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1KG PCA
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# 1KG VCF analysis\n",
"\n",
"1KG VCF 파일의 일부 (22번 염색체에서 5천개 변이 추철)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%matplotlib inline\n",
"import numpy as np\n",
"import pandas as pd\n",
"import matplotlib.pyplot as plt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## VCF 읽기"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"##fileformat=VCFv4.0\r\n",
"##filedat=20101112\r\n",
"##datarelease=20100804\r\n",
"##samples=629\r\n",
"##description=\"Where BI calls are present, genotypes and alleles are from BI. In there absence, UM genotypes are used. If neither are available, no genotype information is present and the alleles are from the NCBI calls.\"\r\n",
"##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">\r\n",
"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth (only filtered reads used for calling)\">\r\n",
"##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic\">\r\n",
"##FORMAT=<ID=GQ,Number=1,Type=Float,Description=\"Genotype Quality\">\r\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n",
"##FORMAT=<ID=GD,Number=1,Type=Float,Description=\"Genotype dosage. Expected count of non-ref alleles [0,2]\">\r\n",
"##FORMAT=<ID=OG,Number=1,Type=String,Description=\"Original Genotype input to Beagle\">\r\n",
"##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">\r\n",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">\r\n",
"##INFO=<ID=CB,Number=.,Type=String,Description=\"List of centres that called, UM (University of Michigan), BI (Broad Institute), BC (Boston College), NCBI\">\r\n",
"##INFO=<ID=EUR_R2,Number=1,Type=Float,Description=\"R2 From Beagle based on European Samples\">\r\n",
"##INFO=<ID=AFR_R2,Number=1,Type=Float,Description=\"R2 From Beagle based on AFRICAN Samples\">\r\n",
"##INFO=<ID=ASN_R2,Number=1,Type=Float,Description=\"R2 From Beagle based on Asian Samples\">\r\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00098\tHG00100\tHG00106\tHG00112\tHG00114\tHG00116\tHG00117\tHG00118\tHG00119\tHG00120\tHG00122\tHG00123\tHG00124\tHG00126\tHG00131\tHG00141\tHG00142\tHG00143\tHG00144\tHG00145\tHG00146\tHG00147\tHG00148\tHG00149\tHG00150\tHG00151\tHG00152\tHG00153\tHG00156\tHG00158\tHG00159\tHG00160\tHG00171\tHG00173\tHG00174\tHG00176\tHG00177\tHG00178\tHG00179\tHG00180\tHG00181\tHG00182\tHG00183\tHG00185\tHG00186\tHG00187\tHG00188\tHG00189\tHG00190\tHG00231\tHG00239\tHG00242\tHG00243\tHG00244\tHG00245\tHG00247\tHG00258\tHG00262\tHG00264\tHG00265\tHG00266\tHG00267\tHG00269\tHG00270\tHG00272\tHG00306\tHG00308\tHG00311\tHG00312\tHG00357\tHG00361\tHG00366\tHG00367\tHG00368\tHG00369\tHG00372\tHG00373\tHG00377\tHG00380\tHG00403\tHG00404\tHG00406\tHG00407\tHG00445\tHG00446\tHG00452\tHG00457\tHG00553\tHG00554\tHG00559\tHG00560\tHG00565\tHG00566\tHG00577\tHG00578\tHG00592\tHG00593\tHG00596\tHG00610\tHG00611\tHG00625\tHG00626\tHG00628\tHG00629\tHG00634\tHG00635\tHG00637\tHG00638\tHG00640\tNA06984\tNA06985\tNA06986\tNA06989\tNA06994\tNA07000\tNA07037\tNA07048\tNA07051\tNA07056\tNA07346\tNA07347\tNA07357\tNA10847\tNA10851\tNA11829\tNA11830\tNA11831\tNA11832\tNA11840\tNA11843\tNA11881\tNA11892\tNA11893\tNA11894\tNA11918\tNA11919\tNA11920\tNA11930\tNA11931\tNA11932\tNA11933\tNA11992\tNA11993\tNA11994\tNA11995\tNA12003\tNA12004\tNA12005\tNA12006\tNA12043\tNA12044\tNA12045\tNA12046\tNA12058\tNA12144\tNA12154\tNA12155\tNA12156\tNA12249\tNA12272\tNA12273\tNA12275\tNA12287\tNA12340\tNA12341\tNA12342\tNA12347\tNA12348\tNA12383\tNA12399\tNA12400\tNA12413\tNA12414\tNA12489\tNA12546\tNA12716\tNA12717\tNA12718\tNA12749\tNA12750\tNA12751\tNA12761\tNA12762\tNA12763\tNA12775\tNA12776\tNA12777\tNA12778\tNA12812\tNA12813\tNA12814\tNA12815\tNA12828\tNA12830\tNA12872\tNA12873\tNA12874\tNA12889\tNA12890\tNA18486\tNA18487\tNA18489\tNA18498\tNA18499\tNA18501\tNA18502\tNA18504\tNA18505\tNA18507\tNA18508\tNA18510\tNA18511\tNA18516\tNA18517\tNA18519\tNA18520\tNA18522\tNA18523\tNA18525\tNA18526\tNA18527\tNA18532\tNA18535\tNA18537\tNA18538\tNA18539\tNA18541\tNA18542\tNA18545\tNA18547\tNA18550\tNA18552\tNA18553\tNA18555\tNA18558\tNA18560\tNA18561\tNA18562\tNA18563\tNA18564\tNA18565\tNA18566\tNA18567\tNA18570\tNA18571\tNA18572\tNA18573\tNA18574\tNA18576\tNA18577\tNA18579\tNA18582\tNA18592\tNA18593\tNA18603\tNA18605\tNA18608\tNA18609\tNA18611\tNA18612\tNA18614\tNA18615\tNA18616\tNA18617\tNA18618\tNA18619\tNA18620\tNA18621\tNA18622\tNA18623\tNA18624\tNA18625\tNA18626\tNA18627\tNA18628\tNA18630\tNA18631\tNA18632\tNA18633\tNA18634\tNA18636\tNA18638\tNA18640\tNA18642\tNA18643\tNA18745\tNA18853\tNA18856\tNA18858\tNA18861\tNA18867\tNA18868\tNA18870\tNA18871\tNA18873\tNA18874\tNA18907\tNA18908\tNA18909\tNA18910\tNA18912\tNA18916\tNA18940\tNA18941\tNA18942\tNA18943\tNA18944\tNA18945\tNA18947\tNA18948\tNA18949\tNA18950\tNA18951\tNA18952\tNA18953\tNA18955\tNA18956\tNA18959\tNA18960\tNA18961\tNA18963\tNA18964\tNA18965\tNA18967\tNA18968\tNA18970\tNA18971\tNA18972\tNA18973\tNA18974\tNA18975\tNA18976\tNA18977\tNA18979\tNA18980\tNA18981\tNA18982\tNA18983\tNA18984\tNA18985\tNA18986\tNA18987\tNA18988\tNA18989\tNA18990\tNA18997\tNA18999\tNA19000\tNA19001\tNA19002\tNA19003\tNA19004\tNA19005\tNA19007\tNA19009\tNA19010\tNA19012\tNA19027\tNA19044\tNA19054\tNA19055\tNA19056\tNA19057\tNA19058\tNA19059\tNA19060\tNA19062\tNA19063\tNA19064\tNA19065\tNA19066\tNA19067\tNA19068\tNA19070\tNA19072\tNA19074\tNA19075\tNA19076\tNA19077\tNA19078\tNA19079\tNA19082\tNA19083\tNA19084\tNA19085\tNA19086\tNA19087\tNA19088\tNA19093\tNA19098\tNA19099\tNA19102\tNA19107\tNA19108\tNA19113\tNA19114\tNA19116\tNA19119\tNA19129\tNA19130\tNA19131\tNA19137\tNA19138\tNA19141\tNA19143\tNA19144\tNA19147\tNA19152\tNA19153\tNA19159\tNA19160\tNA19171\tNA19172\tNA19184\tNA19189\tNA19190\tNA19200\tNA19201\tNA19204\tNA19206\tNA19207\tNA19209\tNA19210\tNA19213\tNA19225\tNA19235\tNA19236\tNA19247\tNA19248\tNA19256\tNA19257\tNA19311\tNA19312\tNA19313\tNA19314\tNA19332\tNA19334\tNA19338\tNA19346\tNA19347\tNA19350\tNA19355\tNA19359\tNA19360\tNA19371\tNA19372\tNA19375\tNA19376\tNA19377\tNA19379\tNA19381\tNA19382\tNA19383\tNA19384\tNA19385\tNA19390\tNA19391\tNA19393\tNA19394\tNA19395\tNA19397\tNA19398\tNA19399\tNA19401\tNA19404\tNA19428\tNA19429\tNA19434\tNA19435\tNA19436\tNA19437\tNA19438\tNA19439\tNA19440\tNA19443\tNA19444\tNA19445\tNA19446\tNA19448\tNA19449\tNA19451\tNA19452\tNA19453\tNA19455\tNA19456\tNA19457\tNA19461\tNA19462\tNA19463\tNA19466\tNA19467\tNA19469\tNA19471\tNA19472\tNA19473\tNA19474\tNA19625\tNA19648\tNA19649\tNA19651\tNA19652\tNA19654\tNA19655\tNA19658\tNA19660\tNA19661\tNA19678\tNA19684\tNA19685\tNA19700\tNA19701\tNA19703\tNA19704\tNA19707\tNA19712\tNA19713\tNA19720\tNA19722\tNA19723\tNA19725\tNA19726\tNA19818\tNA19819\tNA19834\tNA19835\tNA19900\tNA19901\tNA19904\tNA19908\tNA19909\tNA19914\tNA19916\tNA19917\tNA19920\tNA19921\tNA19982\tNA20414\tNA20502\tNA20505\tNA20508\tNA20509\tNA20510\tNA20512\tNA20515\tNA20516\tNA20517\tNA20518\tNA20519\tNA20520\tNA20521\tNA20522\tNA20524\tNA20525\tNA20526\tNA20527\tNA20528\tNA20529\tNA20530\tNA20531\tNA20532\tNA20533\tNA20534\tNA20535\tNA20536\tNA20537\tNA20538\tNA20539\tNA20540\tNA20541\tNA20542\tNA20543\tNA20544\tNA20581\tNA20582\tNA20585\tNA20586\tNA20588\tNA20589\tNA20752\tNA20753\tNA20754\tNA20755\tNA20756\tNA20757\tNA20758\tNA20759\tNA20760\tNA20761\tNA20765\tNA20769\tNA20770\tNA20771\tNA20772\tNA20773\tNA20774\tNA20775\tNA20778\tNA20783\tNA20785\tNA20786\tNA20787\tNA20790\tNA20792\tNA20795\tNA20796\tNA20797\tNA20798\tNA20799\tNA20800\tNA20801\tNA20802\tNA20803\tNA20804\tNA20805\tNA20806\tNA20807\tNA20808\tNA20809\tNA20810\tNA20811\tNA20812\tNA20813\tNA20814\tNA20815\tNA20816\tNA20818\tNA20819\tNA20826\tNA20828\r\n"
]
}
],
"source": [
"!head -n 19 only_rs_22-5000.vcf\n"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>#CHROM</th>\n",
