entrez 0.2.0 → 0.3.0
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- data/README.rdoc +11 -10
- data/lib/entrez.rb +14 -6
- data/lib/entrez/version.rb +1 -1
- data/spec/entrez_spec.rb +9 -3
- metadata +2 -4
- data/spec/support/fixtures/efetch.xml +0 -246
data/README.rdoc
CHANGED
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@@ -6,7 +6,7 @@ Entrez is a simple API for making HTTP requests to Entrez utilities (eutils: htt
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gem install entrez
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or if you use Bundler
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or if you use Bundler:
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# Gemfile
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gem 'entrez'
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@@ -15,17 +15,18 @@ It requires httparty.
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== Usage
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Entrez.
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Entrez.EFetch(<database>, parameters)
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== Example
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Entrez.
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-
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Entrez.EFetch('snp', {id: '9268480', retmode: 'xml'})
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will return an HTTParty response with a body of the xml document with information about rs9268480.
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It's up to you to parse the document.
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== Email & Tool
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NCBI
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NCBI requests that you supply the tool you are using and your email.
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The Entrez gem uses 'ruby' as the tool.
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Email is obtained from an environment variable ENTREZ_EMAIL on your computer.
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I set mine in my ~/.bash_profile:
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@@ -37,12 +38,12 @@ NCBI recommends no more than 3 URL requests per second: http://www.ncbi.nlm.nih.
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This gem respects this limit. It will delay the next request if the last 3 have been made within 1 second.
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The amount of delay time is no more than what is necessary to make the next request "respectful".
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==
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== Supported Utilities
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* EFetch
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* ESummary
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-
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But if you would like to contribute, please feel free.
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After seeing the code, assuming you know how to submit requests to einfo et al,
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It should be easy to implement them here.
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Not yet implemented: EInfo, EPost, ESearch, ELink, EGQuery, ESpell.
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== Compatibility
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data/lib/entrez.rb
CHANGED
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@@ -8,14 +8,18 @@ class Entrez
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8
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class << self
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10
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def
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-
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request_times << Time.now.to_f
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14
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get '/efetch.fcgi', :query => {db: db}.merge(params)
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def EFetch(db, params = {})
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perform '/efetch.fcgi', db, params
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end
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14
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-
def
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18
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def ESummary(db, params = {})
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perform '/esummary.fcgi', db, params
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end
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def perform(utility_path, db, params = {})
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respect_query_limit
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request_times << Time.now.to_f
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get utility_path, :query => {db: db}.merge(params)
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end
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private
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@@ -32,6 +36,10 @@ class Entrez
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end
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end
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def request_times
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@request_times ||= []
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end
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end
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end
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data/lib/entrez/version.rb
CHANGED
data/spec/entrez_spec.rb
CHANGED
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@@ -7,12 +7,18 @@ describe Entrez do
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Entrez.default_params[:email].should_not be_nil
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end
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it '
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Entrez.
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it '#EFetch retrieves results' do
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response = Entrez.EFetch('snp', {id: 9268480})
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response.code.should == 200
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end
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it '#ESummary retrieves results' do
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response = Entrez.ESummary('genomeprj', {id: 62343})
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response.code.should == 200
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end
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it 'should respect query limit' do
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requests = proc { 4.times { Entrez.
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requests = proc { 4.times { Entrez.EFetch('snp', id: 9268480) } }
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requests.should take_longer_than(1.0)
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end
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metadata
CHANGED
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@@ -2,7 +2,7 @@
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name: entrez
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version: !ruby/object:Gem::Version
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prerelease:
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version: 0.
