htsworkflow/pipelines/test/testdata/run_207B2AAXX_2008-04-12.xml

   1 <PipelineRun>
   2   <FlowcellID>207B2AAXX</FlowcellID>
   3   <Firecrest version="1">
   4     <version>1.8.28</version>
   5     <FirstCycle>1</FirstCycle>
   6     <LastCycle>33</LastCycle>
   7     <run_time>1207983600.0</run_time>
   8     <user>diane</user>
   9     <matrix># Auto-generated frequency response matrix
  10 &gt; A
  11 &gt; C
  12 &gt; G
  13 &gt; T
  14 0.77 0.15 -0.04 -0.04
  15 0.76 1.02 -0.05 -0.06
  16 -0.10 -0.10 1.17 -0.03
  17 -0.13 -0.12 0.80 1.27
  18 </matrix>
  19   </Firecrest>
  20   <Bustard version="1">
  21     <version>1.8.28</version>
  22     <run_time>1207983600.0</run_time>
  23     <user>diane</user>
  24     <Parameters>
  25       <Phasing lane="1">
  26         <Phasing>0.0099</Phasing>
  27         <Prephasing>0.0035</Prephasing>
  28       </Phasing>
  29       <Phasing lane="2">
  30         <Phasing>0.0099</Phasing>
  31         <Prephasing>0.0035</Prephasing>
  32       </Phasing>
  33       <Phasing lane="3">
  34         <Phasing>0.0099</Phasing>
  35         <Prephasing>0.0035</Prephasing>
  36       </Phasing>
  37       <Phasing lane="4">
  38         <Phasing>0.0099</Phasing>
  39         <Prephasing>0.0035</Prephasing>
  40       </Phasing>
  41       <Phasing lane="5">
  42         <Phasing>0.0099</Phasing>
  43         <Prephasing>0.0035</Prephasing>
  44       </Phasing>
  45       <Phasing lane="6">
  46         <Phasing>0.0099</Phasing>
  47         <Prephasing>0.0035</Prephasing>
  48       </Phasing>
  49       <Phasing lane="7">
  50         <Phasing>0.0099</Phasing>
  51         <Prephasing>0.0035</Prephasing>
  52       </Phasing>
  53       <Phasing lane="8">
  54         <Phasing>0.0099</Phasing>
  55         <Prephasing>0.0035</Prephasing>
  56       </Phasing>
  57     </Parameters>
  58   </Bustard>
  59   <Gerald version="1">
  60     <RunParameters>
  61       <ChipWideRunParameters>
  62         <ANALYSIS>default</ANALYSIS>
  63         <BAD_LANES />
  64         <BAD_TILES />
  65         <CONTAM_DIR />
  66         <CONTAM_FILE />
  67         <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
  68         <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
  69         <ELAND_REPEAT />
  70         <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
  71         <EMAIL_LIST>diane</EMAIL_LIST>
  72         <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
  73         <EXPT_DIR>/home/diane/gec/080408_HWI-EAS229_0023_207B2AAXX/Data/C1-33_Firecrest1.8.28_12-04-2008_diane/Bustard1.8.28_12-04-2008_diane</EXPT_DIR>
  74         <EXPT_DIR_ROOT>/home/diane/gec</EXPT_DIR_ROOT>
  75         <FORCE>1</FORCE>
  76         <GENOME_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald/../../Genomes</GENOME_DIR>
  77         <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
  78         <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  79         <OUT_DIR>/home/diane/gec/080408_HWI-EAS229_0023_207B2AAXX/Data/C1-33_Firecrest1.8.28_12-04-2008_diane/Bustard1.8.28_12-04-2008_diane/GERALD_12-04-2008_diane</OUT_DIR>
  80         <POST_RUN_COMMAND />
  81         <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
  82         <PURE_BASES>12</PURE_BASES>
  83         <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
  84         <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
  85         <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
  86         <READ_LENGTH>32</READ_LENGTH>
  87         <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
  88         <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
  89         <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
  90         <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
  91         <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
  92         <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
  93         <TILE_ROOT>s</TILE_ROOT>
  94         <TIME_STAMP>Sat Apr 12 08:51:25 2008</TIME_STAMP>
  95         <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
  96         <USE_BASES>all</USE_BASES>
  97         <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
  98       </ChipWideRunParameters>
  99       <LaneSpecificRunParameters>
 100         <ANALYSIS>
 101           <s_1>eland</s_1>
 102           <s_2>eland</s_2>
 103           <s_3>eland</s_3>
 104           <s_4>eland</s_4>
 105           <s_5>eland</s_5>
 106           <s_6>eland</s_6>
 107           <s_7>eland</s_7>
 108           <s_8>eland</s_8>
 109         </ANALYSIS>
 110         <ELAND_GENOME>
 111           <s_1>/data-store01/compbio/genomes/canfam2</s_1>
 112           <s_2>/data-store01/compbio/genomes/equcab1</s_2>
 113           <s_3>/data-store01/compbio/genomes/hg18</s_3>
 114           <s_4>/data-store01/compbio/genomes/hg18</s_4>
 115           <s_5>/data-store01/compbio/genomes/strpur2</s_5>
 116           <s_6>/data-store01/compbio/genomes/elegans170</s_6>
 117           <s_7>/data-store01/compbio/genomes/elegans170</s_7>
 118           <s_8>/data-store01/compbio/genomes/elegans170</s_8>
 119         </ELAND_GENOME>
 120         <READ_LENGTH>
 121           <s_1>32</s_1>
 122           <s_2>32</s_2>
 123           <s_3>32</s_3>
 124           <s_4>32</s_4>
 125           <s_5>32</s_5>
 126           <s_6>32</s_6>
 127           <s_7>32</s_7>
 128           <s_8>32</s_8>
 129         </READ_LENGTH>
 130         <USE_BASES>
 131           <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
 132           <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
 133           <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
 134           <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
 135           <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
 136           <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
 137           <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
 138           <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
 139         </USE_BASES>
 140       </LaneSpecificRunParameters>
 141     </RunParameters>
