src/hg/lib/hapmapPhaseIIISummary.sql 1.1

Index: src/hg/lib/hapmapPhaseIIISummary.sql
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RCS file: src/hg/lib/hapmapPhaseIIISummary.sql
diff -N src/hg/lib/hapmapPhaseIIISummary.sql
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/hapmapPhaseIIISummary.sql	6 Mar 2009 23:34:41 -0000	1.1
@@ -0,0 +1,30 @@
+# hapmapPhaseIIISummary.sql was originally generated by the autoSql program, which also 
+# generated hapmapPhaseIIISummary.c and hapmapPhaseIIISummary.h.  This creates the database representation of
+# an object which can be loaded and saved from RAM in a fairly 
+# automatic way.
+
+#HapMap Phase III allele summaries for filtering (BED 5+)
+CREATE TABLE hapmapPhaseIIISummary (
+    bin smallint not null,      # Bin number for browser speedup
+    chrom varchar(255) not null,	# Chromosome
+    chromStart int unsigned not null,	# Start position in chrom (0 based)
+    chromEnd int unsigned not null,	# End position in chrom (1 based)
+    name varchar(255) not null,	# Reference SNP identifier from dbSnp
+    score int unsigned not null,	# Average of population heterozygosities in parts per thousand (0-500)
+    observed varchar(255) not null,	# Observed string from genotype file
+    overallMajorAllele char(1) not null,	# This allele has been observed in at least half of the populations that have data for this SNP
+    overallMinorAllele char(1) not null,	# This allele may not have been observed in any HapMap sample
+    popCount tinyint unsigned not null,	# How many Phase III populations have data (1-11)
+    phaseIIPopCount tinyint unsigned not null,	# How many Phase II populations have data (0-4)
+    isMixed tinyint unsigned not null,	# 0 if all populations have the same major allele, 1 otherwise.
+    foundInPop longblob not null,	# Got data for each of the 11 Phase III populations?
+    monomorphicInPop longblob not null,	# Monomorphic in each of the 11 Phase III populations?
+    minFreq float not null,	# Minimum minor allele frequency across all populations
+    maxFreq float not null,	# Maximum minor allele frequency across all populations
+    orthoCount int unsigned not null,	# Species for which orthologous alleles have been determined
+    orthoAlleles longblob not null,	# Orthologous allele for each species (or N if not found)
+    orthoQuals longblob not null,	# Base quality score (0-100) for each species
+              #Indices
+    INDEX(chrom(8),bin),
+    INDEX(name(12))
+);