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version: 0.3.0
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platform: ruby
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authors:
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- Jared Ning
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2011-
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date: 2011-05-14 00:00:00 -05:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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@@ -56,7 +56,6 @@ files:
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- lib/entrez/version.rb
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- spec/entrez_spec.rb
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- spec/spec_helper.rb
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- spec/support/fixtures/efetch.xml
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- spec/support/macros.rb
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- spec/support/matchers.rb
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has_rdoc: true
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@@ -90,6 +89,5 @@ summary: HTTP requests to Entrez E-utilities
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test_files:
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- spec/entrez_spec.rb
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- spec/spec_helper.rb
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- spec/support/fixtures/efetch.xml
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- spec/support/macros.rb
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- spec/support/matchers.rb
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@@ -1,246 +0,0 @@
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1
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<?xml version="1.0"?>
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<ExchangeSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns="http://www.ncbi.nlm.nih.gov/SNP/docsum"
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xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/SNP/docsum
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ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.1.xsd"><SourceDatabase taxId="0"
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organism=""/>
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<Rs rsId="9268480" snpClass="snp" snpType="notwithdrawn" molType="genomic" genotype="true" bitField="050368000301050503020100" taxId="9606">
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<Het type="est" value="0.306968957185745" stdError="0.243591338396072"/>
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<Validation byCluster="true" byFrequency="true"></Validation>
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<Create build="118" date="2003-10-31 16:50"/>
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<Update build="132" date="2011-01-04 14:46"/>
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<Sequence exemplarSs="12693244" ancestralAllele="C">
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<Seq5>CCAGTTTAGTCTTCAGATGATTACAGTTTCTAGAATTTTATTGCATTTCTCAGAATTCTAATAACACACTGTGAAACAATGAGCCTTTTGTAAAATATGTAGTAAGATACTCAGATTTCCTTAAAGATATGGTCAATTTTTGAAGATACTGGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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<Observed>C/T</Observed>
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAACAGGTTAGCTGTATATCTTCTCCCACTCTGACGAGGATGGGCTGGGAAGGTCCATTCACTTTTAAAGAAGCTGTTAAATAGAGTGGACAAAACACAATGAAAGAATCAAAATGGAACCAATAATGTCATCTCTAAGAACAGCTCCATTGGA</Seq3>
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</Sequence>
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<Ss ssId="12693244" handle="SI_MHC_SNP" batchId="30080" locSnpId="AL662796.6_71437_CT" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="118" methodClass="sequence" validated="by-cluster">
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<Sequence>
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<Seq5>CCAGTTTAGTCTTCAGATGATTACAGTTTCTAGAATTTTATTGCATTTCTCAGAATTCTAATAACACACTGTGAAACAATGAGCCTTTTGTAAAATATGTAGTAAGATACTCAGATTTCCTTAAAGATATGGTCAATTTTTGAAGATACTGGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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<Observed>C/T</Observed>