 142     <Summary version="2">
 143       <LaneResultSummary lane="1">
 144         <PercentPassFilterClusters deviation="28.34" mean="35.77" />
 145         <PercentIntensityAfter20Cycles deviation="15.88" mean="21.93" />
 146         <Cluster deviation="3170" mean="25167" />
 147         <AverageFirstCycleIntensity deviation="966" mean="7071" />
 148         <AverageAlignmentScore deviation="1198.06" mean="3963.69" />
 149         <PercentPassFilterAlign deviation="6.19" mean="21.2" />
 150         <PercentErrorRate deviation="5.23" mean="4.09" />
 151       </LaneResultSummary>
 152       <LaneResultSummary lane="3">
 153         <PercentPassFilterClusters deviation="17.43" mean="46.52" />
 154         <PercentIntensityAfter20Cycles deviation="3.09" mean="15.96" />
 155         <Cluster deviation="4648" mean="38205" />
 156         <AverageFirstCycleIntensity deviation="669" mean="7476" />
 157         <AverageAlignmentScore deviation="1620.11" mean="7961.24" />
 158         <PercentPassFilterAlign deviation="7.51" mean="39.39" />
 159         <PercentErrorRate deviation="3.76" mean="3.43" />
 160       </LaneResultSummary>
 161       <LaneResultSummary lane="2">
 162         <PercentPassFilterClusters deviation="19.82" mean="46.97" />
 163         <PercentIntensityAfter20Cycles deviation="4.84" mean="15.01" />
 164         <Cluster deviation="3188" mean="29088" />
 165         <AverageFirstCycleIntensity deviation="1006" mean="7253" />
 166         <AverageAlignmentScore deviation="786.73" mean="2113.02" />
 167         <PercentPassFilterAlign deviation="3.9" mean="10.72" />
 168         <PercentErrorRate deviation="2.99" mean="3.39" />
 169       </LaneResultSummary>
 170       <LaneResultSummary lane="5">
 171         <PercentPassFilterClusters deviation="16.39" mean="61.0" />
 172         <PercentIntensityAfter20Cycles deviation="8.67" mean="16.18" />
 173         <Cluster deviation="3367" mean="28208" />
 174         <AverageFirstCycleIntensity deviation="941" mean="8033" />
 175         <AverageAlignmentScore deviation="119.51" mean="416.18" />
 176         <PercentPassFilterAlign deviation="0.55" mean="2.06" />
 177         <PercentErrorRate deviation="2.49" mean="3.16" />
 178       </LaneResultSummary>
 179       <LaneResultSummary lane="4">
 180         <PercentPassFilterClusters deviation="12.44" mean="42.21" />
 181         <PercentIntensityAfter20Cycles deviation="3.55" mean="15.67" />
 182         <Cluster deviation="2935" mean="41543" />
 183         <AverageFirstCycleIntensity deviation="686" mean="7592" />
 184         <AverageAlignmentScore deviation="2286.82" mean="7952.4" />
 185         <PercentPassFilterAlign deviation="10.74" mean="40.31" />
 186         <PercentErrorRate deviation="5.72" mean="3.53" />
 187       </LaneResultSummary>
 188       <LaneResultSummary lane="7">
 189         <PercentPassFilterClusters deviation="9.12" mean="45.97" />
 190         <PercentIntensityAfter20Cycles deviation="3.59" mean="13.44" />
 191         <Cluster deviation="2478" mean="40286" />
 192         <AverageFirstCycleIntensity deviation="699" mean="8193" />
 193         <AverageAlignmentScore deviation="836.97" mean="2786.79" />
 194         <PercentPassFilterAlign deviation="4.99" mean="17.79" />
 195         <PercentErrorRate deviation="4.7" mean="4.77" />
 196       </LaneResultSummary>
 197       <LaneResultSummary lane="6">
 198         <PercentPassFilterClusters deviation="13.76" mean="61.66" />
 199         <PercentIntensityAfter20Cycles deviation="3.67" mean="14.86" />
 200         <Cluster deviation="3541" mean="27049" />
 201         <AverageFirstCycleIntensity deviation="833" mean="8160" />
 202         <AverageAlignmentScore deviation="877.84" mean="2463.72" />
 203         <PercentPassFilterAlign deviation="4.83" mean="14.09" />
 204         <PercentErrorRate deviation="5.77" mean="4.9" />
 205       </LaneResultSummary>
 206       <LaneResultSummary lane="8">
 207         <PercentPassFilterClusters deviation="10.44" mean="54.89" />
 208         <PercentIntensityAfter20Cycles deviation="4.06" mean="21.59" />
 209         <Cluster deviation="3038" mean="35567" />
 210         <AverageFirstCycleIntensity deviation="728" mean="8307" />
 211         <AverageAlignmentScore deviation="2132.04" mean="11771.38" />
 212         <PercentPassFilterAlign deviation="11.62" mean="66.11" />
 213         <PercentErrorRate deviation="2.15" mean="2.03" />
 214       </LaneResultSummary>
 215     </Summary>
 216     <ElandCollection version="1">
 217       <ElandLane id="1" version="1">
 218         <SampleName>s</SampleName>
 219         <LaneID>1</LaneID>
 220         <GenomeMap>
 221           <GenomeItem name="chr20.fa" value="canfam2/chr20.fa" />
 222           <GenomeItem name="chr15.fa" value="canfam2/chr15.fa" />
 223           <GenomeItem name="chr3.fa" value="canfam2/chr3.fa" />
 224           <GenomeItem name="chr4.fa" value="canfam2/chr4.fa" />
 225           <GenomeItem name="chr35.fa" value="canfam2/chr35.fa" />
 226           <GenomeItem name="chr6.fa" value="canfam2/chr6.fa" />
 227           <GenomeItem name="chr36.fa" value="canfam2/chr36.fa" />
 228           <GenomeItem name="chr19.fa" value="canfam2/chr19.fa" />
 229           <GenomeItem name="chr38.fa" value="canfam2/chr38.fa" />
 230           <GenomeItem name="chr26.fa" value="canfam2/chr26.fa" />
 231           <GenomeItem name="chr34.fa" value="canfam2/chr34.fa" />
 232           <GenomeItem name="chr12.fa" value="canfam2/chr12.fa" />
 233           <GenomeItem name="chr1.fa" value="canfam2/chr1.fa" />
 234           <GenomeItem name="chr23.fa" value="canfam2/chr23.fa" />
 235           <GenomeItem name="chr21.fa" value="canfam2/chr21.fa" />
 236           <GenomeItem name="chr8.fa" value="canfam2/chr8.fa" />
 237           <GenomeItem name="chr24.fa" value="canfam2/chr24.fa" />
 238           <GenomeItem name="chr18.fa" value="canfam2/chr18.fa" />
 239           <GenomeItem name="chr30.fa" value="canfam2/chr30.fa" />
 240           <GenomeItem name="chr28.fa" value="canfam2/chr28.fa" />
