{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "Files in folder: (vcf file (resultados.vcf) and ipython notebook (vcf_filter_tassel.ipynb)" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "resultados.vcf vcf_filter_tassel.ipynb\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "##fileformat=VCFv4.0\r\n", "##Tassel=\r\n", "##FORMAT=\r\n" ] } ], "source": [ "!head -n 3 resultados.vcf" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false, "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "15\t18892\tS15_18892\tT\tC\t.\tPASS\tQualityScore=0.0;DP=1199\tGT:AD:DP:GQ:PL\t0/0:13,0:13:99:0,39,255\t0/0:3,0:3:88:0,9,108\t0/0:3,0:3:88:0,9,108\t0/0:1,0:1:66:0,3,36\t0/0:3,0:3:88:0,9,108\t0/0:2,0:2:79:0,6,72\t0/0:2,0:2:79:0,6,72\t1/1:0,6:6:98:216,18,0\t0/0:3,0:3:88:0,9,108\t0/0:6,0:6:98:0,18,216\t0/0:1,0:1:66:0,3,36\t0/0:2,0:2:79:0,6,72\t0/0:16,0:16:99:0,48,255\t0/0:1,0:1:66:0,3,36\t./.:0,0:0\t0/0:7,0:7:99:0,21,252\t0/0:11,0:11:99:0,33,255\t0/0:3,0:3:88:0,9,108\t0/0:4,0:4:94:0,12,144\t0/0:3,0:3:88:0,9,108\t0/0:1,0:1:66:0,3,36\t./.:0,0:0\t0/0:4,0:4:94:0,12,144\t0/0:3,0:3:88:0,9,108\t0/0:5,0:5:96:0,15,180\t0/0:1,0:1:66:0,3,36\t0/0:4,0:4:94:0,12,144\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:4,0:4:94:0,12,144\t0/0:2,0:2:79:0,6,72\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t./.:0,0:0\t./.:0,0:0\t0/0:8,0:8:99:0,24,255\t0/0:19,0:19:99:0,57,255\t0/0:3,0:3:88:0,9,108\t1/1:0,6:6:98:216,18,0\t0/0:3,0:3:88:0,9,108\t0/0:7,0:7:99:0,21,252\t0/0:10,0:10:99:0,30,255\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t0/0:8,0:8:99:0,24,255\t1/1:0,4:4:94:144,12,0\t0/0:3,0:3:88:0,9,108\t1/1:0,4:4:94:144,12,0\t0/0:1,0:1:66:0,3,36\t1/1:0,3:3:88:108,9,0\t0/0:2,0:2:79:0,6,72\t1/1:0,10:10:99:255,30,0\t1/1:0,4:4:94:144,12,0\t1/0:2,3:5:99:93,0,57\t1/1:0,3:3:88:108,9,0\t./.:0,0:0\t./.:0,0:0\t./.:0,0:0\t0/0:8,0:8:99:0,24,255\t0/0:5,0:5:96:0,15,180\t0/0:5,0:5:96:0,15,180\t0/0:14,0:14:99:0,42,255\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t0/0:4,0:4:94:0,12,144\t0/0:6,0:6:98:0,18,216\t0/0:3,0:3:88:0,9,108\t0/0:14,0:14:99:0,42,255\t0/0:1,0:1:66:0,3,36\t1/1:0,3:3:88:108,9,0\t0/0:6,0:6:98:0,18,216\t./.:0,0:0\t0/0:7,0:7:99:0,21,252\t1/1:0,4:4:94:144,12,0\t./.:0,0:0\t0/1:2,1:3:99:27,0,63\t0/0:2,0:2:79:0,6,72\t0/0:2,0:2:79:0,6,72\t1/0:2,2:4:99:60,0,60\t0/0:4,0:4:94:0,12,144\t./.:0,0:0\t0/0:1,0:1:66:0,3,36\t1/1:0,2:2:79:72,6,0\t1/1:0,3:3:88:108,9,0\t./.:0,0:0\t./.:0,0:0\t0/0:2,0:2:79:0,6,72\t0/0:4,0:4:94:0,12,144\t0/0:3,0:3:88:0,9,108\t0/0:3,0:3:88:0,9,108\t0/0:2,0:2:79:0,6,72\t./.:0,0:0\t./.:0,0:0\t0/0:3,0:3:88:0,9,108\t./.:0,0:0\t0/0:2,0:2:79:0,6,72\t0/0:11,0:11:99:0,33,255\t0/0:2,0:2:79:0,6,72\t0/0:8,0:8:99:0,24,255\t0/0:2,0:2:79:0,6,72\t0/0:3,0:3:88:0,9,108\t0/0:2,0:2:79:0,6,72\t0/0:4,0:4:94:0,12,144\t0/0:2,0:2:79:0,6,72\t0/0:1,0:1:66:0,3,36\t0/0:3,0:3:88:0,9,108\t0/0:5,0:5:96:0,15,180\t0/0:10,0:10:99:0,30,255\t0/0:8,0:8:99:0,24,255\t0/0:7,0:7:99:0,21,252\t0/0:3,0:3:88:0,9,108\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t0/0:6,0:6:98:0,18,216\t0/0:7,0:7:99:0,21,252\t0/0:2,0:2:79:0,6,72\t./.:0,0:0\t0/0:4,0:4