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAACAGGTTAGCTGTATATCTTCTCCCACTCTGACGAGGATGGGCTGGGAAGGTCCATTCACTTTTAAAGAAGCTGTTAAATAGAGTGGACAAAACACAATGAAAGAATCAAAATGGAACCAATAATGTCATCTCTAAGAACAGCTCCATTGGA</Seq3>
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</Sequence>
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</Ss>
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<Ss ssId="23138294" handle="FHCRC" batchId="11352" locSnpId="JF16_7049" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="126" methodClass="unknown" validated="by-frequency">
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<Sequence>
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<Seq5>TTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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<Observed>C/T</Observed>
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGT</Seq3>
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</Sequence>
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</Ss>
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<Ss ssId="24650851" handle="PERLEGEN" batchId="12311" locSnpId="afd0292430" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="123" methodClass="hybridize" validated="by-cluster">
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<Sequence>
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<Seq5>TTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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<Observed>C/T</Observed>
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGT</Seq3>
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</Sequence>
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</Ss>
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<Ss ssId="38346936" handle="PULMONOLOGYMSSM" batchId="18500" locSnpId="G16043A" subSnpClass="snp" orient="reverse" strand="top" molType="genomic" buildId="126" methodClass="unknown" validated="by-frequency">
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<Sequence>
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<Seq5>TCGGACGACGGGCAGTACCGCTGCCTTTTTGAAAAAGATGATGTCTACCA</Seq5>
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<Observed>A/G</Observed>
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<Seq3>GAGGCCAGTTTGGATCTGAAGGTGGTAAGTAAGAATTCTAGATAGATATT</Seq3>
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</Sequence>
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</Ss>
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<Ss ssId="44707181" handle="ABI" batchId="18990" locSnpId="hCV2488470" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="126" methodClass="unknown" linkoutUrl="http://myscience.appliedbiosystems.com/servlet/com.celera.web.myab.servlets.MyscienceGateway?source=dbSNP&resource=genotypingAssay&ap2=Celera+SNP&ap1=hCV2488470">
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<Sequence>
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<Seq5>AGTAAGATACTCAGATTTCCTTAAAGATATGGTCAATTTTTGAAGATACTGGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACCTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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<Observed>C/T</Observed>
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAACAGGTTAGCTGTATATCTTCTCCCACTCTGACGAGGATGGGCTGGGAAGGT</Seq3>
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53
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</Sequence>
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</Ss>
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<Ss ssId="52083135" handle="SI_EXO" batchId="30185" locSnpId="NT_007592.14_23222094" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="127" methodClass="unknown">
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<Sequence>
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<Seq5>CCAGTTTAGTCTTCAGATGATTACAGTTTCTAGAATTTTATTGCATTTCTCAGAATTCTAATAACACACTGTGAAACAATGAGCCTTTTGTAAAATATGTAGTAAGATACTCAGATTTCCTTAAAGATATGGTCAATTTTTGAAGATACTGGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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58
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<Observed>C/T</Observed>
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59
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAACAGGTTAGCTGTATATCTTCTCCCACTCTGACGAGGATGGGCTGGGAAGGTCCATTCACTTTTAAAGAAGCTGTTAAATAGAGTGGACAAAACACAATGAAAGAATCAAAATGGAACCAATAATGTCATCTCTAAGAACAGCTCCATTGGA</Seq3>
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60