 241           <GenomeItem name="chr17.fa" value="canfam2/chr17.fa" />
 242           <GenomeItem name="chr33.fa" value="canfam2/chr33.fa" />
 243           <GenomeItem name="chr7.fa" value="canfam2/chr7.fa" />
 244           <GenomeItem name="chrX.fa" value="canfam2/chrX.fa" />
 245           <GenomeItem name="chrM.fa" value="canfam2/chrM.fa" />
 246           <GenomeItem name="chr31.fa" value="canfam2/chr31.fa" />
 247           <GenomeItem name="chr25.fa" value="canfam2/chr25.fa" />
 248           <GenomeItem name="chrUn.fa" value="canfam2/chrUn.fa" />
 249           <GenomeItem name="chr14.fa" value="canfam2/chr14.fa" />
 250           <GenomeItem name="chr13.fa" value="canfam2/chr13.fa" />
 251           <GenomeItem name="chr27.fa" value="canfam2/chr27.fa" />
 252           <GenomeItem name="chr10.fa" value="canfam2/chr10.fa" />
 253           <GenomeItem name="chr11.fa" value="canfam2/chr11.fa" />
 254           <GenomeItem name="chr16.fa" value="canfam2/chr16.fa" />
 255           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 256           <GenomeItem name="chr32.fa" value="canfam2/chr32.fa" />
 257           <GenomeItem name="chr9.fa" value="canfam2/chr9.fa" />
 258           <GenomeItem name="chr2.fa" value="canfam2/chr2.fa" />
 259           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 260           <GenomeItem name="chr37.fa" value="canfam2/chr37.fa" />
 261           <GenomeItem name="chr5.fa" value="canfam2/chr5.fa" />
 262           <GenomeItem name="chr22.fa" value="canfam2/chr22.fa" />
 263           <GenomeItem name="chr29.fa" value="canfam2/chr29.fa" />
 264         </GenomeMap>
 265         <MappedReads>
 266           <MappedItem name="canfam2/chr10.fa" value="29257" />
 267           <MappedItem name="canfam2/chr25.fa" value="16135" />
 268           <MappedItem name="canfam2/chr24.fa" value="18143" />
 269           <MappedItem name="canfam2/chrM.fa" value="1337" />
 270           <MappedItem name="canfam2/chr5.fa" value="35101" />
 271           <MappedItem name="canfam2/chr12.fa" value="19253" />
 272           <MappedItem name="canfam2/chr35.fa" value="10790" />
 273           <MappedItem name="canfam2/chr7.fa" value="25921" />
 274           <MappedItem name="canfam2/chr19.fa" value="11627" />
 275           <MappedItem name="canfam2/chr29.fa" value="8906" />
 276           <MappedItem name="canfam2/chr37.fa" value="9791" />
 277           <MappedItem name="canfam2/chr32.fa" value="7316" />
 278           <MappedItem name="canfam2/chrUn.fa" value="10999" />
 279           <MappedItem name="canfam2/chr14.fa" value="22380" />
 280           <MappedItem name="canfam2/chr13.fa" value="21781" />
 281           <MappedItem name="canfam2/chr30.fa" value="13895" />
 282           <MappedItem name="canfam2/chr16.fa" value="15134" />
 283           <MappedItem name="canfam2/chr17.fa" value="31318" />
 284           <MappedItem name="canfam2/chrX.fa" value="24677" />
 285           <MappedItem name="canfam2/chr2.fa" value="31665" />
 286           <MappedItem name="canfam2/chr9.fa" value="34881" />
 287           <MappedItem name="canfam2/chr20.fa" value="28261" />
 288           <MappedItem name="canfam2/chr6.fa" value="27538" />
 289           <MappedItem name="canfam2/chr11.fa" value="21024" />
 290           <MappedItem name="canfam2/chr23.fa" value="16508" />
 291           <MappedItem name="canfam2/chr22.fa" value="13098" />
 292           <MappedItem name="canfam2/chr27.fa" value="14028" />
 293           <MappedItem name="canfam2/chr33.fa" value="8047" />
 294           <MappedItem name="canfam2/chr36.fa" value="7601" />
 295           <MappedItem name="canfam2/chr31.fa" value="9798" />
 296           <MappedItem name="canfam2/chr8.fa" value="27519" />
 297           <MappedItem name="canfam2/chr34.fa" value="12467" />
 298           <MappedItem name="newcontam_UK.fa" value="291001" />
 299           <MappedItem name="BAC_plus_vector.fa" value="1396" />
 300           <MappedItem name="canfam2/chr21.fa" value="14217" />
 301           <MappedItem name="canfam2/chr26.fa" value="17426" />
 302           <MappedItem name="canfam2/chr1.fa" value="40155" />
 303           <MappedItem name="canfam2/chr4.fa" value="27219" />
 304           <MappedItem name="canfam2/chr28.fa" value="15791" />
 305           <MappedItem name="canfam2/chr18.fa" value="20921" />
 306           <MappedItem name="canfam2/chr38.fa" value="8660" />
 307           <MappedItem name="canfam2/chr3.fa" value="26776" />
 308           <MappedItem name="canfam2/chr15.fa" value="18602" />
 309         </MappedReads>
 310         <MatchCodes>
 311           <Code name="R0" value="85498" />
 312           <Code name="NM" value="5808462" />
 313           <Code name="R2" value="89255" />
 314           <Code name="U1" value="358530" />
 315           <Code name="U0" value="465548" />
 316           <Code name="U2" value="244282" />
 317           <Code name="QC" value="1122557" />
 318           <Code name="RM" value="0" />
 319           <Code name="R1" value="131253" />
 320         </MatchCodes>
 321         <Reads>8305385</Reads>
 322       </ElandLane>
 323       <ElandLane id="3" version="1">
 324         <SampleName>s</SampleName>
 325         <LaneID>3</LaneID>
 326         <GenomeMap>
 327           <GenomeItem name="chr20.fa" value="hg18/chr20.fa" />
 328           <GenomeItem name="chr10_random.fa" value="hg18/chr10_random.fa" />
 329           <GenomeItem name="chr4.fa" value="hg18/chr4.fa" />
 330           <GenomeItem name="chrY.fa" value="hg18/chrY.fa" />
 331           <GenomeItem name="chr4_random.fa" value="hg18/chr4_random.fa" />
 332           <GenomeItem name="chr11_random.fa" value="hg18/chr11_random.fa" />
 333           <GenomeItem name="chr6_random.fa" value="hg18/chr6_random.fa" />
 334           <GenomeItem name="chr6.fa" value="hg18/chr6.fa" />
 335           <GenomeItem name="chrX_random.fa" value="hg18/chrX_random.fa" />
 336           <GenomeItem name="Apetala2.fa" value="Apetala2.fa" />
 337           <GenomeItem name="chr3.fa" value="hg18/chr3.fa" />