" <th>POS</th>\n",
" <th>ID</th>\n",
" <th>REF</th>\n",
" <th>ALT</th>\n",
" <th>QUAL</th>\n",
" <th>FILTER</th>\n",
" <th>INFO</th>\n",
" <th>FORMAT</th>\n",
" <th>HG00098</th>\n",
" <th>...</th>\n",
" <th>NA20811</th>\n",
" <th>NA20812</th>\n",
" <th>NA20813</th>\n",
" <th>NA20814</th>\n",
" <th>NA20815</th>\n",
" <th>NA20816</th>\n",
" <th>NA20818</th>\n",
" <th>NA20819</th>\n",
" <th>NA20826</th>\n",
" <th>NA20828</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>22</td>\n",
" <td>50328528</td>\n",
" <td>rs116643340</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=269;AF=0.010;CB=BI,NCBI;AFR_R2=0.516</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>22</td>\n",
" <td>50328670</td>\n",
" <td>rs114196268</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1089;AF=0.007;CB=UM,BI,BC,NCBI;AFR_R2=0.465</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>22</td>\n",
" <td>50328731</td>\n",
" <td>rs28608875</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=907;AF=0.055;CB=UM,BI,BC,NCBI;EUR_R2=0.751;...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:19.48:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.06:31.02:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-14.93:25.32:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.66:25.58:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.47:22.60:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.31:28.57:./.</td>\n",
" <td>1|0:3,0:3:.:-0.00,-0.90,-10.19:3.84:0/0</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.86:28.57:./.</td>\n",
" <td>0|1:2,0:2:.:-0.00,-0.60,-7.19:5.60:0/0</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-10.16:18.81:./.</td>\n",
" <td>0|0:5,0:3:.:-0.00,-0.91,-9.26:31.14:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>22</td>\n",
" <td>50329119</td>\n",
" <td>rs56008904</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=141;AF=0.390;CB=BI,BC;EUR_R2=0.145;AFR_R2=0...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:3.49:./.</td>\n",
" <td>...</td>\n",
" <td>1|0:.:.:.:.,.,.:3.36:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.17:3.87:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.54:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.54:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.37:5.94:./.</td>\n",
" <td>1|0:0,1:1:.:-3.87,-0.30,-0.00:4.71:1/1</td>\n",
" <td>0|0:.:.:.:.,.,.:3.54:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:1.71:./.</td>\n",
" <td>1|0:.:.:.:.,.,.:3.22:./.</td>\n",
" <td>1|0:.:.:.:.,.,.:3.36:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>22</td>\n",
" <td>50329830</td>\n",
" <td>rs79860705</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=373;AF=0.107;CB=UM,BI,BC,NCBI;EUR_R2=0.507</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:9.26:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.47:11.92:./.</td>\n",
" <td>1|0:1,2:2:.:-6.43,-0.60,-0.00:6.99:1/1</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.50:12.12:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:9.26:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.80:12.12:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.43:5.77:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:9.26:./.</td>\n",
" <td>0|1:.:.:.:.,.,.:5.52:./.</td>\n",
" <td>0|0:3,1:3:.:-0.00,-0.91,-8.99:9.32:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.30:11.93:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>22</td>\n",
" <td>50330186</td>\n",
" <td>rs73444002</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1024;AF=0.026;CB=UM,BI,BC,NCBI;EUR_R2=0.498...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:27.01:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.86:19.92:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.01:41.55:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.67:42.22:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-14.76:46.99:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.26:41.55:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.90:35.23:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:32.76:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.50:15.52:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-17.40:27.64:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.56:16.98:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>22</td>\n",
" <td>50330345</td>\n",
" <td>rs28652639</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1477;AF=0.016;CB=UM,BI,BC,NCBI;EUR_R2=0.605</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:11.33:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.19:18.58:./.</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-5.89:20.27:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.99:20.27:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:11.47:./.</td>\n",
" <td>1|0:2,3:5:.:-9.59,-1.51,-6.07:60:./.</td>\n",
" <td>0|0:6,0:6:.:-0.00,-1.81,-21.59:32.22:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:11.44:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.70:13.38:./.</td>\n",
" <td>0|0:8,0:6:.:-0.01,-1.81,-18.99:26.82:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-7.09:15.63:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>22</td>\n",
" <td>50330546</td>\n",
" <td>rs28516848</td>\n",
" <td>T</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1517;AF=0.061;CB=UM,BI,BC,NCBI;EUR_R2=0.773...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:21.35:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:21.73:./.</td>\n",
" <td>0|0:6,0:6:.:-0.00,-1.81,-19.50:45.23:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-18.62:39.59:./.</td>\n",
" <td>0|0:6,0:6:.:-0.00,-1.81,-21.26:43.01:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.43:33.87:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-17.46:43.01:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:24.67:./.</td>\n",
" <td>1|0:1,1:2:.:-2.80,-0.60,-2.94:43.98:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.93:36.20:./.</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-7.49:30.22:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>22</td>\n",
" <td>50331032</td>\n",
" <td>rs115322211</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1465;AF=0.013;CB=UM,BI,BC,NCBI;AFR_R2=0.711</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>22</td>\n",
" <td>50331164</td>\n",
" <td>rs28690400</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1538;AF=0.299;CB=UM,BI,BC,NCBI;EUR_R2=0.929...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.46:23.76:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.43:24.96:./.</td>\n",
" <td>1|0:4,2:4:.:-2.80,-1.21,-10.48:50:./.</td>\n",
" <td>0|0:9,0:9:.:-0.01,-2.72,-31.86:60:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.61,-6.82:50:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.21,-14.35:60:./.</td>\n",
" <td>1|0:3,3:5:.:-5.97,-1.51,-11.20:60:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.57:43.98:./.</td>\n",
" <td>1|1:0,3:3:.:-8.76,-0.91,-0.01:37.21:./.</td>\n",
" <td>1|0:3,1:4:.:-3.20,-1.21,-11.00:22.73:./.</td>\n",
" <td>0|0:8,0:6:.:-0.00,-1.81,-22.28:42.22:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>22</td>\n",
" <td>50331300</td>\n",
" <td>rs73891184</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1799;AF=0.020;CB=UM,BI,BC,NCBI;AFR_R2=0.759</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>22</td>\n",
" <td>50331475</td>\n",
" <td>rs76433322</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2162;AF=0.009;CB=UM,BI,BC,NCBI;AFR_R2=0.732</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>22</td>\n",
" <td>50331622</td>\n",
" <td>rs28393180</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1952;AF=0.052;CB=UM,BI,BC,NCBI;EUR_R2=0.68;...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:24.96:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:6,0:6:.:-0.01,-1.81,-17.47:60:./.</td>\n",