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</Sequence>
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</Ss>
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<Ss ssId="65847636" handle="KRIBB_YJKIM" batchId="33716" locSnpId="KHS23433" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="127" methodClass="other" validated="by-cluster">
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63
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<Sequence>
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64
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<Seq5>AGTAAGATACTCAGATTTCCTTAAAGATATGGTCAATTTTTGAAGATACTGGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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65
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<Observed>C/T</Observed>
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66
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAACAGGTTAGCTGTATATCTTCTCCCACTCTGACGAGGATGGGCTGGGAAGGT</Seq3>
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67
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</Sequence>
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68
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</Ss>
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<Ss ssId="66383197" handle="AFFY" batchId="33767" locSnpId="SNP_A-2047476" subSnpClass="snp" orient="reverse" strand="top" molType="genomic" buildId="127" methodClass="hybridize" validated="by-cluster" linkoutUrl="http://www.affymetrix.com/support/technical/byproduct.affx?product=100kSNP_A-2047476">
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<Sequence>
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<Seq5>AAGATGATGTCTACCA</Seq5>
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<Observed>A/G</Observed>
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<Seq3>GAGGCCAGTTTGGATC</Seq3>
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</Sequence>
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</Ss>
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<Ss ssId="68972045" handle="PERLEGEN" batchId="38687" locSnpId="PGP00292430" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="127" methodClass="hybridize" validated="by-cluster">
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<Sequence>
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<Seq5>GGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
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<Observed>C/T</Observed>
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80
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<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGA</Seq3>
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81
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</Sequence>
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82
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</Ss>
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83
|
-
<Ss ssId="76118578" handle="AFFY" batchId="52074" locSnpId="AFFY_6_1M_SNP_A-2047476" subSnpClass="snp" orient="reverse" strand="top" molType="genomic" buildId="129" methodClass="hybridize" validated="by-submitter">
|
|
84
|
-
<Sequence>
|
|
85
|
-
<Seq5>AAGATGATGTCTACCA</Seq5>
|
|
86
|
-
<Observed>A/G</Observed>
|
|
87
|
-
<Seq3>GAGGCCAGTTTGGATC</Seq3>
|
|
88
|
-
</Sequence>
|
|
89
|
-
</Ss>
|
|
90
|
-
<Ss ssId="82555304" handle="KRIBB_YJKIM" batchId="52429" locSnpId="KHS279420" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="130" methodClass="hybridize" validated="by-submitter">
|
|
91
|
-
<Sequence>
|
|
92
|
-
<Seq5>TTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
93
|
-
<Observed>C/T</Observed>
|
|
94
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGT</Seq3>
|
|
95
|
-
</Sequence>
|
|
96
|
-
</Ss>
|
|
97
|
-
<Ss ssId="86242140" handle="CORNELL" batchId="58444" locSnpId="hCV2488470" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="129" methodClass="unknown">
|
|
98
|
-
<Sequence>
|
|
99
|
-
<Seq5>AATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
100
|
-
<Observed>C/T</Observed>
|
|
101
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGA</Seq3>
|
|
102
|
-
</Sequence>
|
|
103
|
-
</Ss>
|
|
104
|
-
<Ss ssId="93437732" handle="BCMHGSC_JDW" batchId="59658" locSnpId="JWB-2121515" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="129" methodClass="computed">