 338           <GenomeItem name="chr10.fa" value="hg18/chr10.fa" />
 339           <GenomeItem name="chr15_random.fa" value="hg18/chr15_random.fa" />
 340           <GenomeItem name="chr19.fa" value="hg18/chr19.fa" />
 341           <GenomeItem name="chr22_random.fa" value="hg18/chr22_random.fa" />
 342           <GenomeItem name="OBF5.fa" value="OBF5.fa" />
 343           <GenomeItem name="chr12.fa" value="hg18/chr12.fa" />
 344           <GenomeItem name="EPR-1.fa" value="EPR-1.fa" />
 345           <GenomeItem name="chr1.fa" value="hg18/chr1.fa" />
 346           <GenomeItem name="chr1_random.fa" value="hg18/chr1_random.fa" />
 347           <GenomeItem name="chr16_random.fa" value="hg18/chr16_random.fa" />
 348           <GenomeItem name="chr21.fa" value="hg18/chr21.fa" />
 349           <GenomeItem name="chr2_random.fa" value="hg18/chr2_random.fa" />
 350           <GenomeItem name="chr8.fa" value="hg18/chr8.fa" />
 351           <GenomeItem name="chr8_random.fa" value="hg18/chr8_random.fa" />
 352           <GenomeItem name="chrX.fa" value="hg18/chrX.fa" />
 353           <GenomeItem name="chr17.fa" value="hg18/chr17.fa" />
 354           <GenomeItem name="chr15.fa" value="hg18/chr15.fa" />
 355           <GenomeItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="Lambda-sequence-1-1.--length-=-11936.fa" />
 356           <GenomeItem name="chr7.fa" value="hg18/chr7.fa" />
 357           <GenomeItem name="chr18.fa" value="hg18/chr18.fa" />
 358           <GenomeItem name="chrM.fa" value="hg18/chrM.fa" />
 359           <GenomeItem name="chr21_random.fa" value="hg18/chr21_random.fa" />
 360           <GenomeItem name="chr19_random.fa" value="hg18/chr19_random.fa" />
 361           <GenomeItem name="VATG.fa" value="VATG.fa" />
 362           <GenomeItem name="chr14.fa" value="hg18/chr14.fa" />
 363           <GenomeItem name="chr17_random.fa" value="hg18/chr17_random.fa" />
 364           <GenomeItem name="chr13.fa" value="hg18/chr13.fa" />
 365           <GenomeItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" />
 366           <GenomeItem name="chr11.fa" value="hg18/chr11.fa" />
 367           <GenomeItem name="chr16.fa" value="hg18/chr16.fa" />
 368           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 369           <GenomeItem name="chr9.fa" value="hg18/chr9.fa" />
 370           <GenomeItem name="chr2.fa" value="hg18/chr2.fa" />
 371           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 372           <GenomeItem name="chr18_random.fa" value="hg18/chr18_random.fa" />
 373           <GenomeItem name="chr9_random.fa" value="hg18/chr9_random.fa" />
 374           <GenomeItem name="chr7_random.fa" value="hg18/chr7_random.fa" />
 375           <GenomeItem name="chr5.fa" value="hg18/chr5.fa" />
 376           <GenomeItem name="chr3_random.fa" value="hg18/chr3_random.fa" />
 377           <GenomeItem name="chr5_random.fa" value="hg18/chr5_random.fa" />
 378           <GenomeItem name="PDF.fa" value="PDF.fa" />
 379           <GenomeItem name="chr13_random.fa" value="hg18/chr13_random.fa" />
 380           <GenomeItem name="chr22.fa" value="hg18/chr22.fa" />
 381           <GenomeItem name="AGP.fa" value="AGP.fa" />
 382         </GenomeMap>
 383         <MappedReads>
 384           <MappedItem name="hg18/chr7.fa" value="117975" />
 385           <MappedItem name="hg18/chr17.fa" value="164588" />
 386           <MappedItem name="hg18/chr15_random.fa" value="16" />
 387           <MappedItem name="hg18/chrX_random.fa" value="37" />
 388           <MappedItem name="hg18/chr5_random.fa" value="3" />
 389           <MappedItem name="hg18/chr11.fa" value="162312" />
 390           <MappedItem name="hg18/chr10_random.fa" value="1" />
 391           <MappedItem name="hg18/chrM.fa" value="195939" />
 392           <MappedItem name="hg18/chr18.fa" value="41302" />
 393           <MappedItem name="OBF5.fa" value="19694" />
 394           <MappedItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="701" />
 395           <MappedItem name="EPR-1.fa" value="8" />
 396           <MappedItem name="Apetala2.fa" value="49" />
 397           <MappedItem name="hg18/chr13.fa" value="61916" />
 398           <MappedItem name="hg18/chr21.fa" value="29452" />
 399           <MappedItem name="hg18/chr13_random.fa" value="7" />
 400           <MappedItem name="hg18/chr21_random.fa" value="738" />
 401           <MappedItem name="hg18/chr4.fa" value="95632" />
 402           <MappedItem name="hg18/chr6_random.fa" value="10" />
 403           <MappedItem name="hg18/chr22_random.fa" value="8" />
 404           <MappedItem name="hg18/chr16_random.fa" value="2" />
 405           <MappedItem name="hg18/chr17_random.fa" value="177" />
 406           <MappedItem name="hg18/chr8_random.fa" value="1" />
 407           <MappedItem name="hg18/chr9.fa" value="101134" />
 408           <MappedItem name="hg18/chr2.fa" value="204319" />
 409           <MappedItem name="hg18/chr19.fa" value="138973" />
 410           <MappedItem name="hg18/chr4_random.fa" value="26" />
 411           <MappedItem name="hg18/chr7_random.fa" value="106" />
 412           <MappedItem name="hg18/chr22.fa" value="58352" />
 413           <MappedItem name="hg18/chr12.fa" value="171468" />
 414           <MappedItem name="hg18/chr8.fa" value="95057" />
 415           <MappedItem name="hg18/chr10.fa" value="109113" />
 416           <MappedItem name="hg18/chrY.fa" value="943" />
 417           <MappedItem name="hg18/chr15.fa" value="100694" />
 418           <MappedItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="3" />
 419           <MappedItem name="hg18/chr16.fa" value="99128" />
 420           <MappedItem name="hg18/chr2_random.fa" value="3" />
 421           <MappedItem name="hg18/chr14.fa" value="99959" />
 422           <MappedItem name="newcontam_UK.fa" value="34" />
 423           <MappedItem name="hg18/chr1.fa" value="287927" />
 424           <MappedItem name="BAC_plus_vector.fa" value="106" />
 425           <MappedItem name="hg18/chrX.fa" value="90790" />
 426           <MappedItem name="hg18/chr3.fa" value="171217" />
