930e2ff4a539d4ce430291acb4af9d7190aabf22 hartera Thu Feb 28 10:42:46 2013 -0800 Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount. diff --git src/hg/lib/ucscRetroInfo.sql src/hg/lib/ucscRetroInfo.sql index d79b27a..0595126 100644 --- src/hg/lib/ucscRetroInfo.sql +++ src/hg/lib/ucscRetroInfo.sql @@ -1,65 +1,64 @@ # ucscRetroInfo.sql was originally generated by the autoSql program, which also # generated ucscRetroInfo.c and ucscRetroInfo.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 ucscRetroInfo ( 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 coverage int unsigned not null, # % of bases that align to gene col31 label int not null, # 1=pseudogene,-1 not pseudogene -2 expressed retroGene col32 milliBad int unsigned not null, # milliBad score, pseudogene aligned to genome col33 - oldScore int unsigned not null, # another heuristic col34 - oldIntronCount int not null, # old simple intron count col35 - processedIntrons int not null, # count of introns removed via retrotransposition col36 - conservedSpliceSites int not null, # conserved splice site count col37 - maxOverlap int not null, # largest overlap with another mrna col38 - refSeq varchar(255) not null, # Name of closest regSeq to gene col39 - rStart int not null, # refSeq alignment start position col40 - rEnd int not null, # refSeq alignment end position col41 - mgc varchar(255) not null, # Name of closest mgc to gene col42 - mStart int not null, # mgc alignment start position col43 - mEnd int not null, # mgc alignment end position col44 - kgName varchar(255) not null, # Name of closest knownGene to gene col45 - kStart int not null, # kg alignment start position col46 - kEnd int not null, # kg alignment end position col47 - overName varchar(255) not null, # name of overlapping mrna col48 - overStart int not null, # overlapping mrna start position col49 - overExonCover int not null, # count of overlapping mrna exons col50 - overStrand char(2) not null, # strand of overlapping mrna col51 - posConf float not null, # pvalue for positive col52 - polyAlen int unsigned not null, # length of polyA col53 + alignGapCount int not null, # old simple intron count col34 + processedIntrons int not null, # count of introns removed via retrotransposition col35 + conservedSpliceSites int not null, # conserved splice site count col36 + maxOverlap int not null, # largest overlap with another mrna col37 + refSeq varchar(255) not null, # Name of closest regSeq to gene col38 + rStart int not null, # refSeq alignment start position col39 + rEnd int not null, # refSeq alignment end position col40 + mgc varchar(255) not null, # Name of closest mgc to gene col41 + mStart int not null, # mgc alignment start position col42 + mEnd int not null, # mgc alignment end position col43 + kgName varchar(255) not null, # Name of closest knownGene to gene col44 + kStart int not null, # kg alignment start position col45 + kEnd int not null, # kg alignment end position col46 + overName varchar(255) not null, # name of overlapping mrna col47 + overStart int not null, # overlapping mrna start position col48 + overExonCover int not null, # count of overlapping mrna exons col49 + overStrand char(2) not null, # strand of overlapping mrna col50 + posConf float not null, # pvalue for positive col51 + polyAlen int unsigned not null, # length of polyA col52 #Indices PRIMARY KEY(name), index(kgName(10)), index(refSeq(10)) );