|
|
105
|
-
<Sequence>
|
|
106
|
-
<Seq5>GGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
107
|
-
<Observed>C/T</Observed>
|
|
108
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAAC</Seq3>
|
|
109
|
-
</Sequence>
|
|
110
|
-
</Ss>
|
|
111
|
-
<Ss ssId="98487577" handle="HUMANGENOME_JCVI" batchId="60080" locSnpId="1103652828650" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="130" methodClass="sequence" validated="by-submitter" linkoutUrl="http://huref.jcvi.org/browse.html?search=1103652828650">
|
|
112
|
-
<Sequence>
|
|
113
|
-
<Seq5>GGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACCTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
114
|
-
<Observed>C/T</Observed>
|
|
115
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGCACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAAC</Seq3>
|
|
116
|
-
</Sequence>
|
|
117
|
-
</Ss>
|
|
118
|
-
<Ss ssId="104297553" handle="BGI" batchId="856429" locSnpId="BGI_rs9268480" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="131" methodClass="unknown">
|
|
119
|
-
<Sequence>
|
|
120
|
-
<Seq5>TTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACYTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
121
|
-
<Observed>C/T</Observed>
|
|
122
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGT</Seq3>
|
|
123
|
-
</Sequence>
|
|
124
|
-
</Ss>
|
|
125
|
-
<Ss ssId="133671803" handle="ENSEMBL" batchId="856818" locSnpId="ENSSNP3072269" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="131" methodClass="computed">
|
|
126
|
-
<Sequence>
|
|
127
|
-
<Seq5>ATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
128
|
-
<Observed>C/T</Observed>
|
|
129
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTC</Seq3>
|
|
130
|
-
</Sequence>
|
|
131
|
-
</Ss>
|
|
132
|
-
<Ss ssId="144248004" handle="ENSEMBL" batchId="856818" locSnpId="ENSSNP13882478" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="131" methodClass="computed">
|
|
133
|
-
<Sequence>
|
|
134
|
-
<Seq5>ATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
135
|
-
<Observed>C/T</Observed>
|
|
136
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTC</Seq3>
|
|
137
|
-
</Sequence>
|
|
138
|
-
</Ss>
|
|
139
|
-
<Ss ssId="156753178" handle="GMI" batchId="1048915" locSnpId="GMI_SNP_77301931" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="131" methodClass="sequence" validated="by-submitter">
|
|
140
|
-
<Sequence>
|
|
141
|
-
<Seq5>TTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
142
|
-
<Observed>C/T</Observed>
|
|
143
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGT</Seq3>
|
|
144
|
-
</Sequence>
|
|
145
|
-
</Ss>
|
|
146
|
-
<Ss ssId="159712195" handle="SEATTLESEQ" batchId="1048973" locSnpId="BTNL2-32471822" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="131" methodClass="unknown">
|
|
147
|
-
<Sequence>
|
|
148
|
-
<Seq5>AATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
149
|
-
<Observed>C/T</Observed>
|
|
150
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGA</Seq3>
|
|
151
|
-
</Sequence>
|
|
152
|
-
</Ss>
|
|
153
|
-
<Ss ssId="160970526" handle="ILLUMINA" batchId="1049033" locSnpId="HumanOmni1-Quad_v1-0_B_rs9268480-128_B_F_1561716334" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="131" methodClass="hybridize" validated="by-submitter">
|
|
154
|
-
<Sequence>
|
|
155
|
-
<Seq5>TTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
156
|
-
<Observed>C/T</Observed>
|
|
157
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCA</Seq3>
|
|
158
|
-
</Sequence>
|
|
159
|
-
</Ss>
|
|
160
|
-
<Ss ssId="162203174" handle="COMPLETE_GENOMICS" batchId="1049290" locSnpId="NA07022_36_chr6_32471822" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="132" methodClass="sequence" validated="by-submitter">
|
|
161
|
-
<Sequence>
|
|
162
|
-
<Seq5>GGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
163
|
-
<Observed>C/T</Observed>
|
|
164
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAAC</Seq3>
|
|
165
|
-
</Sequence>
|
|
166
|
-
</Ss>
|
|
167
|
-
<Ss ssId="172560055" handle="AFFY" batchId="1049350" locSnpId="GenomeWideSNP_5_SNP_A-2047476" subSnpClass="snp" orient="reverse" strand="top" molType="genomic" buildId="132" methodClass="hybridize" validated="by-submitter">
|
|
168
|
-
<Sequence>
|
|
169
|
-
<Seq5>AAGATGATGTCTACCA</Seq5>
|
|
170
|
-
<Observed>A/G</Observed>
|
|
171
|
-
<Seq3>GAGGCCAGTTTGGATC</Seq3>
|
|
172
|
-
</Sequence>
|
|
173
|
-
