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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-. </p></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/helpsnpfaq/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpsnpfaq-lrg.png" alt="Cover of SNP FAQ Archive" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>SNP FAQ Archive [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK573517_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK573517_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2005-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpsnpfaq/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsnpfaq/Cnt_Double_Hit_SNP/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsnpfaq/Cnt_Heterozygosity/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK573517_"><span class="title" itemprop="name">Hardy Weinberg Equilibrium Data</span></h1><p class="small">Created: <span itemprop="datePublished">July 23, 2005</span>; Last Update: <span itemprop="dateModified">February 18, 2014</span>.</p><p><em>Estimated reading time: 2 minutes</em></p></div><div class="body-content whole_rhythm" itemprop="text"><ul class="simple-list"><li><p><a href="#Cnt_HardyWeinberg_Eq.i_am_having_trouble">I am having trouble understanding how the Hardy-Weinburg Probability (HWP) value is calculated for SNP records. I’m no statistician, so it would be helpful if you could include an example.</a></p></li><li><p><a href="#Cnt_HardyWeinberg_Eq.how_is_hwp_hardy_we">How is HWP (Hardy Weinberg Probability) found in the Population Diversity section of the refSNP report determined, and how does it relate to genotype data?</a></p></li><li><p><a href="#Cnt_HardyWeinberg_Eq.your_hardy_weinberg">Your Hardy Weinberg probabilities are calculated using 2 df—an incorrect calculation. Because only one independent parameter is being used to estimate (p=1-q), = there should only be 1 df.</a></p></li><li><p><a href="#Cnt_HardyWeinberg_Eq.the_displayed_value">The displayed value for HWP on your web page is different than the FAQ which calculates it. Am I using the correct calculation method?</a></p></li></ul><div><h4 id="Cnt_HardyWeinberg_Eq.i_am_having_trouble">I am having trouble understanding how the Hardy-Weinburg Probability (HWP) value is calculated for SNP records. I’m no statistician, so it would be helpful if you could include an example.</h4><blockquote><p>A good explanation of HWP and how it is calculated can be found in an online <a href="http://en.wikipedia.org/wiki/Hardy-Weinberg_principle" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Wikipedia article</a>.</p><p>Currently, we use the chi-square and p-value in our HWP calculations. Here is an example of how we calculate the HWP for <a href="/SNP/snp_ss.cgi?ss=ss221" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">ss221</a> in a population (population id as 506) following the HWP equation.</p><div id="Cnt_HardyWeinberg_Eq.T." class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T./?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">GtyFreq</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
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<u>subsnp_id</u>
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</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
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<u>pop_id</u>
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</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_4" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
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<u>gty_str</u>
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</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_5" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">
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<u>cnt</u>
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</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.411</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A/G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">37.000000</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.144</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A/A</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">13.000000</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.444</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G/G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">40.000000</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._1" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._1/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._1_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">cnt</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">AlleleFreq</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_4" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_5" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">allele</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">117.000000</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.650</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">63.000000</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.350</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._1_1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._2" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._2/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._2_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._2_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._2_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._2_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">ind_cnt</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._2_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._2_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._2_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">90.000000</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._3" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._3/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._3_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._3_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._3_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._3_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">chr_cnt</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._3_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._3_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._3_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">180.000000</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._4" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._4/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._4_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._4_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._4_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._4_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Degree of