 427           <MappedItem name="hg18/chr20.fa" value="63909" />
 428           <MappedItem name="VATG.fa" value="1108" />
 429           <MappedItem name="hg18/chr1_random.fa" value="42" />
 430           <MappedItem name="hg18/chr6.fa" value="170063" />
 431           <MappedItem name="hg18/chr3_random.fa" value="1" />
 432           <MappedItem name="hg18/chr9_random.fa" value="14" />
 433           <MappedItem name="hg18/chr5.fa" value="154456" />
 434           <MappedItem name="AGP.fa" value="5" />
 435         </MappedReads>
 436         <MatchCodes>
 437           <Code name="R0" value="337169" />
 438           <Code name="NM" value="7043627" />
 439           <Code name="R2" value="348468" />
 440           <Code name="U1" value="1097126" />
 441           <Code name="U0" value="958773" />
 442           <Code name="U2" value="953619" />
 443           <Code name="QC" value="1482479" />
 444           <Code name="RM" value="0" />
 445           <Code name="R1" value="386670" />
 446         </MatchCodes>
 447         <Reads>12607931</Reads>
 448       </ElandLane>
 449       <ElandLane id="2" version="1">
 450         <SampleName>s</SampleName>
 451         <LaneID>2</LaneID>
 452         <GenomeMap>
 453           <GenomeItem name="chr20.fa" value="equcab1/chr20.fa" />
 454           <GenomeItem name="chr3.fa" value="equcab1/chr3.fa" />
 455           <GenomeItem name="chr4.fa" value="equcab1/chr4.fa" />
 456           <GenomeItem name="chr6.fa" value="equcab1/chr6.fa" />
 457           <GenomeItem name="chr10.fa" value="equcab1/chr10.fa" />
 458           <GenomeItem name="chr19.fa" value="equcab1/chr19.fa" />
 459           <GenomeItem name="chr26.fa" value="equcab1/chr26.fa" />
 460           <GenomeItem name="chr12.fa" value="equcab1/chr12.fa" />
 461           <GenomeItem name="chr1.fa" value="equcab1/chr1.fa" />
 462           <GenomeItem name="chr23.fa" value="equcab1/chr23.fa" />
 463           <GenomeItem name="chr21.fa" value="equcab1/chr21.fa" />
 464           <GenomeItem name="chr8.fa" value="equcab1/chr8.fa" />
 465           <GenomeItem name="chr24.fa" value="equcab1/chr24.fa" />
 466           <GenomeItem name="chrX.fa" value="equcab1/chrX.fa" />
 467           <GenomeItem name="chr30.fa" value="equcab1/chr30.fa" />
 468           <GenomeItem name="chr28.fa" value="equcab1/chr28.fa" />
 469           <GenomeItem name="chr17.fa" value="equcab1/chr17.fa" />
 470           <GenomeItem name="chr15.fa" value="equcab1/chr15.fa" />
 471           <GenomeItem name="chr7.fa" value="equcab1/chr7.fa" />
 472           <GenomeItem name="chr18.fa" value="equcab1/chr18.fa" />
 473           <GenomeItem name="chrM.fa" value="equcab1/chrM.fa" />
 474           <GenomeItem name="chr31.fa" value="equcab1/chr31.fa" />
 475           <GenomeItem name="chr25.fa" value="equcab1/chr25.fa" />
 476           <GenomeItem name="chrUn.fa" value="equcab1/chrUn.fa" />
 477           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 478           <GenomeItem name="chr13.fa" value="equcab1/chr13.fa" />
 479           <GenomeItem name="chr27.fa" value="equcab1/chr27.fa" />
 480           <GenomeItem name="chr11.fa" value="equcab1/chr11.fa" />
 481           <GenomeItem name="chr16.fa" value="equcab1/chr16.fa" />
 482           <GenomeItem name="chr14.fa" value="equcab1/chr14.fa" />
 483           <GenomeItem name="chr9.fa" value="equcab1/chr9.fa" />
 484           <GenomeItem name="chr2.fa" value="equcab1/chr2.fa" />
 485           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 486           <GenomeItem name="chr5.fa" value="equcab1/chr5.fa" />
 487           <GenomeItem name="chr22.fa" value="equcab1/chr22.fa" />
 488           <GenomeItem name="chr29.fa" value="equcab1/chr29.fa" />
 489         </GenomeMap>
 490         <MappedReads>
 491           <MappedItem name="equcab1/chr29.fa" value="3477" />
 492           <MappedItem name="equcab1/chr19.fa" value="5877" />
 493           <MappedItem name="equcab1/chr1.fa" value="19106" />
 494           <MappedItem name="equcab1/chr15.fa" value="8959" />
 495           <MappedItem name="equcab1/chrX.fa" value="2711" />
 496           <MappedItem name="equcab1/chr13.fa" value="2369" />
 497           <MappedItem name="equcab1/chr4.fa" value="8773" />
 498           <MappedItem name="equcab1/chr20.fa" value="6009" />
 499           <MappedItem name="equcab1/chr26.fa" value="3634" />
 500           <MappedItem name="equcab1/chr3.fa" value="10735" />
 501           <MappedItem name="equcab1/chr6.fa" value="8951" />
 502           <MappedItem name="equcab1/chr7.fa" value="8640" />
 503           <MappedItem name="equcab1/chr30.fa" value="1838" />
 504           <MappedItem name="equcab1/chr18.fa" value="5345" />
 505           <MappedItem name="equcab1/chr8.fa" value="9190" />
 506           <MappedItem name="equcab1/chr24.fa" value="5158" />
 507           <MappedItem name="equcab1/chr17.fa" value="6443" />
 508           <MappedItem name="equcab1/chr23.fa" value="3805" />
 509           <MappedItem name="equcab1/chr28.fa" value="4860" />
 510           <MappedItem name="equcab1/chrUn.fa" value="43941" />
 511           <MappedItem name="equcab1/chr12.fa" value="2961" />
 512           <MappedItem name="equcab1/chr2.fa" value="11605" />
 513           <MappedItem name="equcab1/chr9.fa" value="7042" />
 514           <MappedItem name="equcab1/chr11.fa" value="8124" />
 515           <MappedItem name="equcab1/chr14.fa" value="9885" />
 516           <MappedItem name="equcab1/chr16.fa" value="9479" />
 517           <MappedItem name="equcab1/chrM.fa" value="58" />
 518           <MappedItem name="equcab1/chr31.fa" value="2826" />
 519           <MappedItem name="newcontam_UK.fa" value="378598" />
 520           <MappedItem name="equcab1/chr25.fa" value="4883" />
 521           <MappedItem name="equcab1/chr22.fa" value="6565" />
 522           <MappedItem name="BAC_plus_vector.fa" value="687" />
 523           <MappedItem name="equcab1/chr27.fa" value="3240" />
 524           <MappedItem name="equcab1/chr21.fa" value="4781" />
 525           <MappedItem name="equcab1/chr10.fa" value="8299" />
