<?xml version="1.0" encoding="UTF-8"?>
<!--$Id: assay_submission_data-inconsistencies.xml,v 1.7 2004/03/23 11:57:11 mummi Exp $ -->
<assay_submission 
    lsid="urn:lsid:dcc.hapmap.cshl.org:Batch:29432:1" 
    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>2003-09-14</date_created>
        <contact>
            <name>mummi</name>
            <email>mummi@cshl.org</email>
        </contact>
        <comment> This is a test submission datafile that is well-formed and schema-valid and does
            not violate db-constraints, thus it should get imported into the tracking database.
            However, each record has some kind of consistency problem, e.g. strand discrepancy or
            oligos that don't align to the original SNP sequence and therefore will fail in the consistency
            test suite. Last updated: $Date: 2003/10/15
            11:05:13 $ </comment>
    </batch_info>
    <assays>

<!-- assay with an invalid SNP reference -->
    <assay lsid="urn:lsid:wicgr.hapmap.org:Assay:inconsistent_bad_snpref:1">
      <snp_assayed lsid="urn:lsid:ncbi.nlm.nih.gov:dbSNP;refSNP:invalid_snpref:199"/>
      <protocol_used lsid="urn:lsid:wicgr.hapmap.org:Protocol:assay_design_1:1"/>
      <batch type="multiplex-pool">batch_2003-02-11</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <sequenom_platform>
          <seq_for_oligo_design>tgaaaNtgcctttgtaagactaatgaaaaatgacaagattaggctatgggaggtgcctttcatagcatgcctttctataattgtttactgcaccagaagtcacaagatttgtgactctcccaactgatcctatagataacatcatattgtagaatctaagattggtcttttgagatgtgtttcaaacctttgcattctagtgactgactgactccacctggatttgtgcctcatgattcagcccatcctgtggtcccatctagaggcagactcagctcatgcataaggatagttttccctatgatttaattccccaacgaatcagcagcacacattccctagccccactgcctgccaaccctagcctgtgagttctcagggaggctgatttgagtaataaactccatctacNacttggctagcaNtgcattaattaagctctttatttGCTaaatttcagttagttcagaggaataagttcaagagatctattgtacattatggtgattatagttaataacatatattgtataattgaaaattgctgagagtatattttaagtgcaaaatataagcatgtgaggtgattcatatgctaattagcttgatttagccagcccacaatgtatatatatatcataacatcatgctgtatctcatgaacatatacaatttttatctgtcaattaagaagaaTTAAAATAAATAAATCTGTAATTTCATTGACCATTTCTCACAGGTTGTTTTAAAGCATAAGTTAAGGTGATCAACATATTCTTCTCTTTGTTATACTTTTCCCTACTTGATATATTAGTGAGAATATTAATTATCACCTCATTCTCAATGACTAGGTTAATTACTACAATTATTTTAACTAATATAACTTTAAATACTACTNTAGAGTTTCTACTCTTAGTATGCTTTATTTGTGGATAAACACTTTTAGTTATCTAGGTACATTTTTATGGCACTTGGATTTGATGGGAATAAAAAGAAATTA[T/G]CCTGATCTAAATCTTTAGTCTTTCTTTGTATTCTCCATATATTAGTCATGGTTTCCATGTTGTTGAATTGTCCTTTTTTGGAGTTAACATGCCTGATTTCTGTTTACATTGGCCAATAAGAGGATGTAGAACTGCAGCTGGTATTTAATTCTAATTATTTGCATTTTTCAATAACATTTATTTCAGAAAAATTTTTCAAGATTATTTTTTGCTAAGCACAAGATATTTGCTATTCTGTACCATGTTCCCTAAAAGCATAATGCTAATAGAAATCTGCACCTTGattaatttttatattaaaaaaCAAGTggctaggcacagtggctcacatctgtaatcccaacactttgggaggctgaggtgggtgatcacttgaggtgaggagttcaagaccagcctagccaacatggtgaaaccctatctccactaaaaatacaaaaattagctgggcatggttgtgcacgcctgtaatcccGGGCAACAGAGCAAGACTCTGTTTCAAAAAACA</seq_for_oligo_design>
        </sequenom_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <sequenom_platform>
          <pcr_primer_forward>ATGGCACTTGGATTTGATGG</pcr_primer_forward>
          <pcr_primer_reverse>ACAACATGGAAACCATGACT</pcr_primer_reverse>
          <extension_probe>GAAAGACTAAAGATTTAGATCAGG</extension_probe>
        </sequenom_platform>
      </output_design>
    </assay>