</Ss>
|
|
174
|
-
<Ss ssId="201632426" handle="BUSHMAN" batchId="1050084" locSnpId="BUSHMAN-chr6-32471821" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="132" methodClass="unknown">
|
|
175
|
-
<Sequence>
|
|
176
|
-
<Seq5>TTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
177
|
-
<Observed>C/T</Observed>
|
|
178
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCG</Seq3>
|
|
179
|
-
</Sequence>
|
|
180
|
-
</Ss>
|
|
181
|
-
<Ss ssId="207457298" handle="BCM-HGSC-SUB" batchId="1050312" locSnpId="BCM_CMT_1011-1284727" subSnpClass="snp" orient="forward" strand="bottom" molType="genomic" buildId="132" methodClass="sequence" validated="by-submitter">
|
|
182
|
-
<Sequence>
|
|
183
|
-
<Seq5>GGAAAAGATACAAGTTATATGCCCAAATAATTAAATTTCATCCATTTGAGTTTGTGGATTTTAAGTAACTATGACAGTTTCACACACTGGAGGATTTGATATAAATTTGATGATGAATAAGCATTAAGAAAATTTCAAATGTCAGAGAAATTGTCCAGGAACTAGCATATTAAAGTGGCAGGAGCAGGTATTGAATACAAAATATCTATCTAGAATTCTTACTTACCACCTTCAGATCCAAACTGGCCTC</Seq5>
|
|
184
|
-
<Observed>C/T</Observed>
|
|
185
|
-
<Seq3>TGGTAGACATCATCTTTTTCAAAAAGGCAGCGGTACTGCCCGTCGTCCGAAGGTCTGGCACTGAGTATCTGCAGGGTCAGTCTGCCCTCGTCAATGGCGTCACTCACCAGTACAGTCCTCCCTCTGTACTCTGCCATCTGCTCTCCAGCCACATGGTCCCCATCCATATACACATGCACAGCAGGGTAACGGTGGGATCGGTCCCACCTCACCTCCATGCTCTGTGCATTCGCCTTGGGGGACAGGTAAC</Seq3>
|
|
186
|
-
</Sequence>
|
|
187
|
-
</Ss>
|
|
188
|
-
<Assembly dbSnpBuild="132" genomeBuild="37_1" groupLabel="Celera" current="true">
|
|
189
|
-
<Component componentType="contig" ctgId="88999178" accession="NW_923073.1" name="NW_923073.1" chromosome="6" start="28535679" end="58908290" orientation="fwd" gi="88999178" groupTerm="Celera" contigLabel="Celera">
|
|
190
|
-
<MapLoc asnFrom="5394909" asnTo="5394909" locType="exact" alnQuality="0.998325" orient="forward" physMapInt="33930588" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="5394908" rightContigNeighborPos="5394910" numberOfMismatches="2" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
191
|
-
</Component>
|
|
192
|
-
<SnpStat mapWeight="unique-in-contig" chromCount="1" placedContigCount="1" unplacedContigCount="0" seqlocCount="1" hapCount="0"/>
|
|
193
|
-
</Assembly>
|
|
194
|
-
<Assembly dbSnpBuild="132" genomeBuild="37_1" groupLabel="GRCh37" current="true" reference="true">
|
|
195
|
-
<Component componentType="contig" ctgId="224514668" accession="NT_007592.15" name="NT_007592.15" chromosome="6" start="60000" end="58780165" orientation="fwd" gi="224514668" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
196
|
-
<MapLoc asnFrom="32303843" asnTo="32303843" locType="exact" alnQuality="1" orient="forward" physMapInt="32363843" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="32303842" rightContigNeighborPos="32303844" numberOfMismatches="1" numberOfDeletions="0" numberOfInsertions="0">
|
|
197
|
-
<FxnSet geneId="56244" symbol="BTNL2" mrnaAcc="NM_019602" mrnaVer="1" protAcc="NP_062548" protVer="1" fxnClass="coding-synonymous" readingFrame="3" allele="A" residue="Q" aaPosition="349"/>
|
|
198
|
-
<FxnSet geneId="56244" symbol="BTNL2" mrnaAcc="NM_019602" mrnaVer="1" protAcc="NP_062548" protVer="1" fxnClass="reference" readingFrame="3" allele="G" residue="Q" aaPosition="349"/>
|
|
199
|
-
</MapLoc>
|
|
200
|
-
</Component>
|
|
201
|
-
<Component componentType="contig" ctgId="224515576" accession="NT_167244.1" name="NT_167244.1" chromosome="6" orientation="fwd" gi="224515576" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
202
|
-
<MapLoc asnFrom="3678213" asnTo="3678213" locType="exact" alnQuality="1" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3678212" rightContigNeighborPos="3678214" numberOfMismatches="1" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
203
|
-
</Component>
|
|
204
|
-
<Component componentType="contig" ctgId="224515577" accession="NT_113891.2" name="NT_113891.2" chromosome="6" orientation="fwd" gi="224515577" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
205
|
-
<MapLoc asnFrom="3834264" asnTo="3834264" locType="exact" alnQuality="1" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3834263" rightContigNeighborPos="3834265" numberOfMismatches="1" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
206
|
-
</Component>
|
|
207
|
-
<Component componentType="contig" ctgId="224515578" accession="NT_167245.1" name="NT_167245.1" chromosome="6" orientation="fwd" gi="224515578" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
208
|
-
