src/hg/lib/hapmapPhaseIIISummary.as 1.1

Index: src/hg/lib/hapmapPhaseIIISummary.as
===================================================================
RCS file: src/hg/lib/hapmapPhaseIIISummary.as
diff -N src/hg/lib/hapmapPhaseIIISummary.as
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/hapmapPhaseIIISummary.as	6 Mar 2009 23:34:41 -0000	1.1
@@ -0,0 +1,24 @@
+table hapmapPhaseIIISummary
+"HapMap Phase III allele summaries for filtering (BED 5+)"
+    (
+    string  chrom;      "Chromosome"
+    uint    chromStart; "Start position in chrom (0 based)"
+    uint    chromEnd;   "End position in chrom (1 based)"
+    string  name;       "Reference SNP identifier from dbSnp"
+    uint    score;      "Average of population heterozygosities in parts per thousand (0-500)"
+
+    string  observed;            "Observed string from genotype file"
+    char    overallMajorAllele;  "This allele has been observed in at least half of the populations that have data for this SNP"
+    char    overallMinorAllele;  "This allele may not have been observed in any HapMap sample"
+    ubyte   popCount;            "How many Phase III populations have data (1-11)"
+    ubyte   phaseIIPopCount;     "How many Phase II populations have data (0-4)"
+    ubyte   isMixed;             "0 if all populations have the same major allele, 1 otherwise."
+    ubyte[11] foundInPop;        "Got data for each of the 11 Phase III populations?"
+    ubyte[11] monomorphicInPop;  "Monomorphic in each of the 11 Phase III populations?"
+    float   minFreq;             "Minimum minor allele frequency across all populations"
+    float   maxFreq;             "Maximum minor allele frequency across all populations"
+
+    uint     orthoCount;           "Species for which orthologous alleles have been determined"
+    char[orthoCount] orthoAlleles; "Orthologous allele for each species (or N if not found)"
+    ushort[orthoCount] orthoQuals; "Base quality score (0-100) for each species"
+    )