Freedom</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._4_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._4_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._4_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">1</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._5" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._5/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._5_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">exp_gtyFreq</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_4" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">exp_gtyCnt</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_5" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">allele_1</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_6" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">allele_2</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_7" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">gty_str</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.422</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">38.025</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_6" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_7" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G/G</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.455</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">40.950</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_6" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_7" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A/G</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.122</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">11.025</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_5" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_6" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._5_1_1_1_7" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A/A</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._6" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._6/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._6_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">gty_str</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_4" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">observed_gtyCnt</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">G/G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">40.00</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A/G</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">37.00</td></tr><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">A/A</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._6_1_1_1_4" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">13.00</td></tr></tbody></table></div></div><div id="Cnt_HardyWeinberg_Eq.T._7" class="table"><div class="caption"><p>_</p></div><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK573517/table/Cnt_HardyWeinberg_Eq.T._7/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__Cnt_HardyWeinberg_Eq.T._7_lrgtbl__"><table><thead><tr><th id="hd_h_Cnt_HardyWeinberg_Eq.T._7_1_1_1_1" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">subsnp_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._7_1_1_1_2" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">pop_id</th><th id="hd_h_Cnt_HardyWeinberg_Eq.T._7_1_1_1_3" scope="col" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Chi-square</th></tr></thead><tbody><tr><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._7_1_1_1_1" scope="row" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">221</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._7_1_1_1_2" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">506</td><td headers="hd_h_Cnt_HardyWeinberg_Eq.T._7_1_1_1_3" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">0.837</td></tr></tbody></table></div></div><p>After obtaining the chi-square value, calculate the p-value using the degrees of freedom via the gamma function, or many websites offer <a href="http://www.danielsoper.com/statcalc/calc11.aspx" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">p-value calculators</a>. (<b>9/11/07</b>)</p></blockquote></div><div><h4 id="Cnt_HardyWeinberg_Eq.how_is_hwp_hardy_we">How is HWP (Hardy Weinberg Probability) found in the Population Diversity section of the refSNP report determined, and how does it relate to genotype data?</h4><blockquote><p>A good explanation of HWP and how it is calculated can be found <a href="http://en.wikipedia.org/wiki/Hardy-Weinberg_principle" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">online</a>. The next question in this section also contains information you should find useful. (<b>6/4/07</b>)</p></blockquote></div><div><h4 id="Cnt_HardyWeinberg_Eq.your_hardy_weinberg">Your Hardy Weinberg probabilities are calculated using 2 df—an incorrect calculation. Because only one independent parameter is being used to estimate (p=1-q), = there should only be 1 df.</h4><blockquote><p>Thanks for pointing out the inclusion of failed assays in the Hardy Weinberg estimates for refSNP (rs) clusters appearing on rs cluster reports as well as in the genotype and allele frequency reports. We will exclude such genotypes in the Hardy Weinberg equilibrium calculations for the release of dbSNP build 120.</p><p>Many of the assumptions of the Hardy Weinberg equilibrium are not necessarily met in the submissions to the dbSNP, but we do believe that there is utility (although limited) in calculation of Hardy Weinberg equilibrium over rs clusters. Please see the Hardy Weinberg equilibrium performed over submitted SNPs (ss) by population. These are listed in the submitted SNP details page as well as in the genotype and allele frequency report. Please be aware, however, that the population in the context of dbSNP may (or may not) differ from a population as defined in a population genetics context.</p></blockquote></div><div><h4 id="Cnt_HardyWeinberg_Eq.the_displayed_value">The displayed value for HWP on your web page is different than the FAQ which calculates it. Am I using the correct calculation method?</h4><blockquote><p>To speed up database update, we have used a lookup table which is binned. This is a contributory factor as to why the P value is not exact but should be close. To calculate the P value (chi-square distribution), we used the Gamma Function. I think we got the C algorithm from Numeric Recipe book.</p><p>If you are interested in HWE, have you looked at Fisher Exact test? From what biologists have told us, the Fisher Exact test is a better way to estimate HWP especially when sample size is small. When time allows, we hope to switch our HWE calculations from the Chi-square test to the Fisher Exact test.(<b>08/01/08</b>)</p></blockquote></div><div id="bk_toc_contnr"></div></div></div>
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<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK573517</span></div><div style="margin-top:2em" class="bk_noprnt"><a class="bk_cntns" href="/books/n/helpsnpfaq/">Contents</a><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsnpfaq/Cnt_Double_Hit_SNP/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsnpfaq/Cnt_Heterozygosity/" title="Next page in this title">Next ></a></div></div></div></div>
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