" <td>0|0:13,0:11:.:-0.02,-3.33,-30.65:60:./.</td>\n",
" <td>0|0:16,0:16:.:-0.02,-4.83,-49.96:60:./.</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-5.66:50:./.</td>\n",
" <td>0|0:8,0:7:.:-0.01,-2.11,-20.85:43.01:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.10:60:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.90:28.96:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.33:60:./.</td>\n",
" <td>0|0:8,0:7:.:-0.01,-2.11,-22.39:60:./.</td>\n",
" <td>0|0:6,0:4:.:-0.00,-1.21,-12.77:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>22</td>\n",
" <td>50332005</td>\n",
" <td>rs28460675</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2228;AF=0.144;CB=UM,BI,BC,NCBI;EUR_R2=0.918...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.40:17.77:./.</td>\n",
" <td>...</td>\n",
" <td>1|0:1,5:5:.:-13.57,-1.51,-2.80:50:./.</td>\n",
" <td>0|0:6,0:4:.:-0.01,-1.21,-11.77:50:./.</td>\n",
" <td>0|0:18,0:17:.:-0.02,-5.13,-53.88:60:./.</td>\n",
" <td>0|0:6,0:4:.:-0.00,-1.21,-11.66:46.99:./.</td>\n",
" <td>0|0:6,0:5:.:-0.01,-1.51,-16.23:26.78:./.</td>\n",
" <td>0|0:5,0:5:.:-0.01,-1.51,-15.63:60:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.06:28.54:./.</td>\n",
" <td>1|0:4,1:5:.:-3.90,-1.51,-12.42:43.01:./.</td>\n",
" <td>0|0:6,0:6:.:-0.01,-1.81,-17.97:46.99:./.</td>\n",
" <td>1|0:5,2:6:.:-3.90,-1.81,-15.46:39.21:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>22</td>\n",
" <td>50332022</td>\n",
" <td>rs28470489</td>\n",
" <td>T</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2210;AF=0.438;CB=UM,BI,BC,NCBI;EUR_R2=0.972...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.94:16.89:./.</td>\n",
" <td>...</td>\n",
" <td>1|0:2,3:5:.:-10.04,-1.51,-6.48:60:./.</td>\n",
" <td>1|0:4,3:6:.:-6.94,-1.81,-13.38:60:./.</td>\n",
" <td>0|0:17,0:16:.:-0.01,-4.82,-58.10:60:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-18.06:45.23:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-19.09:50:./.</td>\n",
" <td>1|0:4,5:8:.:-14.36,-2.41,-13.48:60:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.70:27.93:./.</td>\n",
" <td>1|1:0,7:6:.:-20.45,-1.81,-0.00:60:./.</td>\n",
" <td>1|0:2,3:5:.:-10.48,-1.51,-6.60:60:./.</td>\n",
" <td>1|0:6,3:9:.:-11.04,-2.71,-20.50:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>22</td>\n",
" <td>50332097</td>\n",
" <td>rs77228592</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2104;AF=0.020;CB=UM,BI,BC,NCBI;EUR_R2=0.483...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:21.60:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.06:30.56:./.</td>\n",
" <td>0|0:10,0:7:.:-0.01,-2.11,-21.06:45.23:./.</td>\n",
" <td>0|0:19,0:19:.:-0.02,-5.73,-60.41:60:./.</td>\n",
" <td>0|0:10,0:8:.:-0.01,-2.41,-26.40:45.23:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-5.46:27.93:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.21,-12.20:36.58:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:21.56:./.</td>\n",
" <td>0|0:8,0:6:.:-0.01,-1.81,-17.99:60:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-9.76:33.57:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-16.43:39.59:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>22</td>\n",
" <td>50332242</td>\n",
" <td>rs28451805</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3101;AF=0.426;CB=UM,BI,BC,NCBI;EUR_R2=0.969...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:17.48:./.</td>\n",
" <td>...</td>\n",
" <td>1|0:7,3:9:.:-8.00,-2.72,-23.94:60:./.</td>\n",
" <td>1|0:7,2:9:.:-6.07,-2.72,-23.15:60:./.</td>\n",
" <td>0|0:31,0:30:.:-0.02,-9.04,-109.61:60:./.</td>\n",
" <td>0|0:11,0:11:.:-0.01,-3.32,-40.19:60:./.</td>\n",
" <td>0|0:18,0:16:.:-0.02,-4.83,-57.14:60:./.</td>\n",
" <td>1|0:7,5:12:.:-18.26,-3.62,-24.95:60:./.</td>\n",
" <td>0|0:7,0:7:.:-0.01,-2.12,-22.43:50:./.</td>\n",
" <td>1|1:0,4:4:.:-14.33,-1.20,-0.00:33.28:./.</td>\n",
" <td>1|0:13,6:19:.:-23.89,-5.73,-47.23:60:./.</td>\n",
" <td>1|0:11,2:12:.:-7.08,-3.62,-35.26:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>22</td>\n",
" <td>50332324</td>\n",
" <td>rs28523661</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3435;AF=0.587;CB=UM,BI,BC,NCBI;EUR_R2=0.755...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:4.64:./.</td>\n",
" <td>...</td>\n",
" <td>1|1:0,15:14:.:-45.50,-4.22,-0.02:60:./.</td>\n",
" <td>1|0:14,13:24:.:-32.97,-7.24,-45.55:60:./.</td>\n",
" <td>0|1:25,24:44:.:-64.95,-13.26,-90.40:60:./.</td>\n",
" <td>0|0:10,0:9:.:-0.01,-2.72,-32.25:30.71:./.</td>\n",
" <td>0|0:17,0:17:.:-0.02,-5.13,-60.28:60:./.</td>\n",
" <td>1|1:0,12:10:.:-31.71,-3.01,-0.01:23.48:./.</td>\n",
" <td>0|1:3,2:4:.:-2.67,-1.21,-10.78:11.43:./.</td>\n",
" <td>1|1:0,2:2:.:-7.36,-0.60,-0.00:18.29:./.</td>\n",
" <td>1|0:19,12:28:.:-40.16,-8.44,-62.12:60:./.</td>\n",
" <td>1|0:12,3:15:.:-10.84,-4.52,-45.63:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>22</td>\n",
" <td>50332377</td>\n",
" <td>rs114353012</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3208;AF=0.003;CB=UM,BC,NCBI</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>22</td>\n",
" <td>50332472</td>\n",
" <td>rs115364094</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3376;AF=0.003;CB=UM,BI,BC,NCBI;AFR_R2=0.824</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>22</td>\n",
" <td>50333130</td>\n",
" <td>rs77002698</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1951;AF=0.081;CB=UM,BI,BC,NCBI;EUR_R2=0.886...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:30.97:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-6.16:40.46:./.</td>\n",
" <td>1|0:6,3:6:.:-7.14,-1.81,-12.28:60:./.</td>\n",
" <td>0|0:10,0:10:.:-0.01,-3.01,-32.30:60:./.</td>\n",
" <td>0|0:8,0:5:.:-0.00,-1.51,-16.60:46.99:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.91,-9.36:41.55:./.</td>\n",
" <td>1|0:7,5:8:.:-3.76,-2.41,-22.63:28.66:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.06:37.45:./.</td>\n",
" <td>0|1:2,2:2:.:-7.23,-0.60,-0.00:60:1/1</td>\n",
" <td>1|0:7,3:7:.:-11.48,-2.11,-11.99:60:./.</td>\n",
" <td>0|0:9,0:7:.:-0.01,-2.11,-21.89:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>22</td>\n",
" <td>50333253</td>\n",
" <td>rs116837852</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2488;AF=0.010;CB=UM,BI,BC,NCBI;AFR_R2=0.822</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>22</td>\n",
" <td>50333415</td>\n",
" <td>rs4073387</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2144;AF=0.087;CB=UM,BI,BC,NCBI;EUR_R2=0.967...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.80:26.09:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-9.03:34.81:./.</td>\n",
" <td>1|0:4,4:6:.:-14.77,-1.81,-5.67:60:./.</td>\n",
" <td>0|0:6,0:6:.:-0.01,-1.81,-18.69:40.97:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-9.66:32.29:./.</td>\n",
" <td>0|0:6,0:6:.:-0.01,-1.81,-17.65:41.55:./.</td>\n",
" <td>1|0:6,3:9:.:-10.60,-2.72,-17.67:60:./.</td>\n",
" <td>0|0:4,0:4:.:-0.01,-1.21,-11.86:35.09:./.</td>\n",
" <td>0|1:1,0:1:.:-0.00,-0.30,-2.80:26.13:0/0</td>\n",
" <td>1|0:4,3:7:.:-11.69,-2.11,-12.10:60:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-16.25:41.55:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>22</td>\n",
" <td>50333697</td>\n",
" <td>rs4073388</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1957;AF=0.073;CB=UM,BI,BC,NCBI;EUR_R2=0.885...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-4.05:23.48:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-11.94:31.87:./.</td>\n",
" <td>1|0:5,2:5:.:-4.20,-1.51,-14.08:40.46:./.</td>\n",
" <td>0|0:10,0:8:.:-0.01,-2.42,-31.35:43.98:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.89:23.68:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.89:23.97:./.</td>\n",