 526           <MappedItem name="equcab1/chr5.fa" value="7383" />
 527         </MappedReads>
 528         <MatchCodes>
 529           <Code name="R0" value="35424" />
 530           <Code name="NM" value="7290197" />
 531           <Code name="R2" value="87472" />
 532           <Code name="U1" value="217832" />
 533           <Code name="U0" value="246856" />
 534           <Code name="U2" value="171549" />
 535           <Code name="QC" value="1456243" />
 536           <Code name="RM" value="0" />
 537           <Code name="R1" value="93723" />
 538         </MatchCodes>
 539         <Reads>9599296</Reads>
 540       </ElandLane>
 541       <ElandLane id="5" version="1">
 542         <SampleName>s</SampleName>
 543         <LaneID>5</LaneID>
 544         <GenomeMap>
 545           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 546           <GenomeItem name="strPur2.fa" value="strpur2/strPur2.fa" />
 547           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 548         </GenomeMap>
 549         <MappedReads>
 550           <MappedItem name="strpur2/strPur2.fa" value="48599" />
 551           <MappedItem name="BAC_plus_vector.fa" value="86173" />
 552           <MappedItem name="newcontam_UK.fa" value="4811" />
 553         </MappedReads>
 554         <MatchCodes>
 555           <Code name="R0" value="25456" />
 556           <Code name="NM" value="8637432" />
 557           <Code name="R2" value="11528" />
 558           <Code name="U1" value="44902" />
 559           <Code name="U0" value="58232" />
 560           <Code name="U2" value="36449" />
 561           <Code name="QC" value="482671" />
 562           <Code name="RM" value="0" />
 563           <Code name="R1" value="12299" />
 564         </MatchCodes>
 565         <Reads>9308969</Reads>
 566       </ElandLane>
 567       <ElandLane id="4" version="1">
 568         <SampleName>s</SampleName>
 569         <LaneID>4</LaneID>
 570         <GenomeMap>
 571           <GenomeItem name="chr20.fa" value="hg18/chr20.fa" />
 572           <GenomeItem name="chr10_random.fa" value="hg18/chr10_random.fa" />
 573           <GenomeItem name="chr4.fa" value="hg18/chr4.fa" />
 574           <GenomeItem name="chrY.fa" value="hg18/chrY.fa" />
 575           <GenomeItem name="chr4_random.fa" value="hg18/chr4_random.fa" />
 576           <GenomeItem name="chr11_random.fa" value="hg18/chr11_random.fa" />
 577           <GenomeItem name="chr6_random.fa" value="hg18/chr6_random.fa" />
 578           <GenomeItem name="chr6.fa" value="hg18/chr6.fa" />
 579           <GenomeItem name="chrX_random.fa" value="hg18/chrX_random.fa" />
 580           <GenomeItem name="Apetala2.fa" value="Apetala2.fa" />
 581           <GenomeItem name="chr3.fa" value="hg18/chr3.fa" />
 582           <GenomeItem name="chr10.fa" value="hg18/chr10.fa" />
 583           <GenomeItem name="chr15_random.fa" value="hg18/chr15_random.fa" />
 584           <GenomeItem name="chr19.fa" value="hg18/chr19.fa" />
 585           <GenomeItem name="chr22_random.fa" value="hg18/chr22_random.fa" />
 586           <GenomeItem name="OBF5.fa" value="OBF5.fa" />
 587           <GenomeItem name="chr12.fa" value="hg18/chr12.fa" />
 588           <GenomeItem name="EPR-1.fa" value="EPR-1.fa" />
 589           <GenomeItem name="chr1.fa" value="hg18/chr1.fa" />
 590           <GenomeItem name="chr1_random.fa" value="hg18/chr1_random.fa" />
 591           <GenomeItem name="chr16_random.fa" value="hg18/chr16_random.fa" />
 592           <GenomeItem name="chr21.fa" value="hg18/chr21.fa" />
 593           <GenomeItem name="chr2_random.fa" value="hg18/chr2_random.fa" />
 594           <GenomeItem name="chr8.fa" value="hg18/chr8.fa" />
 595           <GenomeItem name="chr8_random.fa" value="hg18/chr8_random.fa" />
 596           <GenomeItem name="chrX.fa" value="hg18/chrX.fa" />
 597           <GenomeItem name="chr17.fa" value="hg18/chr17.fa" />
 598           <GenomeItem name="chr15.fa" value="hg18/chr15.fa" />
 599           <GenomeItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="Lambda-sequence-1-1.--length-=-11936.fa" />
 600           <GenomeItem name="chr7.fa" value="hg18/chr7.fa" />
 601           <GenomeItem name="chr18.fa" value="hg18/chr18.fa" />
 602           <GenomeItem name="chrM.fa" value="hg18/chrM.fa" />
 603           <GenomeItem name="chr21_random.fa" value="hg18/chr21_random.fa" />
 604           <GenomeItem name="chr19_random.fa" value="hg18/chr19_random.fa" />
 605           <GenomeItem name="VATG.fa" value="VATG.fa" />
 606           <GenomeItem name="chr14.fa" value="hg18/chr14.fa" />
 607           <GenomeItem name="chr17_random.fa" value="hg18/chr17_random.fa" />
 608           <GenomeItem name="chr13.fa" value="hg18/chr13.fa" />
 609           <GenomeItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" />
 610           <GenomeItem name="chr11.fa" value="hg18/chr11.fa" />
 611           <GenomeItem name="chr16.fa" value="hg18/chr16.fa" />
 612           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 613           <GenomeItem name="chr9.fa" value="hg18/chr9.fa" />
 614           <GenomeItem name="chr2.fa" value="hg18/chr2.fa" />
 615           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 616           <GenomeItem name="chr18_random.fa" value="hg18/chr18_random.fa" />
 617           <GenomeItem name="chr9_random.fa" value="hg18/chr9_random.fa" />
 618           <GenomeItem name="chr7_random.fa" value="hg18/chr7_random.fa" />
 619           <GenomeItem name="chr5.fa" value="hg18/chr5.fa" />
 620           <GenomeItem name="chr3_random.fa" value="hg18/chr3_random.fa" />
 621           <GenomeItem name="chr5_random.fa" value="hg18/chr5_random.fa" />
 622           <GenomeItem name="PDF.fa" value="PDF.fa" />
 623           <GenomeItem name="chr13_random.fa" value="hg18/chr13_random.fa" />
 624           <GenomeItem name="chr22.fa" value="hg18/chr22.fa" />
 625           <GenomeItem name="AGP.fa" value="AGP.fa" />
 626         </GenomeMap>
 627         <MappedReads>
 628           <MappedItem name="hg18/chr7.fa" value="159684" />
