAlign75mer	75mer alignability ENCODE/CRG(Guigo)	\N	7	14	0	\N


  		





  
  91
  
    
ILS_test_File	Phillip Test Track	\N	4	12	0	\N


  		












  

    
      b/mm9/makeDb.sql
    
  






  34
  34
  
    
"3,http://vizhub.wustl.edu/hubSample/mm9/wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdSig.gz,1,http://vizhub.wustl.edu/hubSample/mm9/bed.gz,5,http://vizhub.wustl.edu/hubSample/mm9/wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdAlnRep2.gz,100,http://vizhub.wustl.edu/hubSample/mm9/hub.txt",


  		





  35
  35
  
    
"chr6,51999773,chr6,52368420",


  		





  36
  36
  
    
"longrange,encode",


  		





  37
  
  
    
"knownGene,rmsk_ensemble",


  		





  
  37
  
    
"knownGene,rmsk_ensemble,ILS_test_File",


  		





  38
  38
  
    
"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY,chrM",


  		





  39
  39
  
    
\N,\N,


  		





  40
  40
  
    
true,


  		












  

    
      b/mm9/track2Categorical
    
  






  1
  1
  
    
rmsk_ensemble	1:['SINE - short interspersed nuclear elements','#cc0000'], 2:['LINE - long interspersed nuclear element','#FF6600'], 3:['LTR - long terminal repeat element','#006600'], 4:['DNA transposon','#4A72E8'], 5:['Simple repeat, micro-satellite','#AB833B'], 7:['Low complexity repeat','#663333'], 6:['Satellite repeat','#660000'], 9:['Other repeats','#488E8E'],8:['RNA repeat','#cc33ff'], 10:['Unknown','#5C5C5C']


  		





  
  2
  
    
ILS_test_File	24:['type24','#ffffff'], 25:['type25','#ffffff'], 20:['type20','#afeeee'], 21:['type21','#e0ffff'], 22:['type22','#ffffff'], 23:['type23','#ffffff'], 1:['type1','#e9967a'], 3:['type3','#ff0000'], 2:['type2','#dc143c'], 5:['type5','#b22222'], 4:['type4','#ff4500'], 7:['type7','#008000'], 6:['type6','#b22222'], 9:['type9','#adff2f'], 8:['type8','#008000'], 11:['type11','#ffa500'], 10:['type10','#adff2f'], 13:['type13','#ffa500'], 12:['type12','#ffa500'], 15:['type15','#ffff00'], 14:['type14','#ffa500'], 17:['type17','#c0c0c0'], 16:['type16','#dcdcdc'], 19:['type19','#4682b4'], 18:['type18','#5f9ea0'], 26:['type26','#e9967a'], 27:['type27','#ff0000'], 28:['type28','#dc143c'], 29:['type29','#b22222']


  		












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