" <td>1|0:2,3:4:.:-7.20,-1.21,-7.09:60:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.69:23.29:./.</td>\n",
" <td>0|1:.:.:.:.,.,.:11.50:./.</td>\n",
" <td>1|0:1,3:3:.:-7.84,-0.91,-3.79:50:./.</td>\n",
" <td>0|0:5,0:4:.:-0.00,-1.21,-15.77:35.69:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>22</td>\n",
" <td>50333748</td>\n",
" <td>rs114900897</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2417;AF=0.022;CB=UM,BI,BC,NCBI;AFR_R2=0.818</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>22</td>\n",
" <td>50334208</td>\n",
" <td>rs4073885</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2555;AF=0.022;CB=UM,BI,BC,NCBI;AFR_R2=0.75</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>22</td>\n",
" <td>50334409</td>\n",
" <td>rs28376035</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2092;AF=0.059;CB=UM,BI;EUR_R2=0.815;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:31.43:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:5,0:2:.:-0.00,-0.60,-8.23:40.46:./.</td>\n",
" <td>1|0:5,4:6:.:-5.50,-1.81,-13.56:46.99:./.</td>\n",
" <td>0|0:6,0:3:.:-0.01,-0.91,-9.48:40.46:./.</td>\n",
" <td>0|0:9,0:5:.:-0.00,-1.51,-19.71:46.99:./.</td>\n",
" <td>0|0:8,0:5:.:-0.00,-1.51,-18.92:46.99:./.</td>\n",
" <td>1|0:7,2:4:.:-5.99,-1.21,-7.33:60:./.</td>\n",
" <td>0|0:7,0:4:.:-0.01,-1.21,-12.22:43.01:./.</td>\n",
" <td>0|1:7,0:1:.:-0.00,-0.30,-3.97:7.52:0/0</td>\n",
" <td>1|0:3,5:5:.:-9.76,-1.51,-7.94:60:./.</td>\n",
" <td>0|0:11,0:7:.:-0.01,-2.11,-26.55:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>22</td>\n",
" <td>50334415</td>\n",
" <td>rs28405006</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2200;AF=0.055;CB=UM,BI,BC;AFR_R2=0.651</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:60:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-6.74:60:./.</td>\n",
" <td>0|0:10,0:6:.:-0.01,-1.81,-18.07:60:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-15.08:60:./.</td>\n",
" <td>0|0:10,0:6:.:-0.00,-1.81,-19.77:60:./.</td>\n",
" <td>0|0:7,0:3:.:-0.00,-0.90,-9.83:60:./.</td>\n",
" <td>0|0:11,0:5:.:-0.00,-1.51,-16.20:60:./.</td>\n",
" <td>0|0:6,0:3:.:-0.01,-0.91,-8.59:60:./.</td>\n",
" <td>0|0:6,0:3:.:-0.00,-0.91,-9.43:60:./.</td>\n",
" <td>0|0:9,0:6:.:-0.01,-1.81,-18.67:60:./.</td>\n",
" <td>0|0:12,0:8:.:-0.01,-2.41,-25.90:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>22</td>\n",
" <td>50334443</td>\n",
" <td>rs28612446</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2398;AF=0.069;CB=UM,BI,BC,NCBI;EUR_R2=0.907...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:28.39:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:7,0:7:.:-0.00,-2.11,-26.13:50:./.</td>\n",
" <td>1|0:7,5:8:.:-11.93,-2.42,-13.84:60:./.</td>\n",
" <td>0|0:7,1:6:.:-0.00,-1.81,-22.49:46.99:./.</td>\n",
" <td>0|0:11,0:11:.:-0.01,-3.32,-40.97:60:./.</td>\n",
" <td>0|0:5,0:3:.:-0.00,-0.90,-10.89:37.21:./.</td>\n",
" <td>1|0:8,5:10:.:-9.36,-3.01,-26.04:60:./.</td>\n",
" <td>0|0:7,0:5:.:-0.00,-1.51,-18.51:43.01:./.</td>\n",
" <td>0|1:4,2:4:.:-2.57,-1.21,-11.88:23.38:./.</td>\n",
" <td>1|0:3,3:5:.:-9.29,-1.51,-7.43:60:./.</td>\n",
" <td>0|0:8,0:5:.:-0.00,-1.51,-19.78:46.99:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>22</td>\n",
" <td>50334680</td>\n",
" <td>rs62234028</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2743;AF=0.099;CB=UM,BI,BC,NCBI;EUR_R2=0.98;...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-8.02:39.21:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-18.40:60:./.</td>\n",
" <td>1|0:1,5:5:.:-10.79,-1.51,-3.68:60:./.</td>\n",
" <td>0|0:11,0:9:.:-0.00,-2.71,-33.87:60:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-19.51:50:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-11.89:45.23:./.</td>\n",
" <td>1|0:7,3:9:.:-6.00,-2.71,-25.63:60:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.86:38.24:./.</td>\n",
" <td>0|1:0,1:1:.:-2.77,-0.30,-0.00:42.22:1/1</td>\n",
" <td>1|0:3,4:6:.:-9.73,-1.81,-11.39:60:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.92:43.98:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4970</th>\n",
" <td>22</td>\n",
" <td>51217134</td>\n",
" <td>rs117417021</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1636;AF=0.080;CB=BI,BC;EUR_R2=0.423;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:6.73:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:9.80:./.</td>\n",
" <td>0|0:4,1:3:.:-0.00,-0.91,-10.29:22.85:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:8.07:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-11.08:20.32:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-11.29:22.06:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:5.15:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:6.92:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.62:15.65:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.20,-16.16:24.93:./.</td>\n",
" <td>0|0:6,0:6:.:-0.00,-1.81,-23.76:32.01:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4971</th>\n",
" <td>22</td>\n",
" <td>51217954</td>\n",
" <td>rs9616974</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2572;AF=0.066;CB=UM,BI;EUR_R2=0.925;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.04:10.47:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:8,0:3:.:-0.00,-0.90,-11.16:40.97:./.</td>\n",
" <td>0|0:4,0:1:.:-0.00,-0.30,-3.20:34.32:./.</td>\n",
" <td>0|1:2,1:2:.:-2.87,-0.61,-3.47:34.81:./.</td>\n",
" <td>0|0:5,0:1:.:-0.00,-0.30,-4.00:34.56:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.81:40.46:./.</td>\n",
" <td>0|0:12,0:4:.:-0.01,-1.21,-12.57:45.23:./.</td>\n",
" <td>0|0:2,0:3:.:-2.80,-3.31,-8.58:26.29:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.80:34.69:./.</td>\n",
" <td>0|0:10,0:7:.:-0.00,-2.11,-25.06:50:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:31.14:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4972</th>\n",
" <td>22</td>\n",
" <td>51218224</td>\n",
" <td>rs9616975</td>\n",
" <td>C</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2741;AF=0.050;CB=UM,BI,BC,NCBI;EUR_R2=0.699...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:12.69:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:10,0:4:.:-0.00,-1.21,-13.47:43.98:./.</td>\n",
" <td>0|0:9,0:4:.:-0.00,-1.21,-12.66:43.01:./.</td>\n",
" <td>0|1:4,3:4:.:-5.23,-1.21,-6.86:60:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:31.74:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:31.49:./.</td>\n",
" <td>0|0:7,0:3:.:-0.00,-0.90,-9.92:40:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:27.19:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:30.71:./.</td>\n",
" <td>0|0:11,0:4:.:-0.00,-1.21,-12.40:43.98:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:30.86:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4973</th>\n",
" <td>22</td>\n",
" <td>51218615</td>\n",
" <td>rs117845379</td>\n",
" <td>T</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2071;AF=0.067;CB=UM,BI,BC,NCBI;EUR_R2=0.765...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-4.00:11.69:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:10,0:9:.:-0.01,-2.71,-29.75:60:./.</td>\n",
" <td>0|0:7,0:6:.:-0.00,-1.81,-20.37:50:./.</td>\n",
" <td>0|1:6,1:7:.:-3.70,-2.11,-20.97:21.16:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.10:36.99:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.91,-9.40:38.24:./.</td>\n",
" <td>0|0:10,0:9:.:-0.01,-2.71,-30.25:60:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-15.97:35.23:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.98:40.46:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.44:40.46:./.</td>\n",
" <td>0|0:5,0:5:.:-0.01,-1.51,-16.19:46.99:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4974</th>\n",
" <td>22</td>\n",
" <td>51218957</td>\n",
