Differences

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--- pgd_unaligned_mixedreads [2008/12/09 09:59] – created heidi
+++ pgd_unaligned_mixedreads [2011/05/05 17:30] (current) – heidi
@@ Line 10: / Line 10: @@
     <organism> homo sapiens sapiens </organism>
     <numPop> 3 </numPop>
-    <numReads> mixed </numReads>
+    <ploidy> 1 </ploidy>
     <aligned> no </aligned>
     <missing> ? </missing>
@@ Line 16: / Line 16: @@
   </header>
-  <loci>
+  <dataDescription>
-    <lociNum> 2 </lociNum>
+    <numLoci> 2 </numLoci>
-    <lociDataType> DNA </lociDataType>
+    <dataType> DNA </dataType>
     <locus id="loci one">
-      <locusChromosom> 3 </locusChromosom>
+      <locusChromosome> 3 </locusChromosome>
       <locusLocation> Hs8_23892 </locusLocation>
       <locusGenic> coding </locusGenic>
@@ Line 31: / Line 31: @@
       <locusGenic> noncoding </locusGenic>
     </locus>
-  </loci>
+  </dataDescription>
   <population name="pop 1">
     <popSize> 3 </popSize>
-    <popNumReads> mixed </popNumReads>
     <ind name="1">
       <indGeogCoord> 35, 4 </indGeogCoord>
       <indLingGroup> African </indLingGroup>
-      <indLocus> loci one </indLocus>
+      <indLoci> loci one </indLoci>
-      <indNumReads> 2 </indNumReads>
       <indFreq> 10 </indFreq>
       <read>
@@ Line 57: / Line 55: @@
       <indGeogCoord> 36, 4 </indGeogCoord>
       <indLingGroup> Africanic </indLingGroup>
-      <indLocus> loci one </indLocus>
+      <indLoci> loci one </indLoci>
-      <indNumReads> 1 </indNumReads>
       <indFreq> 11 </indFreq>
       <read>
@@ Line 70: / Line 67: @@
       <indGeogCoord> 35, 5 </indGeogCoord>
       <indLingGroup> African </indLingGroup>
-      <indLocus> loci one </indLocus>
+      <indLoci> loci one </indLoci>
       <indNumReads> 3 </indNumReads>
       <read>
@@ Line 96: / Line 93: @@
     <popGeogCoord> 8, 48 </popGeogCoord>
     <popLingGroup> European </popLingGroup>
-    <popLocus> loci two </popLocus>
+    <popLoci> loci two </popLoci>
-    <popNumReads> 1 </popNumReads>
     <ind name="4">
       <read>
@@ Line 117: / Line 113: @@
   <population name="pop 3">
     <popSize> 3 </popSize>
-    <popNumReads> mixed </popNumReads>
+    <popLoci> loci 3 </popLoci>
-    <popLocus> loci 3 </popLocus>
     <ind name="1">
       <indGeogCoord> 35, 4 </indGeogCoord>
       <indLingGroup> African </indLingGroup>
-      <indNumReads> 2 </indNumReads>
       <read>
         <start> 230 </start>
@@ Line 138: / Line 132: @@
       <indGeogCoord> 36, 4 </indGeogCoord>
       <indLingGroup> Africanic </indLingGroup>
-      <indNumReads> 1 </indNumReads>
       <indFreq> 10 </indFreq>
       <read>
@@ Line 174: / Line 167: @@
     <group name="two"> pop 2, pop 3 </group>
   </structure>
 </PGD>
 </code>