 629           <MappedItem name="hg18/chr17.fa" value="171017" />
 630           <MappedItem name="hg18/chr22_random.fa" value="29" />
 631           <MappedItem name="hg18/chrX_random.fa" value="18" />
 632           <MappedItem name="hg18/chr5_random.fa" value="9" />
 633           <MappedItem name="hg18/chr11.fa" value="182860" />
 634           <MappedItem name="hg18/chr10_random.fa" value="2" />
 635           <MappedItem name="hg18/chrM.fa" value="221083" />
 636           <MappedItem name="hg18/chr18.fa" value="42295" />
 637           <MappedItem name="OBF5.fa" value="19911" />
 638           <MappedItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="710" />
 639           <MappedItem name="EPR-1.fa" value="7" />
 640           <MappedItem name="Apetala2.fa" value="46" />
 641           <MappedItem name="hg18/chr13.fa" value="39566" />
 642           <MappedItem name="hg18/chr21.fa" value="36381" />
 643           <MappedItem name="hg18/chr13_random.fa" value="84" />
 644           <MappedItem name="hg18/chr21_random.fa" value="1022" />
 645           <MappedItem name="hg18/chr4.fa" value="104306" />
 646           <MappedItem name="hg18/chr6_random.fa" value="22" />
 647           <MappedItem name="hg18/chr16_random.fa" value="8" />
 648           <MappedItem name="hg18/chr17_random.fa" value="104" />
 649           <MappedItem name="hg18/chr8_random.fa" value="1" />
 650           <MappedItem name="hg18/chr9.fa" value="100436" />
 651           <MappedItem name="hg18/chr2.fa" value="212111" />
 652           <MappedItem name="hg18/chr19.fa" value="146631" />
 653           <MappedItem name="hg18/chr4_random.fa" value="345" />
 654           <MappedItem name="hg18/chr7_random.fa" value="587" />
 655           <MappedItem name="hg18/chr22.fa" value="65577" />
 656           <MappedItem name="hg18/chr15_random.fa" value="22" />
 657           <MappedItem name="hg18/chr12.fa" value="176515" />
 658           <MappedItem name="hg18/chr8.fa" value="99621" />
 659           <MappedItem name="hg18/chr10.fa" value="118216" />
 660           <MappedItem name="hg18/chrY.fa" value="1158" />
 661           <MappedItem name="hg18/chr15.fa" value="92333" />
 662           <MappedItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="3" />
 663           <MappedItem name="hg18/chr16.fa" value="110237" />
 664           <MappedItem name="hg18/chr14.fa" value="74253" />
 665           <MappedItem name="newcontam_UK.fa" value="78" />
 666           <MappedItem name="hg18/chr19_random.fa" value="3" />
 667           <MappedItem name="hg18/chr1.fa" value="366404" />
 668           <MappedItem name="BAC_plus_vector.fa" value="18" />
 669           <MappedItem name="hg18/chrX.fa" value="101675" />
 670           <MappedItem name="hg18/chr3.fa" value="163755" />
 671           <MappedItem name="hg18/chr20.fa" value="67691" />
 672           <MappedItem name="VATG.fa" value="1164" />
 673           <MappedItem name="hg18/chr1_random.fa" value="54" />
 674           <MappedItem name="hg18/chr6.fa" value="190720" />
 675           <MappedItem name="hg18/chr9_random.fa" value="186" />
 676           <MappedItem name="hg18/chr5.fa" value="161049" />
 677           <MappedItem name="AGP.fa" value="1" />
 678         </MappedReads>
 679         <MatchCodes>
 680           <Code name="R0" value="449286" />
 681           <Code name="NM" value="7840273" />
 682           <Code name="R2" value="277380" />
 683           <Code name="U1" value="1063696" />
 684           <Code name="U0" value="1343130" />
 685           <Code name="U2" value="823182" />
 686           <Code name="QC" value="1553370" />
 687           <Code name="RM" value="0" />
 688           <Code name="R1" value="359163" />
 689         </MatchCodes>
 690         <Reads>13709480</Reads>
 691       </ElandLane>
 692       <ElandLane id="7" version="1">
 693         <SampleName>s</SampleName>
 694         <LaneID>7</LaneID>
 695         <GenomeMap>
 696           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 697           <GenomeItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="Lambda-sequence-1-1.--length-=-11936.fa" />
 698           <GenomeItem name="chrX.fa" value="elegans170/chrX.fa" />
 699           <GenomeItem name="chrm.fa" value="elegans170/chrm.fa" />
 700           <GenomeItem name="chrV.fa" value="elegans170/chrV.fa" />
 701           <GenomeItem name="chrII.fa" value="elegans170/chrII.fa" />
 702           <GenomeItem name="Apetala2.fa" value="Apetala2.fa" />
 703           <GenomeItem name="PDF.fa" value="PDF.fa" />
 704           <GenomeItem name="chrIII.fa" value="elegans170/chrIII.fa" />
 705           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 706           <GenomeItem name="VATG.fa" value="VATG.fa" />
 707           <GenomeItem name="chrI.fa" value="elegans170/chrI.fa" />
 708           <GenomeItem name="chrIV.fa" value="elegans170/chrIV.fa" />
 709           <GenomeItem name="OBF5.fa" value="OBF5.fa" />
 710           <GenomeItem name="EPR-1.fa" value="EPR-1.fa" />
 711           <GenomeItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" />
 712           <GenomeItem name="AGP.fa" value="AGP.fa" />
 713         </GenomeMap>
 714         <MappedReads>
 715           <MappedItem name="elegans170/chrX.fa" value="158885" />
 716           <MappedItem name="newcontam_UK.fa" value="374301" />
 717           <MappedItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="7" />
 718           <MappedItem name="BAC_plus_vector.fa" value="544" />
 719           <MappedItem name="elegans170/chrV.fa" value="188118" />
 720           <MappedItem name="elegans170/chrm.fa" value="335" />
 721           <MappedItem name="elegans170/chrIV.fa" value="169430" />
 722           <MappedItem name="elegans170/chrI.fa" value="184814" />
 723           <MappedItem name="elegans170/chrII.fa" value="164709" />
 724           <MappedItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="3" />
 725           <MappedItem name="elegans170/chrIII.fa" value="174952" />
 726         </MappedReads>
 727         <MatchCodes>