" <td>rs116323389</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3192;AF=0.015;CB=UM,BI,BC,NCBI;AFR_R2=0.867</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-4.07:33.57:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.20,-15.63:37.45:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.21,-13.55:38.86:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.21,-13.56:40.97:./.</td>\n",
" <td>0|0:8,0:8:.:-0.00,-2.41,-30.60:50:./.</td>\n",
" <td>0|0:7,0:7:.:-0.00,-2.11,-26.21:46.99:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-18.50:41.55:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.76:32.52:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.21,-13.35:38.24:./.</td>\n",
" <td>0|0:10,0:10:.:-0.00,-3.01,-37.71:60:./.</td>\n",
" <td>0|0:8,0:7:.:-0.00,-2.11,-26.22:46.99:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4975</th>\n",
" <td>22</td>\n",
" <td>51219006</td>\n",
" <td>rs28729663</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3270;AF=0.200;CB=UM,BI,BC,NCBI;EUR_R2=0.871...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|1:0,1:1:.:-3.77,-0.30,-0.00:7.51:1/1</td>\n",
" <td>...</td>\n",
" <td>0|0:8,0:7:.:-0.00,-2.11,-22.66:35.69:./.</td>\n",
" <td>0|0:6,0:5:.:-0.01,-1.51,-14.95:30:./.</td>\n",
" <td>0|1:3,2:5:.:-7.21,-1.51,-10.29:60:./.</td>\n",
" <td>0|0:8,0:10:.:-6.24,-8.71,-30.87:40:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.21,-12.30:26.99:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-15.80:29.96:./.</td>\n",
" <td>1|0:2,1:3:.:-3.87,-0.90,-6.49:38.54:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.73:23.74:./.</td>\n",
" <td>0|0:9,0:9:.:-0.01,-2.71,-29.33:42.22:./.</td>\n",
" <td>0|0:5,0:5:.:-0.01,-1.51,-15.33:30.71:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4976</th>\n",
" <td>22</td>\n",
" <td>51219216</td>\n",
" <td>rs6010087</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3115;AF=0.002;CB=UM,BI,NCBI;AFR_R2=0.794</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4977</th>\n",
" <td>22</td>\n",
" <td>51219382</td>\n",
" <td>rs118066233</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2889;AF=0.000;CB=BI,BC,NCBI;AFR_R2=0.957</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.50:60:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:8,0:8:.:-0.00,-2.41,-26.36:60:./.</td>\n",
" <td>0|0:7,0:6:.:-0.01,-1.81,-17.14:60:./.</td>\n",
" <td>0|0:9,0:9:.:-0.00,-2.71,-29.83:60:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.30:60:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-10.36:60:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.40:60:./.</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-6.34:60:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.06:60:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.20,-15.28:60:./.</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-6.44:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4978</th>\n",
" <td>22</td>\n",
" <td>51219387</td>\n",
" <td>rs9616832</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2796;AF=0.069;CB=UM,BI,BC,NCBI;EUR_R2=0.952...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-4.06:10.25:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:10,0:9:.:-0.00,-2.71,-34.55:60:./.</td>\n",
" <td>0|0:7,0:6:.:-0.00,-1.81,-21.99:50:./.</td>\n",
" <td>0|1:7,2:7:.:-3.17,-2.11,-23.27:46.99:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.86:34.69:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-11.58:40.46:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.86:38.24:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-11.69:26.80:./.</td>\n",
" <td>0|0:3,0:2:.:-0.00,-0.60,-7.12:37.96:./.</td>\n",
" <td>0|0:4,0:4:.:-0.00,-1.20,-15.82:43.98:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-11.40:39.59:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4979</th>\n",
" <td>22</td>\n",
" <td>51220441</td>\n",
" <td>rs76759269</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1857;AF=1.000;CB=UM,BI,BC</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>1|1:0,1:1:.:-2.80,-0.30,-0.00:36.58:./.</td>\n",
" <td>...</td>\n",
" <td>1|1:0,2:2:.:-5.96,-0.60,-0.00:38.24:./.</td>\n",
" <td>1|1:0,7:5:.:-14.73,-1.51,-0.01:46.99:./.</td>\n",
" <td>1|1:0,13:9:.:-27.58,-2.71,-0.01:60:./.</td>\n",
" <td>1|1:0,8:3:.:-8.83,-0.90,-0.00:40.97:./.</td>\n",
" <td>1|1:0,5:4:.:-11.73,-1.21,-0.01:43.98:./.</td>\n",
" <td>1|1:0,6:6:.:-18.17,-1.81,-0.01:50:./.</td>\n",
" <td>1|1:0,1:1:.:-3.07,-0.30,-0.00:36.20:./.</td>\n",
" <td>1|1:0,7:5:.:-15.10,-1.51,-0.00:46.99:./.</td>\n",
" <td>1|1:0,4:4:.:-12.56,-4.54,-3.95:37.96:./.</td>\n",
" <td>1|1:0,4:3:.:-8.93,-0.91,-0.00:40.97:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4980</th>\n",
" <td>22</td>\n",
" <td>51220848</td>\n",
" <td>rs9616981</td>\n",
" <td>C</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3053;AF=0.126;CB=UM,BI,BC;EUR_R2=0.607;AFR_...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,2:1:.:-0.00,-0.30,-3.66:10.88:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:14,1:14:.:-0.01,-4.22,-44.95:60:./.</td>\n",
" <td>0|0:7,0:7:.:-0.01,-2.11,-20.53:31.80:./.</td>\n",
" <td>0|0:5,1:5:.:-0.00,-1.51,-16.56:18.25:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.46:12.84:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-16.37:25.21:./.</td>\n",
" <td>0|0:17,1:17:.:-0.01,-5.12,-55.22:60:./.</td>\n",
" <td>0|0:5,0:4:.:-0.00,-1.21,-11.96:20.55:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.56:16.09:./.</td>\n",
" <td>0|0:12,0:12:.:-0.00,-3.61,-41.70:46.99:./.</td>\n",
" <td>0|0:9,2:9:.:-0.01,-2.71,-30.09:37.96:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4981</th>\n",
" <td>22</td>\n",
" <td>51220938</td>\n",
" <td>rs78802599</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=4787;AF=0.220;CB=BI,BC,NCBI;EUR_R2=0.667;AF...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,1:1:.:-0.00,-0.30,-4.07:6.93:./.</td>\n",
" <td>...</td>\n",
" <td>0|1:5,1:6:.:-3.40,-1.81,-19.62:12.98:./.</td>\n",
" <td>0|0:6,1:6:.:-0.00,-1.81,-20.77:21.40:./.</td>\n",
" <td>0|0:11,2:11:.:-3.30,-3.32,-37.84:3.99:./.</td>\n",
" <td>1|0:4,2:3:.:-3.50,-0.90,-8.03:22.92:./.</td>\n",
" <td>0|0:13,0:13:.:-0.01,-3.92,-48.33:60:./.</td>\n",
" <td>0|0:13,3:13:.:-3.17,-3.92,-44.70:11.14:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-11.18:12.39:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.53:9.72:./.</td>\n",
" <td>0|0:9,0:9:.:-0.00,-2.71,-35.56:30.41:./.</td>\n",
" <td>0|0:6,1:6:.:-0.00,-1.81,-24.48:21.42:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4982</th>\n",
" <td>22</td>\n",
" <td>51221731</td>\n",
" <td>rs115055839</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2518;AF=0.059;CB=UM,BI,BC,NCBI;EUR_R2=0.807...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:10.76:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:4,0:4:.:-0.01,-1.21,-14.17:31.74:./.</td>\n",
" <td>0|0:8,0:8:.:-0.01,-2.41,-27.82:45.23:./.</td>\n",
" <td>0|1:7,11:17:.:-32.13,-5.12,-26.47:60:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.17:19.80:./.</td>\n",
" <td>0|0:7,0:7:.:-0.00,-2.11,-26.33:42.22:./.</td>\n",
" <td>0|0:5,0:5:.:-0.00,-1.51,-18.14:36.78:./.</td>\n",
" <td>0|0:9,0:9:.:-0.01,-2.72,-31.78:45.23:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-16.91:34.32:./.</td>\n",
" <td>0|0:12,0:12:.:-0.01,-3.62,-44.65:60:./.</td>\n",
" <td>0|0:10,0:9:.:-0.01,-2.72,-32.28:50:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4983</th>\n",
" <td>22</td>\n",
" <td>51222052</td>\n",
" <td>rs2879915</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=979;AF=0.190;CB=UM,BI,BC,NCBI;EUR_R2=0.314;...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:3.02:./.</td>\n",
" <td>...</td>\n",
" <td>1|1:2,4:3:.:-9.18,-0.91,-0.01:4:./.</td>\n",
" <td>0|0:3,0:1:.:-0.00,-0.30,-3.07:5.90:./.</td>\n",
" <td>0|1:2,2:2:.:-3.76,-0.60,-2.70:26.09:./.</td>\n",
" <td>1|0:2,5:2:.:-7.52,-0.60,-0.00:3.70:1/1</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.46:8.15:./.</td>\n",
