src/hg/lib/retroMrnaInfo.sql 1.2

Index: src/hg/lib/retroMrnaInfo.sql
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/retroMrnaInfo.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/lib/retroMrnaInfo.sql	1 Mar 2007 00:01:41 -0000	1.1
+++ src/hg/lib/retroMrnaInfo.sql	2 Dec 2009 00:38:56 -0000	1.2
@@ -1,67 +1,67 @@
 # retroMrnaInfo.sql was originally generated by the autoSql program, which also 
 # generated retroMrnaInfo.c and retroMrnaInfo.h.  This creates the database representation of
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
 #Retrogenes based on cDNA alignments that are expressed or processed pseudogenes.
-CREATE TABLE retroMrnaInfo (
+CREATE TABLE retroMrnaInfoXX (
     chrom varchar(255) not null,	# Reference sequence chromosome or scaffold col1
     chromStart int unsigned not null,	# pseudogene alignment start position col2
     chromEnd int unsigned not null,	# pseudogene alignment end position col3
     name varchar(255) not null,	# Name of pseudogene col4
     score int unsigned not null,	# score of pseudogene with gene col5
     strand char(2) not null,	# + or -
     thickStart int unsigned not null,	# Start of where display should be thick (start codon)
     thickEnd int unsigned not null,	# End of where display should be thick (stop codon)
     reserved int unsigned not null,	# Always zero for now
     blockCount int not null,	# Number of blocks
     blockSizes longblob not null,	# Comma separated list of block sizes
     chromStarts longblob not null,	# Start positions relative to chromStart
     retroExonCount int not null,	# number of exons in retroGene col13
     axtScore int not null,	# blastz score, parent mrna aligned to pseudogene col14
     type varchar(255) not null,	# type of evidence col15
     gChrom varchar(255) not null,	# Chromosome name col16
     gStart int not null,	# gene alignment start position col17
     gEnd int not null,	# gene alignment end position col18
     gStrand char(2) not null,	# strand of gene col19
     parentSpliceCount int unsigned not null,	# # of splice sites in parent gene col20
     geneOverlap int unsigned not null,	# bases overlapping col21
     polyA int unsigned not null,	# count of As in polyA col22
     polyAstart int not null,	# start of polyA, relative to end of pseudogene col23
     exonCover int not null,	# number of exons in Gene covered col24
     intronCount int unsigned not null,	# number of introns in pseudogene col25
     bestAliCount int unsigned not null,	# number of good mrnas aligning col26
     matches int unsigned not null,	# matches + repMatches col27
     qSize int unsigned not null,	# aligning bases in pseudogene col28
     qEnd int unsigned not null,	# end of cdna alignment col29
     tReps int unsigned not null,	# repeats in gene col30
     overlapRhesus int not null,	# percent of retro that breaks net relative to Rhesus col31
     overlapMouse int not null,	# percent of retro that breaks net relative to Mouse col32
     coverage int unsigned not null,	# % of bases that align to gene col33
     label int not null,	# 1=pseudogene,-1 not pseudogene -2 expressed retroGene col34
     milliBad int unsigned not null,	# milliBad score, pseudogene aligned to genome col35
     oldScore int unsigned not null,	# another heuristic col36
     oldIntronCount int not null,	# old simple intron count col37
     processedIntrons int not null,	# count of introns removed via retrotransposition col38
     conservedSpliceSites int not null,	# conserved splice site count col39
     maxOverlap int not null,	# largest overlap with another mrna col40
     refSeq varchar(255) not null,	# Name of closest regSeq to gene col41
     rStart int not null,	# refSeq alignment start position col42
     rEnd int not null,	# refSeq alignment end position col43
     mgc varchar(255) not null,	# Name of closest mgc to gene col44
     mStart int not null,	# mgc alignment start position col45
     mEnd int not null,	# mgc alignment end position col46
     kgName varchar(255) not null,	# Name of closest knownGene to gene col47
     kStart int not null,	# kg alignment start position col48
     kEnd int not null,	# kg alignment end position col49
     overName varchar(255) not null,	# name of overlapping mrna col50
     overStart int not null,	# overlapping mrna start position col51
     overExonCover int not null,	# count of overlapping mrna exons col52
     overStrand char(2) not null,	# strand of overlapping mrna col53
     overlapDog int not null,	# percent of retro that breaks net relative to dog col54
     posConf float not null,	# pvalue for positive col55
     polyAlen int unsigned not null,	# length of polyA col56
     kaku float not null,	# ratio of substitutions between coding and utr wrt parent gene
               #Indices
     PRIMARY KEY(name)
 );