src/hg/lib/snp125.as 1.7

Index: src/hg/lib/snp125.as
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/snp125.as,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/lib/snp125.as	22 Apr 2006 00:32:49 -0000	1.6
+++ src/hg/lib/snp125.as	8 Mar 2010 19:42:31 -0000	1.7
@@ -3,19 +3,19 @@
     (
     string   chrom;      "Reference sequence chromosome or scaffold"
     uint     chromStart; "Start position in chrom"
     uint     chromEnd;   "End position in chrom"
-    string   name;       "Reference SNP identifier or Affy SNP name"
+    string   name;       "dbSNP Reference SNP identifier"
     uint     score;      "Not used"
     string   strand;     "Which DNA strand contains the observed alleles"
-    lstring  refNCBI;  	"Reference genomic from dbSNP"
-    lstring  refUCSC;   "Reference genomic from nib lookup"
+    lstring  refNCBI;  	 "Reference genomic sequence from dbSNP"
+    lstring  refUCSC;    "Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd"
     string   observed;   "The sequences of the observed alleles from rs-fasta files"
-    string   molType;    "Sample type from exemplar ss"
-    string   class;      "The class of variant (simple, insertion, deletion, range, etc.)"
-    string   valid;      "The validation status of the SNP"
-    float    avHet;      "The average heterozygosity from all observations"
-    float    avHetSE;    "The Standard Error for the average heterozygosity"
-    string   func;       "The functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)"
-    string   locType;    "How the variant affects the reference sequence"
-    uint     weight;     "The quality of the alignment"
+    string   molType;    "Sample type from exemplar submitted sequence (ss)"
+    string   class;      "Class of variant (single, in-del, named, mixed, etc.)"
+    string   valid;      "Validation status of the SNP"
+    float    avHet;      "Average heterozygosity from all observations"
+    float    avHetSE;    "Standard Error for the average heterozygosity"
+    string   func;       "Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)"
+    string   locType;    "Type of mapping inferred from size on reference; may not agree with class"
+    uint     weight;     "The quality of the alignment: 1 = unique mapping, 2 = non-unique, 3 = many matches"
     )