" <td>1|1:0,6:4:.:-14.32,-1.21,-0.00:6.43:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.07:./.</td>\n",
" <td>0|1:5,1:5:.:-3.36,-1.51,-12.50:17.28:./.</td>\n",
" <td>1|0:0,1:1:.:-3.86,-0.30,-0.00:5.98:1/1</td>\n",
" <td>0|0:10,0:8:.:-0.01,-2.41,-24.49:25.70:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4984</th>\n",
" <td>22</td>\n",
" <td>51222100</td>\n",
" <td>rs114553188</td>\n",
" <td>G</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=840;AF=0.082;CB=UM,BI;EUR_R2=0.393;AFR_R2=0...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:9.42:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:9.82:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-9.57:18.88:./.</td>\n",
" <td>0|0:5,0:4:.:-0.01,-1.21,-11.76:21.34:./.</td>\n",
" <td>0|0:4,0:1:.:-0.00,-0.30,-2.70:13.09:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.11:15.88:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-8.86:18.88:./.</td>\n",
" <td>1|0:.:.:.:.,.,.:1.94:./.</td>\n",
" <td>0|0:3,1:2:.:-0.00,-0.60,-7.21:15.75:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-6.06:15.99:./.</td>\n",
" <td>0|0:5,0:4:.:-0.01,-1.21,-12.22:21.89:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4985</th>\n",
" <td>22</td>\n",
" <td>51223848</td>\n",
" <td>rs2519470</td>\n",
" <td>C</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2632;AF=0.020;CB=BI,BC;AFR_R2=0.782</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-4.49:60:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:6,1:5:.:-0.01,-1.51,-19.73:60:./.</td>\n",
" <td>0|0:8,0:7:.:-0.01,-2.11,-27.90:60:./.</td>\n",
" <td>0|0:9,0:7:.:-0.01,-2.11,-28.36:60:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-20.18:60:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-20.12:60:./.</td>\n",
" <td>0|0:7,0:6:.:-0.00,-1.81,-25.01:60:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-19.17:60:./.</td>\n",
" <td>0|0:5,0:5:.:-0.01,-1.51,-18.37:60:./.</td>\n",
" <td>0|0:12,0:12:.:-0.01,-3.62,-49.18:60:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.91,-11.78:60:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4986</th>\n",
" <td>22</td>\n",
" <td>51224208</td>\n",
" <td>rs116656403</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3100;AF=0.024;CB=UM,BI,NCBI;AFR_R2=0.936</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.06:37.45:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.43:40.46:./.</td>\n",
" <td>0|0:9,0:9:.:-0.01,-2.72,-28.91:60:./.</td>\n",
" <td>0|0:11,0:11:.:-0.01,-3.32,-36.33:60:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-6.46:37.45:./.</td>\n",
" <td>0|0:5,0:4:.:-0.00,-1.21,-13.36:43.98:./.</td>\n",
" <td>0|0:14,0:13:.:-0.02,-3.92,-40.44:60:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-6.64:37.45:./.</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.40:34.56:./.</td>\n",
" <td>0|0:8,0:8:.:-0.00,-2.41,-26.71:60:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-16.03:46.99:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4987</th>\n",
" <td>22</td>\n",
" <td>51224947</td>\n",
" <td>rs6009969</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3023;AF=0.078;CB=UM,BI,BC;EUR_R2=0.346;AFR_...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:6.17:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:6.17:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:6.17:./.</td>\n",
" <td>0|0:2,2:1:.:-0.00,-0.30,-3.16:8.88:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:6.17:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:6.17:./.</td>\n",
" <td>0|0:5,0:1:.:-0.00,-0.30,-4.07:8.88:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-7.33:11.59:./.</td>\n",
" <td>0|0:5,0:2:.:-0.00,-0.60,-7.11:11.59:./.</td>\n",
" <td>0|0:10,0:5:.:-0.00,-1.51,-19.50:20.41:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:6.17:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4988</th>\n",
" <td>22</td>\n",
" <td>51224993</td>\n",
" <td>rs2595141</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2322;AF=0.020;CB=BI,BC;EUR_R2=0.59;AFR_R2=0...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:20.55:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:20.55:./.</td>\n",
" <td>0|0:6,1:4:.:-0.00,-1.21,-16.22:32.60:./.</td>\n",
" <td>0|0:2,1:2:.:-0.00,-0.60,-8.84:26.54:./.</td>\n",
" <td>0|0:5,0:3:.:-0.00,-0.90,-13.43:29.51:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-13.43:29.51:./.</td>\n",
" <td>0|0:6,0:6:.:-0.00,-1.81,-24.96:38.54:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-12.78:29.51:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:20.55:./.</td>\n",
" <td>0|0:10,0:8:.:-0.00,-2.41,-35.26:45.23:./.</td>\n",
" <td>0|0:2,2:1:.:-0.00,-0.30,-3.85:23.54:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4989</th>\n",
" <td>22</td>\n",
" <td>51227891</td>\n",
" <td>rs6010091</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1953;AF=0.264;CB=UM,BI,BC;EUR_R2=0.429;AFR_...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-2.90:6.41:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:2.29:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-5.54:12.11:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:1.97:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.76:./.</td>\n",
" <td>1|0:0,1:1:.:-3.66,-0.30,-0.00:9.76:1/1</td>\n",
" <td>1|1:0,6:1:.:-3.66,-0.30,-0.00:2.23:./.</td>\n",
" <td>1|0:0,3:2:.:-7.61,-0.60,-0.00:5.61:1/1</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.30:8.43:./.</td>\n",
" <td>0|0:6,3:6:.:-0.01,-1.81,-18.29:18.11:./.</td>\n",
" <td>0|0:4,0:2:.:-0.00,-0.60,-6.46:11.17:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4990</th>\n",
" <td>22</td>\n",
" <td>51227937</td>\n",
" <td>rs6009970</td>\n",
" <td>A</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=1066;AF=0.997;CB=UM,BI;EUR_R2=0.21;AFR_R2=0...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>1|1:.:.:.:.,.,.:12.86:./.</td>\n",
" <td>...</td>\n",
" <td>1|1:.:.:.:.,.,.:12.22:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:12.97:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:13.98:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:11.92:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:7.93:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:12.42:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:7.31:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:12.38:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:13.35:./.</td>\n",
" <td>1|1:.:.:.:.,.,.:13.02:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4991</th>\n",
" <td>22</td>\n",
" <td>51229805</td>\n",
" <td>rs9616985</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=3300;AF=0.085;CB=UM,BI,BC;EUR_R2=0.724;AFR_...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-4.17:10.71:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:6,1:5:.:-0.00,-1.51,-18.51:23.10:./.</td>\n",
" <td>0|0:12,1:12:.:-0.01,-3.62,-42.46:45.23:./.</td>\n",
" <td>0|1:6,4:6:.:-9.86,-1.81,-11.68:60:./.</td>\n",
" <td>0|0:10,0:5:.:-0.00,-1.51,-18.61:23.21:./.</td>\n",
" <td>0|0:10,0:8:.:-0.01,-2.41,-28.27:32.01:./.</td>\n",
" <td>0|0:9,0:8:.:-0.01,-2.41,-28.88:31.94:./.</td>\n",
" <td>0|0:14,0:12:.:-0.01,-3.62,-44.52:45.23:./.</td>\n",
" <td>0|0:6,0:5:.:-0.00,-1.51,-18.92:23.31:./.</td>\n",
" <td>0|0:8,0:6:.:-0.00,-1.81,-23.46:26.11:./.</td>\n",
" <td>0|0:10,0:7:.:-0.00,-2.11,-26.83:29.28:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4992</th>\n",
" <td>22</td>\n",
" <td>51233312</td>\n",
" <td>rs62240043</td>\n",
" <td>A</td>\n",
" <td>G</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2252;AF=0.078;CB=UM,BI;EUR_R2=0.321;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.61:13.84:./.</td>\n",
" <td>...</td>\n",
" <td>1|1:0,2:1:.:-3.17,-0.30,-0.00:3.28:./.</td>\n",