 728           <Code name="R0" value="32042" />
 729           <Code name="NM" value="10820174" />
 730           <Code name="R2" value="43465" />
 731           <Code name="U1" value="522658" />
 732           <Code name="U0" value="413309" />
 733           <Code name="U2" value="480131" />
 734           <Code name="QC" value="944609" />
 735           <Code name="RM" value="0" />
 736           <Code name="R1" value="38077" />
 737         </MatchCodes>
 738         <Reads>13294465</Reads>
 739       </ElandLane>
 740       <ElandLane id="6" version="1">
 741         <SampleName>s</SampleName>
 742         <LaneID>6</LaneID>
 743         <GenomeMap>
 744           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 745           <GenomeItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="Lambda-sequence-1-1.--length-=-11936.fa" />
 746           <GenomeItem name="chrX.fa" value="elegans170/chrX.fa" />
 747           <GenomeItem name="chrm.fa" value="elegans170/chrm.fa" />
 748           <GenomeItem name="chrV.fa" value="elegans170/chrV.fa" />
 749           <GenomeItem name="chrII.fa" value="elegans170/chrII.fa" />
 750           <GenomeItem name="Apetala2.fa" value="Apetala2.fa" />
 751           <GenomeItem name="PDF.fa" value="PDF.fa" />
 752           <GenomeItem name="chrIII.fa" value="elegans170/chrIII.fa" />
 753           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 754           <GenomeItem name="VATG.fa" value="VATG.fa" />
 755           <GenomeItem name="chrI.fa" value="elegans170/chrI.fa" />
 756           <GenomeItem name="chrIV.fa" value="elegans170/chrIV.fa" />
 757           <GenomeItem name="OBF5.fa" value="OBF5.fa" />
 758           <GenomeItem name="EPR-1.fa" value="EPR-1.fa" />
 759           <GenomeItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" />
 760           <GenomeItem name="AGP.fa" value="AGP.fa" />
 761         </GenomeMap>
 762         <MappedReads>
 763           <MappedItem name="elegans170/chrX.fa" value="84643" />
 764           <MappedItem name="newcontam_UK.fa" value="12553" />
 765           <MappedItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="17085" />
 766           <MappedItem name="BAC_plus_vector.fa" value="67778" />
 767           <MappedItem name="elegans170/chrV.fa" value="103998" />
 768           <MappedItem name="elegans170/chrm.fa" value="46" />
 769           <MappedItem name="elegans170/chrIV.fa" value="166323" />
 770           <MappedItem name="elegans170/chrI.fa" value="191515" />
 771           <MappedItem name="elegans170/chrII.fa" value="99396" />
 772           <MappedItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="14057" />
 773           <MappedItem name="elegans170/chrIII.fa" value="148865" />
 774         </MappedReads>
 775         <MatchCodes>
 776           <Code name="R0" value="32337" />
 777           <Code name="NM" value="7238860" />
 778           <Code name="R2" value="104357" />
 779           <Code name="U1" value="328165" />
 780           <Code name="U0" value="203188" />
 781           <Code name="U2" value="374906" />
 782           <Code name="QC" value="588784" />
 783           <Code name="RM" value="0" />
 784           <Code name="R1" value="55854" />
 785         </MatchCodes>
 786         <Reads>8926451</Reads>
 787       </ElandLane>
 788       <ElandLane id="8" version="1">
 789         <SampleName>s</SampleName>
 790         <LaneID>8</LaneID>
 791         <GenomeMap>
 792           <GenomeItem name="newcontam_UK.fa" value="newcontam_UK.fa" />
 793           <GenomeItem name="Lambda-sequence-1-1.--length-=-11936.fa" value="Lambda-sequence-1-1.--length-=-11936.fa" />
 794           <GenomeItem name="chrX.fa" value="elegans170/chrX.fa" />
 795           <GenomeItem name="chrm.fa" value="elegans170/chrm.fa" />
 796           <GenomeItem name="chrV.fa" value="elegans170/chrV.fa" />
 797           <GenomeItem name="chrII.fa" value="elegans170/chrII.fa" />
 798           <GenomeItem name="Apetala2.fa" value="Apetala2.fa" />
 799           <GenomeItem name="PDF.fa" value="PDF.fa" />
 800           <GenomeItem name="chrIII.fa" value="elegans170/chrIII.fa" />
 801           <GenomeItem name="BAC_plus_vector.fa" value="BAC_plus_vector.fa" />
 802           <GenomeItem name="VATG.fa" value="VATG.fa" />
 803           <GenomeItem name="chrI.fa" value="elegans170/chrI.fa" />
 804           <GenomeItem name="chrIV.fa" value="elegans170/chrIV.fa" />
 805           <GenomeItem name="OBF5.fa" value="OBF5.fa" />
 806           <GenomeItem name="EPR-1.fa" value="EPR-1.fa" />
 807           <GenomeItem name="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" value="Lambda-sequence-2,3-2.-length-=-9786nts-.fa" />
 808           <GenomeItem name="AGP.fa" value="AGP.fa" />
 809         </GenomeMap>
 810         <MappedReads>
 811           <MappedItem name="elegans170/chrX.fa" value="970545" />
 812           <MappedItem name="newcontam_UK.fa" value="26971" />
 813           <MappedItem name="BAC_plus_vector.fa" value="150" />
 814           <MappedItem name="elegans170/chrV.fa" value="1090880" />
 815           <MappedItem name="elegans170/chrm.fa" value="11651" />
 816           <MappedItem name="elegans170/chrIV.fa" value="859262" />
 817           <MappedItem name="elegans170/chrI.fa" value="870480" />
 818           <MappedItem name="elegans170/chrII.fa" value="835119" />
 819           <MappedItem name="elegans170/chrIII.fa" value="747421" />
 820         </MappedReads>
 821         <MatchCodes>
 822           <Code name="R0" value="420530" />
 823           <Code name="NM" value="5019224" />
 824           <Code name="R2" value="171357" />
 825           <Code name="U1" value="1529191" />
 826           <Code name="U0" value="2960409" />
 827           <Code name="U2" value="922879" />
 828           <Code name="QC" value="457936" />
 829           <Code name="RM" value="0" />
 830           <Code name="R1" value="255660" />
 831         </MatchCodes>
 832         <Reads>11737186</Reads>
 833       </ElandLane>
 834     </ElandCollection>
 835   </Gerald>
 836 </PipelineRun>