<!-- assay with primary oligo strand vs. assay strand discrepancy-->
    <assay lsid="urn:lsid:wicgr.hapmap.org:Assay:inconsistent_bad_poligo_strand:1">
      <snp_assayed lsid="urn:lsid:ncbi.nlm.nih.gov:dbSNP;refSNP:rs1528272:88"/>
      <protocol_used lsid="urn:lsid:wicgr.hapmap.org:Protocol:assay_design_1:1"/>
      <batch type="multiplex-pool">batch_2003-02-11</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <sequenom_platform>
          <seq_for_oligo_design>tgaaaNtgcctttgtaagactaatgaaaaatgacaagattaggctatgggaggtgcctttcatagcatgcctttctataattgtttactgcaccagaagtcacaagatttgtgactctcccaactgatcctatagataacatcatattgtagaatctaagattggtcttttgagatgtgtttcaaacctttgcattctagtgactgactgactccacctggatttgtgcctcatgattcagcccatcctgtggtcccatctagaggcagactcagctcatgcataaggatagttttccctatgatttaattccccaacgaatcagcagcacacattccctagccccactgcctgccaaccctagcctgtgagttctcagggaggctgatttgagtaataaactccatctacNacttggctagcaNtgcattaattaagctctttatttGCTaaatttcagttagttcagaggaataagttcaagagatctattgtacattatggtgattatagttaataacatatattgtataattgaaaattgctgagagtatattttaagtgcaaaatataagcatgtgaggtgattcatatgctaattagcttgatttagccagcccacaatgtatatatatatcataacatcatgctgtatctcatgaacatatacaatttttatctgtcaattaagaagaaTTAAAATAAATAAATCTGTAATTTCATTGACCATTTCTCACAGGTTGTTTTAAAGCATAAGTTAAGGTGATCAACATATTCTTCTCTTTGTTATACTTTTCCCTACTTGATATATTAGTGAGAATATTAATTATCACCTCATTCTCAATGACTAGGTTAATTACTACAATTATTTTAACTAATATAACTTTAAATACTACTNTAGAGTTTCTACTCTTAGTATGCTTTATTTGTGGATAAACACTTTTAGTTATCTAGGTACATTTTTATGGCACTTGGATTTGATGGGAATAAAAAGAAATTA[T/G]CCTGATCTAAATCTTTAGTCTTTCTTTGTATTCTCCATATATTAGTCATGGTTTCCATGTTGTTGAATTGTCCTTTTTTGGAGTTAACATGCCTGATTTCTGTTTACATTGGCCAATAAGAGGATGTAGAACTGCAGCTGGTATTTAATTCTAATTATTTGCATTTTTCAATAACATTTATTTCAGAAAAATTTTTCAAGATTATTTTTTGCTAAGCACAAGATATTTGCTATTCTGTACCATGTTCCCTAAAAGCATAATGCTAATAGAAATCTGCACCTTGattaatttttatattaaaaaaCAAGTggctaggcacagtggctcacatctgtaatcccaacactttgggaggctgaggtgggtgatcacttgaggtgaggagttcaagaccagcctagccaacatggtgaaaccctatctccactaaaaatacaaaaattagctgggcatggttgtgcacgcctgtaatcccGGGCAACAGAGCAAGACTCTGTTTCAAAAAACA</seq_for_oligo_design>
        </sequenom_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <sequenom_platform>
          <pcr_primer_forward>ATGGCACTTGGATTTGATGG</pcr_primer_forward>
          <pcr_primer_reverse>ACAACATGGAAACCATGACT</pcr_primer_reverse>
          <extension_probe>GAAAGACTAAAGATTTAGATCAGG</extension_probe>
        </sequenom_platform>
      </output_design>
    </assay>

    <!-- assay with oligo(s) not mapping to the SNP sequence-->
        <assay lsid="urn:lsid:illumina.hapmap.org:Assay:inconsistent_bad_oligos: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>
                <pass/>
            </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>ATTTAGATTTTTTATTCCCGCGGGGGGG</allele1_combined_seq>
                    <allele2_combined_seq>AAAAAATTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT</allele2_combined_seq>
                    <common_combined_seq>CACACACAACCCCCCCCCCCCCCCTTTTTTTTTTTTTTT</common_combined_seq>
                    <illumina_strand>bottom</illumina_strand>
                </beadarray_platform>
            </output_design>
        </assay>
    </assays>
</assay_submission>