" <td>0|0:2,0:1:.:-0.00,-0.30,-3.36:11.02:./.</td>\n",
" <td>0|1:6,2:1:.:-0.00,-0.30,-3.17:2.96:0/0</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.07:11.02:./.</td>\n",
" <td>0|1:3,4:1:.:-0.00,-0.30,-3.66:2.84:0/0</td>\n",
" <td>0|1:2,4:1:.:-2.77,-0.30,-0.00:10.71:1/1</td>\n",
" <td>0|0:.:.:.:.,.,.:8.23:./.</td>\n",
" <td>0|0:6,0:3:.:-0.00,-0.91,-10.07:16.85:./.</td>\n",
" <td>0|0:8,1:1:.:-0.00,-0.30,-3.76:12.02:./.</td>\n",
" <td>0|0:5,0:1:.:-0.00,-0.30,-3.86:12.68:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4993</th>\n",
" <td>22</td>\n",
" <td>51233347</td>\n",
" <td>rs62240044</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2566;AF=0.010;CB=UM,BI;EUR_R2=0.072;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-8.23:10.09:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>1|0:5,3:1:.:-3.10,-0.30,-0.00:7.46:1/1</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:4.91:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4994</th>\n",
" <td>22</td>\n",
" <td>51234159</td>\n",
" <td>rs8138356</td>\n",
" <td>T</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2851;AF=0.021;CB=UM,BI;EUR_R2=0.548;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.64:27.72:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:5,0:2:.:-0.00,-0.60,-7.70:27.72:./.</td>\n",
" <td>0|0:5,0:1:.:-0.00,-0.30,-3.40:24.74:./.</td>\n",
" <td>0|0:10,0:5:.:-0.00,-1.51,-17.03:36.78:./.</td>\n",
" <td>0|0:10,0:4:.:-0.00,-1.21,-13.99:33.77:./.</td>\n",
" <td>0|0:10,0:7:.:-0.01,-2.11,-23.25:43.01:./.</td>\n",
" <td>0|0:7,0:1:.:-0.00,-0.30,-3.60:24.74:./.</td>\n",
" <td>0|0:5,0:1:.:-0.00,-0.30,-3.40:24.74:./.</td>\n",
" <td>0|0:7,0:3:.:-0.00,-0.90,-9.84:30.71:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-10.24:30.71:./.</td>\n",
" <td>0|0:5,0:1:.:-0.00,-0.30,-3.44:24.74:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4995</th>\n",
" <td>22</td>\n",
" <td>51234199</td>\n",
" <td>rs6010092</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2463;AF=0.006;CB=UM,BI;EUR_R2=0.648;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.96:25.48:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:1,0:1:.:-0.00,-0.30,-3.97:25.48:./.</td>\n",
" <td>0|0:6,0:6:.:-0.00,-1.81,-21.60:40.46:./.</td>\n",
" <td>0|0:11,0:11:.:-0.01,-3.32,-41.93:60:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.62:28.48:./.</td>\n",
" <td>0|0:11,0:9:.:-0.01,-2.72,-32.46:50:./.</td>\n",
" <td>0|0:11,0:10:.:-0.00,-3.01,-36.92:50:./.</td>\n",
" <td>0|0:6,0:5:.:-0.01,-1.51,-17.11:37.45:./.</td>\n",
" <td>0|0:8,0:7:.:-0.00,-2.11,-25.95:43.98:./.</td>\n",
" <td>0|0:10,0:10:.:-0.00,-3.01,-38.82:50:./.</td>\n",
" <td>0|0:8,0:8:.:-0.00,-2.41,-29.28:46.99:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4996</th>\n",
" <td>22</td>\n",
" <td>51234632</td>\n",
" <td>rs6010093</td>\n",
" <td>G</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2243;AF=0.003;CB=UM,BI;AFR_R2=0.658</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>...</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" <td>./.:.:.:.:.,.,.:.:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4997</th>\n",
" <td>22</td>\n",
" <td>51235344</td>\n",
" <td>rs114148499</td>\n",
" <td>G</td>\n",
" <td>A</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2322;AF=0.030;CB=UM,BI,BC;EUR_R2=0.548;AFR_...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.26:14.83:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.19:14.62:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.91,-8.43:17.62:./.</td>\n",
" <td>0|0:4,0:3:.:-0.00,-0.90,-9.11:17.63:./.</td>\n",
" <td>0|0:3,0:1:.:-0.00,-0.30,-3.50:11.85:./.</td>\n",
" <td>0|0:3,0:3:.:-0.00,-0.90,-9.03:17.60:./.</td>\n",
" <td>0|0:6,0:3:.:-0.00,-0.90,-9.63:17.62:./.</td>\n",
" <td>0|0:2,0:2:.:-0.00,-0.60,-7.49:14.71:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:9:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:9.08:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:8.86:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4998</th>\n",
" <td>22</td>\n",
" <td>51237063</td>\n",
" <td>rs3896457</td>\n",
" <td>T</td>\n",
" <td>C</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2410;AF=0.136;CB=UM,BI;EUR_R2=0.25;AFR_R2=0.46</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:3.27:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" <td>0|1:2,1:1:.:-3.37,-0.30,-0.00:5.39:1/1</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" <td>1|1:1,2:2:.:-5.96,-0.60,-0.00:2.80:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" <td>0|1:4,2:1:.:-3.27,-0.30,-0.00:5.39:1/1</td>\n",
" <td>0|0:.:.:.:.,.,.:3.06:./.</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4999</th>\n",
" <td>22</td>\n",
" <td>51238831</td>\n",
" <td>rs62240048</td>\n",
" <td>C</td>\n",
" <td>T</td>\n",
" <td>.</td>\n",
" <td>PASS</td>\n",
" <td>DP=2392;AF=0.268;CB=UM,BI;EUR_R2=0.392;AFR_R2=...</td>\n",
" <td>GT:AD:DP:GD:GL:GQ:OG</td>\n",
" <td>0|0:.:.:.:.,.,.:8.45:./.</td>\n",
" <td>...</td>\n",
" <td>0|0:4,2:4:.:-0.00,-1.21,-12.40:20.10:./.</td>\n",
" <td>0|0:.:.:.:.,.,.:8.45:./.</td>\n",
" <td>0|0:3,4:2:.:-0.00,-0.60,-6.14:14.13:./.</td>\n",
" <td>0|1:0,2:1:.:-3.97,-0.30,-0.00:11.31:1/1</td>\n",
" <td>0|0:6,2:4:.:-0.01,-1.21,-11.53:20:./.</td>\n",
" <td>0|0:8,1:6:.:-0.01,-1.81,-18.14:25.97:./.</td>\n",
" <td>0|0:1,3:1:.:-0.00,-0.30,-2.77:11.29:./.</td>\n",
" <td>0|0:2,2:1:.:-0.00,-0.30,-2.97:11.29:./.</td>\n",
" <td>0|0:7,0:5:.:-0.01,-1.51,-14.73:22.97:./.</td>\n",
" <td>0|0:5,0:3:.:-0.00,-0.91,-8.93:17.14:./.</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5000 rows × 638 columns</p>\n",
"</div>"
],
"text/plain": [
" #CHROM POS ID REF ALT QUAL FILTER \\\n",
"0 22 50328528 rs116643340 G C . PASS \n",
"1 22 50328670 rs114196268 G A . PASS \n",
"2 22 50328731 rs28608875 C T . PASS \n",
"3 22 50329119 rs56008904 C T . PASS \n",
"4 22 50329830 rs79860705 G A . PASS \n",
"5 22 50330186 rs73444002 G T . PASS \n",
"6 22 50330345 rs28652639 G A . PASS \n",
"7 22 50330546 rs28516848 T G . PASS \n",
"8 22 50331032 rs115322211 G A . PASS \n",
"9 22 50331164 rs28690400 T C . PASS \n",
"10 22 50331300 rs73891184 T C . PASS \n",
"11 22 50331475 rs76433322 A G . PASS \n",
"12 22 50331622 rs28393180 C T . PASS \n",
"13 22 50332005 rs28460675 G T . PASS \n",
"14 22 50332022 rs28470489 T A . PASS \n",
"15 22 50332097 rs77228592 C T . PASS \n",
"16 22 50332242 rs28451805 A G . PASS \n",
"17 22 50332324 rs28523661 T C . PASS \n",
"18 22 50332377 rs114353012 C T . PASS \n",
"19 22 50332472 rs115364094 C G . PASS \n",
"20 22 50333130 rs77002698 G A . PASS \n",
"21 22 50333253 rs116837852 G A . PASS \n",
"22 22 50333415 rs4073387 G A . PASS \n",
"23 22 50333697 rs4073388 C G . PASS \n",
"24 22 50333748 rs114900897 C T . PASS \n",
"25 22 50334208 rs4073885 C T . PASS \n",
"26 22 50334409 rs28376035 A G . PASS \n",
"27 22 50334415 rs28405006 C T . PASS \n",
"28 22 50334443 rs28612446 T C . PASS \n",
"29 22 50334680 rs62234028 A G . PASS \n",
"... ... ... ... .. .. ... ... \n",
"4970 22 51217134 rs117417021 A G . PASS \n",
"4971 22 51217954 rs9616974 G A . PASS \n",
"4972 22 51218224 rs9616975 C A . PASS \n",
"4973 22 51218615 rs117845379 T A . PASS \n",
"4974 22 51218957 rs116323389 A G . PASS \n",
"4975 22 51219006 rs28729663 G A . PASS \n",
"4976 22 51219216 rs6010087 G A . PASS \n",
"4977 22 51219382 rs118066233 G A . PASS \n",
"4978 22 51219387 rs9616832 T C . PASS \n",
"4979 22 51220441 rs76759269 T C . PASS \n",
"4980 22 51220848 rs9616981 C A . PASS \n",
"4981 22 51220938 rs78802599 A G . PASS \n",
"4982 22 51221731 rs115055839 T C . PASS \n",
"4983 22 51222052 rs2879915 G A . PASS \n",
"4984 22 51222100 rs114553188 G T . PASS \n",
"4985 22 51223848 rs2519470 C G . PASS \n",
"4986 22 51224208 rs116656403 G A . PASS \n",
"4987 22 51224947 rs6009969 A G . PASS \n",
"4988 22 51224993 rs2595141 G C . PASS \n",
