<?xml version="1.0" encoding="UTF-8"?>
<!--$Id: assay_submission_failure_codes.xml,v 1.11 2004/03/23 11:57:11 mummi Exp $-->
<assay_submission lsid="urn:lsid:dcc.hapmap.cshl.org:Batch:2343200:1"
  xmlns="http://www.hapmap.org"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
    xsi:schemaLocation="http://www.hapmap.org http://www.hapmap.org/xml-schema/2003-11-04/hapmap.xsd">
  <batch_info>
    <class>NEW</class>
    <date_created>2003-09-23</date_created>
    <contact>
      <name>mummi</name>
      <email>mummi@cshl.org</email>
    </contact>
    <comment> This a test submission file that has valid XML and consistent
      assay data, but the assays have been flagged as failed. This file should
      pass the upload-processing tests, get imported into the tracking database,
      but should not get into the main database because of the fail flags. Last
      updated: $Date: 2004/03/23 11:57:11 $</comment>
  </batch_info>
  <assays>
    <assay lsid="urn:lsid:illumina.hapmap.org:Assay:failcode_1:1">
      <snp_assayed lsid="urn:LSID:ncbi.nlm.nih.gov:dbSNP;refSNP:rs1455353:88"/>
      <protocol_used lsid="urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_assay_design_1.0.0:1"/>
      <batch type="multiplex-pool">pool-13_2003-02-11</batch>
      <status>
        <fail code="1">assay design failure</fail>
      </status>
      <input_parameters>
        <beadarray_platform>
          <seq_for_oligo_design>ATAGGCATATTCCCTGTGCTTCAGGATCCCGTCCAACAATAAGGACCCATTAACACACACACATGACAGACGCAACTGGCCAATTTTTTAAGTCTAATCTGAAAAGCATTCTTGATTGCC[C/T]GCTAGCATAAAGAATCCCCTTTAAACTCTGTATCAAACAAGACAATACCAAAAAGCTACTCATAAAATCATATATACTATTCAATTCCCAATATATATAAAATTAAATATGAAAA</seq_for_oligo_design>
        </beadarray_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <beadarray_platform>
          <allele1_combined_seq>ACTTCGTCAGTAACGGACTCTGAAAAGCATTCTTGATTGCCT</allele1_combined_seq>
          <allele2_combined_seq>GAGTCGAGGTCATATCGTTCTGAAAAGCATTCTTGATTGCCC</allele2_combined_seq>
          <common_combined_seq>CTAGCATAAAGAATCCCCTTTAACTCAATCTTTGCGAGACACGTCGGTCTGCCTATAGTGAGTC</common_combined_seq>
          <illumina_strand>bottom</illumina_strand>
        </beadarray_platform>
      </output_design>
    </assay>
    <assay lsid="urn:lsid:illumina.hapmap.org:Assay:failcode_2:1">
      <snp_assayed lsid="urn:LSID:ncbi.nlm.nih.gov:dbSNP;refSNP:rs1455353:88"/>
      <protocol_used lsid="urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_assay_design_1.0.0:1"/>
      <batch type="multiplex-pool">pool-13_2003-02-11</batch>
      <status>
        <fail code="2">polymorphic flanking sequence</fail>
      </status>
      <input_parameters>
        <beadarray_platform>
          <seq_for_oligo_design>ATAGGCATATTCCCTGTGCTTCAGGATCCCGTCCAACAATAAGGACCCATTAACACACACACATGACAGACGCAACTGGCCAATTTTTTAAGTCTAATCTGAAAAGCATTCTTGATTGCC[C/T]GCTAGCATAAAGAATCCCCTTTAAACTCTGTATCAAACAAGACAATACCAAAAAGCTACTCATAAAATCATATATACTATTCAATTCCCAATATATATAAAATTAAATATGAAAA</seq_for_oligo_design>
        </beadarray_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <beadarray_platform>
          <allele1_combined_seq>ACTTCGTCAGTAACGGACTCTGAAAAGCATTCTTGATTGCCT</allele1_combined_seq>
          <allele2_combined_seq>GAGTCGAGGTCATATCGTTCTGAAAAGCATTCTTGATTGCCC</allele2_combined_seq>
          <common_combined_seq>CTAGCATAAAGAATCCCCTTTAACTCAATCTTTGCGAGACACGTCGGTCTGCCTATAGTGAGTC</common_combined_seq>
          <illumina_strand>bottom</illumina_strand>
        </beadarray_platform>
      </output_design>
    </assay>
    <assay lsid="urn:lsid:illumina.hapmap.org:Assay:failcode_0:1">
      <snp_assayed lsid="urn:LSID:ncbi.nlm.nih.gov:dbSNP;refSNP:rs1455353:88"/>
      <protocol_used lsid="urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_assay_design_1.0.0:1"/>
      <batch type="multiplex-pool">pool-13_2003-02-11</batch>
      <status>
        <fail code="0">not specified</fail>
      </status>
      <input_parameters>
        <beadarray_platform>
          <seq_for_oligo_design>ATAGGCATATTCCCTGTGCTTCAGGATCCCGTCCAACAATAAGGACCCATTAACACACACACATGACAGACGCAACTGGCCAATTTTTTAAGTCTAATCTGAAAAGCATTCTTGATTGCC[C/T]GCTAGCATAAAGAATCCCCTTTAAACTCTGTATCAAACAAGACAATACCAAAAAGCTACTCATAAAATCATATATACTATTCAATTCCCAATATATATAAAATTAAATATGAAAA</seq_for_oligo_design>
        </beadarray_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <beadarray_platform>
          <allele1_combined_seq>ACTTCGTCAGTAACGGACTCTGAAAAGCATTCTTGATTGCCT</allele1_combined_seq>
          <allele2_combined_seq>GAGTCGAGGTCATATCGTTCTGAAAAGCATTCTTGATTGCCC</allele2_combined_seq>
          <common_combined_seq>CTAGCATAAAGAATCCCCTTTAACTCAATCTTTGCGAGACACGTCGGTCTGCCTATAGTGAGTC</common_combined_seq>
          <illumina_strand>bottom</illumina_strand>
        </beadarray_platform>
      </output_design>
    </assay>
  </assays>
</assay_submission>