<MapLoc asnFrom="3642742" asnTo="3642742" locType="exact" alnQuality="1" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3642741" rightContigNeighborPos="3642743" numberOfMismatches="1" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
209
|
-
</Component>
|
|
210
|
-
<Component componentType="contig" ctgId="224515579" accession="NT_167246.1" name="NT_167246.1" chromosome="6" orientation="fwd" gi="224515579" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
211
|
-
<MapLoc asnFrom="3706679" asnTo="3706679" locType="exact" alnQuality="0.993719" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3706678" rightContigNeighborPos="3706680" numberOfMismatches="6" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
212
|
-
</Component>
|
|
213
|
-
<Component componentType="contig" ctgId="224515580" accession="NT_167247.1" name="NT_167247.1" chromosome="6" orientation="fwd" gi="224515580" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
214
|
-
<MapLoc asnFrom="3743401" asnTo="3743401" locType="exact" alnQuality="0.995894" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3743400" rightContigNeighborPos="3743402" numberOfMismatches="4" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
215
|
-
</Component>
|
|
216
|
-
<Component componentType="contig" ctgId="224515581" accession="NT_167248.1" name="NT_167248.1" chromosome="6" orientation="fwd" gi="224515581" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
217
|
-
<MapLoc asnFrom="3624701" asnTo="3624701" locType="exact" alnQuality="1" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3624700" rightContigNeighborPos="3624702" numberOfMismatches="1" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
218
|
-
</Component>
|
|
219
|
-
<Component componentType="contig" ctgId="224515582" accession="NT_167249.1" name="NT_167249.1" chromosome="6" orientation="fwd" gi="224515582" groupTerm="GRCh37" contigLabel="GRCh37">
|
|
220
|
-
<MapLoc asnFrom="3711286" asnTo="3711286" locType="exact" alnQuality="0.995894" orient="forward" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="3711285" rightContigNeighborPos="3711287" numberOfMismatches="4" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
221
|
-
</Component>
|
|
222
|
-
<SnpStat mapWeight="unique-in-contig" chromCount="1" placedContigCount="1" unplacedContigCount="0" seqlocCount="8" hapCount="0"/>
|
|
223
|
-
</Assembly>
|
|
224
|
-
<Assembly dbSnpBuild="132" genomeBuild="37_1" groupLabel="HuRef" current="true">
|
|
225
|
-
<Component componentType="contig" ctgId="157696541" accession="NW_001838980.1" name="NW_001838980.1" chromosome="6" start="26727691" end="39531031" orientation="fwd" gi="157696541" groupTerm="HuRef" contigLabel="HuRef">
|
|
226
|
-
<MapLoc asnFrom="5390074" asnTo="5390074" locType="exact" alnQuality="0.995894" orient="forward" physMapInt="32117765" leftFlankNeighborPos="399" rightFlankNeighborPos="401" leftContigNeighborPos="5390073" rightContigNeighborPos="5390075" numberOfMismatches="4" numberOfDeletions="0" numberOfInsertions="0"></MapLoc>
|
|
227
|
-
</Component>
|
|
228
|
-
<SnpStat mapWeight="unique-in-contig" chromCount="1" placedContigCount="1" unplacedContigCount="0" seqlocCount="1" hapCount="0"/>
|
|
229
|
-
</Assembly>
|
|
230
|
-
<PrimarySequence dbSnpBuild="132" gi="9624968" source="remap" accession="NM_019602">
|
|
231
|
-
<MapLoc asnFrom="1049" asnTo="1049" locType="exact" alnQuality="1" orient="reverse" leftContigNeighborPos="1048" rightContigNeighborPos="1050"></MapLoc>
|
|
232
|
-
</PrimarySequence>
|
|
233
|
-
<RsStruct protAcc="NP_062548" protGi="9624969" protLoc="350" protResidue="Q" rsResidue="Q" structGi="209870436" structLoc="111" structResidue="E"/>
|
|
234
|
-
<RsStruct protAcc="NP_062548" protGi="9624969" protLoc="350" protResidue="Q" rsResidue="H" structGi="209870436" structLoc="111" structResidue="E"/>
|
|
235
|
-
<RsStruct protAcc="NP_062548" protGi="9624969" protLoc="350" protResidue="Q" rsResidue="H" structGi="209870436" structLoc="111" structResidue="E"/>
|
|
236
|
-
<RsLinkout resourceId="1" linkValue="9268480"/>
|
|
237
|
-
<MergeHistory rsId="57538739" buildId="130"/>
|
|
238
|
-
<MergeHistory rsId="17423795" buildId="123"/>
|
|
239
|
-
<MergeHistory rsId="17208804" buildId="126"/>
|
|
240
|
-
<hgvs>NM_019602.1:c.1050G>A</hgvs>
|
|
241
|
-
<hgvs>NT_007592.15:g.32303844C>T</hgvs>
|
|
242
|
-
</Rs>
|
|
243
|
-
|
|
244
|
-
|
|
245
|
-
|
|
246
|
-
<Summary/><BaseURL></BaseURL></ExchangeSet>
|