"4989 22 51227891 rs6010091 G A . PASS \n",
"4990 22 51227937 rs6009970 A C . PASS \n",
"4991 22 51229805 rs9616985 T C . PASS \n",
"4992 22 51233312 rs62240043 A G . PASS \n",
"4993 22 51233347 rs62240044 T C . PASS \n",
"4994 22 51234159 rs8138356 T A . PASS \n",
"4995 22 51234199 rs6010092 T C . PASS \n",
"4996 22 51234632 rs6010093 G C . PASS \n",
"4997 22 51235344 rs114148499 G A . PASS \n",
"4998 22 51237063 rs3896457 T C . PASS \n",
"4999 22 51238831 rs62240048 C T . PASS \n",
"\n",
" INFO FORMAT \\\n",
"0 DP=269;AF=0.010;CB=BI,NCBI;AFR_R2=0.516 GT:AD:DP:GD:GL:GQ:OG \n",
"1 DP=1089;AF=0.007;CB=UM,BI,BC,NCBI;AFR_R2=0.465 GT:AD:DP:GD:GL:GQ:OG \n",
"2 DP=907;AF=0.055;CB=UM,BI,BC,NCBI;EUR_R2=0.751;... GT:AD:DP:GD:GL:GQ:OG \n",
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"23 DP=1957;AF=0.073;CB=UM,BI,BC,NCBI;EUR_R2=0.885... GT:AD:DP:GD:GL:GQ:OG \n",
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"27 DP=2200;AF=0.055;CB=UM,BI,BC;AFR_R2=0.651 GT:AD:DP:GD:GL:GQ:OG \n",
"28 DP=2398;AF=0.069;CB=UM,BI,BC,NCBI;EUR_R2=0.907... GT:AD:DP:GD:GL:GQ:OG \n",
"29 DP=2743;AF=0.099;CB=UM,BI,BC,NCBI;EUR_R2=0.98;... GT:AD:DP:GD:GL:GQ:OG \n",
"... ... ... \n",
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"\n",
" HG00098 \\\n",
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"3 0|0:.:.:.:.,.,.:3.49:./. \n",
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"17 0|0:.:.:.:.,.,.:4.64:./. \n",
"18 ./.:.:.:.:.,.,.:.:./. \n",
"19 ./.:.:.:.:.,.,.:.:./. \n",
"20 0|0:.:.:.:.,.,.:30.97:./. \n",
"21 ./.:.:.:.:.,.,.:.:./. \n",
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"23 0|0:1,0:1:.:-0.00,-0.30,-4.05:23.48:./. \n",
"24 ./.:.:.:.:.,.,.:.:./. \n",
"25 ./.:.:.:.:.,.,.:.:./. \n",
"26 0|0:.:.:.:.,.,.:31.43:./. \n",
"27 0|0:.:.:.:.,.,.:60:./. \n",
"28 0|0:.:.:.:.,.,.:28.39:./. \n",
"29 0|0:2,0:2:.:-0.00,-0.60,-8.02:39.21:./. \n",
"... ... \n",
"4970 0|0:.:.:.:.,.,.:6.73:./. \n",
"4971 0|0:2,0:2:.:-0.00,-0.60,-6.04:10.47:./. \n",
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"4975 0|1:0,1:1:.:-3.77,-0.30,-0.00:7.51:1/1 \n",
"4976 ./.:.:.:.:.,.,.:.:./. \n",
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"4981 0|0:1,1:1:.:-0.00,-0.30,-4.07:6.93:./. \n",
"4982 0|0:.:.:.:.,.,.:10.76:./. \n",
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"4985 0|0:2,0:1:.:-0.00,-0.30,-4.49:60:./. \n",
"4986 0|0:2,0:2:.:-0.00,-0.60,-7.06:37.45:./. \n",
"4987 0|0:.:.:.:.,.,.:6.17:./. \n",
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"4990 1|1:.:.:.:.,.,.:12.86:./. \n",
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"4995 0|0:1,0:1:.:-0.00,-0.30,-3.96:25.48:./. \n",
"4996 ./.:.:.:.:.,.,.:.:./. \n",
"4997 0|0:2,0:2:.:-0.00,-0.60,-7.26:14.83:./. \n",
"4998 0|0:.:.:.:.,.,.:3.27:./. \n",
"4999 0|0:.:.:.:.,.,.:8.45:./. \n",
"\n",
" ... \\\n",
"0 ... \n",
"1 ... \n",
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"4970 ... \n",
"4971 ... \n",
"4972 ... \n",
"4973 ... \n",
"4974 ... \n",
"4975 ... \n",
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"4977 ... \n",
"4978 ... \n",
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"4980 ... \n",
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"4990 ... \n",
"4991 ... \n",
"4992 ... \n",
"4993 ... \n",
"4994 ... \n",
"4995 ... \n",
"4996 ... \n",
"4997 ... \n",
"4998 ... \n",
"4999 ... \n",
"\n",
" NA20811 \\\n",
"0 ./.:.:.:.:.,.,.:.:./. \n",
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"7 0|0:.:.:.:.,.,.:21.73:./. \n",
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"10 ./.:.:.:.:.,.,.:.:./. \n",
"11 ./.:.:.:.:.,.,.:.:./. \n",
"12 0|0:6,0:6:.:-0.01,-1.81,-17.47:60:./. \n",
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"17 1|1:0,15:14:.:-45.50,-4.22,-0.02:60:./. \n",
"18 ./.:.:.:.:.,.,.:.:./. \n",
"19 ./.:.:.:.:.,.,.:.:./. \n",
"20 0|0:3,0:2:.:-0.00,-0.60,-6.16:40.46:./. \n",
"21 ./.:.:.:.:.,.,.:.:./. \n",
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"23 0|0:4,0:3:.:-0.00,-0.90,-11.94:31.87:./. \n",
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"26 0|0:5,0:2:.:-0.00,-0.60,-8.23:40.46:./. \n",
"27 0|0:4,0:2:.:-0.00,-0.60,-6.74:60:./. \n",
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"29 0|0:5,0:5:.:-0.00,-1.51,-18.40:60:./. \n",
"... ... \n",
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"4999 0|0:4,2:4:.:-0.00,-1.21,-12.40:20.10:./. \n",
"\n",
" NA20812 \\\n",
"0 ./.:.:.:.:.,.,.:.:./. \n",
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"19 ./.:.:.:.:.,.,.:.:./. \n",
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"21 ./.:.:.:.:.,.,.:.:./. \n",
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"25 ./.:.:.:.:.,.,.:.:./. \n",
"26 1|0:5,4:6:.:-5.50,-1.81,-13.56:46.99:./. \n",
"27 0|0:10,0:6:.:-0.01,-1.81,-18.07:60:./. \n",
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"... ... \n",
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" NA20813 \\\n",
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" NA20814 \\\n",
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"... ... \n",
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"\n",
" NA20815 \\\n",
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"... ... \n",
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"\n",
" NA20816 \\\n",
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"... ... \n",
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" NA20818 \\\n",
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" NA20819 \\\n",
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" NA20826 \\\n",
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"... ... \n",
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"\n",
" NA20828 \n",
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"... ... \n",
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"4992 0|0:5,0:1:.:-0.00,-0.30,-3.86:12.68:./. \n",
"4993 0|0:.:.:.:.,.,.:4.91:./. \n",
"4994 0|0:5,0:1:.:-0.00,-0.30,-3.44:24.74:./. \n",
"4995 0|0:8,0:8:.:-0.00,-2.41,-29.28:46.99:./. \n",
"4996 ./.:.:.:.:.,.,.:.:./. \n",
"4997 0|0:.:.:.:.,.,.:8.86:./. \n",
"4998 0|0:.:.:.:.,.,.:3.06:./. \n",
"4999 0|0:5,0:3:.:-0.00,-0.91,-8.93:17.14:./. \n",
"\n",
"[5000 rows x 638 columns]"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df = pd.read_table('only_rs_22-5000.vcf', skiprows=18)\n",
"df\n"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"629"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sample_ids = list(df.columns[9:])\n",
"len(sample_ids)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 유전자형을 숫자료 표시 (AA:0, AB:1, BB:2)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"sample_ids_number = ['{} num'.format(s) for s in sample_ids]\n",
"\n",
"def get_number(ref, alt):\n",
" if ',' in alt or '.' in ref or '.' in alt:\n",
" return np.nan\n",
" return sum(map(int, [ref, alt]))\n",
"\n",
"def call_genotype_number(row):\n",
" return pd.Series(\n",
" [get_number(row[s][0], row[s][2]) for s in sample_ids if s], \n",
" index=sample_ids_number)\n",
"\n",
"df[sample_ids_number] = df.apply(call_genotype_number, axis=1)\n"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <th>HG00098 num</th>\n",
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" <td>NaN</td>\n",
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" <th>HG00123 num</th>\n",
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" <th>HG00124 num</th>\n",
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" <td>0.0</td>\n",
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" <th>HG00131 num</th>\n",
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" <tr>\n",
" <th>HG00141 num</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <tr>\n",
" <th>HG00142 num</th>\n",
" <td>NaN</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>HG00143 num</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",