pgd_ngs
PGD file example
NGS data of two loci from three haploid populations:
<?xml version="1.0" encoding="iso-8859-1" ?> <?xml-stylesheet type="text/xsl" href="stylesheet_PGD.xsl"?> <PGD xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="PGD_schema.xsd"> <header title="faked example data"> <organism> homo sapiens sapiens </organism> <numPop> 3 </numPop> <ploidy> 1 </ploidy> <missing> ? </missing> <gap> - </gap> </header> <dataDescription> <numLoci> 2 </numLoci> <dataType> DNA </dataType> <locus id="loci one"> <locusChromosome> 3 </locusChromosome> <locusLocation> Hs8_23892 </locusLocation> <locusGenic> coding </locusGenic> <locusLinks> www.loci.ch/faked_adress/ </locusLinks> <locusComments> faked </locusComments> </locus> <locus id="loci two"> <locusChromosome> 3 </locusChromosome> <locusLocation> Hs8_23992 </locusLocation> <locusGenic> noncoding </locusGenic> </locus> </dataDescription> <population name="pop 1"> <popSize> 3 </popSize> <ind name="1"> <indGeogCoord> 35, 4 </indGeogCoord> <indLingGroup> African </indLingGroup> <indLoci> loci one </indLoci> <indFreq> 10 </indFreq> <read> <start> 230 </start> <length> 100 </length> <data> ATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> <read> <start> 240 </start> <length> 90 </length> <data> AAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> <ind name="2"> <indGeogCoord> 36, 4 </indGeogCoord> <indLingGroup> Africanic </indLingGroup> <indLoci> loci one </indLoci> <indFreq> 11 </indFreq> <read> <start> 273 </start> <length> 57 </length> <data> TCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> <ind name="3"> <indGeogCoord> 35, 5 </indGeogCoord> <indLingGroup> African </indLingGroup> <indLoci> loci one </indLoci> <read> <start> 256 </start> <length> 74 </length> <data> TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> <read> <start> 260 </start> <length> 70 </length> <data> AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> <read> <start> 250 </start> <length> 80 </length> <data> AAACCCTTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> </population> <population name="pop 2"> <popSize> 2 </popSize> <popGeogCoord> 8, 48 </popGeogCoord> <popLingGroup> European </popLingGroup> <popLoci> loci two </popLoci> <ind name="4"> <read> <start> 265 </start> <length> 65 </length> <data> TTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> <ind name="5"> <read> <start> 250 </start> <length> 80 </length> <data> TTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> </population> <population name="pop 3"> <popSize> 3 </popSize> <popLoci> loci 3 </popLoci> <ind name="1"> <indGeogCoord> 35, 4 </indGeogCoord> <indLingGroup> African </indLingGroup> <read> <start> 230 </start> <length> 100 </length> <data> ATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> <read> <start> 240 </start> <length> 90 </length> <data> AAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> <ind name="2"> <indGeogCoord> 36, 4 </indGeogCoord> <indLingGroup> Africanic </indLingGroup> <indFreq> 10 </indFreq> <read> <start> 273 </start> <length> 57 </length> <data> TCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> </ind> <ind name="3"> <indGeogCoord> 35, 5 </indGeogCoord> <indLingGroup> African </indLingGroup> <read> <start> 256 </start> <length> 74 </length> <data> TTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> <read> <start> 250 </start> <length> 80 </length> <data> AAACCCTTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAT </data> </read> <read> <start> 260 </start> <length> 65 </length> <data> AACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCAT </data> </read> </ind> </population> <structure name="faked"> <numGroups> 2 </numGroups> <group name="one"> pop 1 </group> <group name="two"> pop 2, pop 3 </group> </structure> </PGD>
pgd_ngs.txt · Last modified: 2011/10/11 15:52 by heidi