:94:0,12,144\t0/0:3,0:3:88:0,9,108\t0/0:3,0:3:88:0,9,108\t0/0:8,0:8:99:0,24,255\t0/0:5,0:5:96:0,15,180\t0/0:1,0:1:66:0,3,36\t0/0:3,0:3:88:0,9,108\t0/0:8,0:8:99:0,24,255\t0/0:3,0:3:88:0,9,108\t0/0:8,0:8:99:0,24,255\t0/0:7,0:7:99:0,21,252\t0/0:1,0:1:66:0,3,36\t0/0:3,0:3:88:0,9,108\t0/0:19,0:19:99:0,57,255\t0/0:3,0:3:88:0,9,108\t0/0:13,0:13:99:0,39,255\t0/0:1,0:1:66:0,3,36\t0/0:10,0:10:99:0,30,255\t0/0:12,0:12:99:0,36,255\t0/0:9,0:9:99:0,27,255\t0/0:9,0:9:99:0,27,255\t0/0:1,0:1:66:0,3,36\t0/1:8,5:13:99:141,0,249\t0/0:8,0:8:99:0,24,255\t0/0:1,0:1:66:0,3,36\t0/0:4,0:4:94:0,12,144\t0/0:9,0:9:99:0,27,255\t0/0:5,0:5:96:0,15,180\t0/0:3,0:3:88:0,9,108\t0/0:4,0:4:94:0,12,144\t0/0:2,0:2:79:0,6,72\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t0/0:4,0:4:94:0,12,144\t0/0:2,0:2:79:0,6,72\t0/0:1,0:1:66:0,3,36\t0/0:6,0:6:98:0,18,216\t0/0:4,0:4:94:0,12,144\t0/0:10,0:10:99:0,30,255\t0/0:4,0:4:94:0,12,144\t1/1:0,5:5:96:180,15,0\t0/0:1,0:1:66:0,3,36\t0/0:7,0:7:99:0,21,252\t0/0:5,0:5:96:0,15,180\t0/0:2,0:2:79:0,6,72\t1/0:2,7:9:99:225,0,45\t0/0:1,0:1:66:0,3,36\t0/0:2,0:2:79:0,6,72\t0/0:3,0:3:88:0,9,108\t./.:0,0:0\t0/0:3,0:3:88:0,9,108\t0/0:2,0:2:79:0,6,72\t0/0:2,0:2:79:0,6,72\t./.:0,0:0\t0/0:1,0:1:66:0,3,36\t0/1:2,1:3:99:27,0,63\t0/0:6,0:6:98:0,18,216\t0/0:1,0:1:66:0,3,36\t0/0:10,0:10:99:0,30,255\t0/0:11,0:11:99:0,33,255\t0/1:3,1:4:99:24,0,96\t0/1:7,4:11:99:111,0,219\t0/0:19,0:19:99:0,57,255\t0/0:8,0:8:99:0,24,255\t0/0:5,0:5:96:0,15,180\t1/1:0,5:5:96:180,15,0\t0/0:3,0:3:88:0,9,108\t0/0:9,0:9:99:0,27,255\t0/0:11,0:11:99:0,33,255\t0/0:8,0:8:99:0,24,255\t0/0:3,0:3:88:0,9,108\t0/0:9,0:9:99:0,27,255\t0/1:7,5:12:99:144,0,216\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t0/0:3,0:3:88:0,9,108\t0/0:4,0:4:94:0,12,144\t0/0:1,0:1:66:0,3,36\t0/0:4,0:4:94:0,12,144\t0/0:1,0:1:66:0,3,36\t./.:0,0:0\t0/0:9,0:9:99:0,27,255\t0/0:2,0:2:79:0,6,72\t0/0:4,0:4:94:0,12,144\t0/0:1,0:1:66:0,3,36\t0/0:9,0:9:99:0,27,255\t0/0:4,0:4:94:0,12,144\t0/0:8,0:8:99:0,24,255\t0/0:20,0:20:99:0,60,255\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:12,0:12:99:0,36,255\t0/0:1,0:1:66:0,3,36\t0/0:8,0:8:99:0,24,255\t0/0:5,0:5:96:0,15,180\t0/0:2,0:2:79:0,6,72\t1/1:0,1:1:66:36,3,0\t0/0:6,0:6:98:0,18,216\t0/0:1,0:1:66:0,3,36\t0/0:5,0:5:96:0,15,180\t1/1:0,3:3:88:108,9,0\t0/0:10,0:10:99:0,30,255\t1/1:0,2:2:79:72,6,0\t0/0:3,0:3:88:0,9,108\t0/0:5,0:5:96:0,15,180\t0/0:6,0:6:98:0,18,216\t0/1:3,2:5:99:57,0,93\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:1,0:1:66:0,3,36\t0/0:3,0:3:88:0,9,108\t0/0:2,0:2:79:0,6,72\t0/0:8,0:8:99:0,24,255\t1/1:0,2:2:79:72,6,0\t1/1:0,4:4:94:144,12,0\t0/0:3,0:3:88:0,9,108\t0/0:5,0:5:96:0,15,180\t0/0:2,0:2:79:0,6,72\t1/1:0,1:1:66:36,3,0\t0/0:2,0:2:79:0,6,72\t0/1:3,1:4:99:24,0,96\t./.:0,0:0\t1/1:0,4:4:94:144,12,0\t0/0:4,0:4:94:0,12,144\t0/1:10,5:15:99:135,0,255\t0/0:10,0:10:99:0,30,255\t./.:0,0:0\t0/1:2,1:3:99:27,0,63\t1/1:0,2:2:79:72,6,0\t0/0:1,0:1:66:0,3,36\t0/0:10,0:10:99:0,30,255\t1/1:0,2:2:79:72,6,0\t1/0:2,2:4:99:60,0,60\t0/0:10,0:10:99:0,30,255\t0/0:20,0:20:99:0,60,255\t0/0:13,0:13:99:0,39,255\t0/0:9,0:9:99:0,27,255\t0/0:2,0:2:79:0,6,72\t0/0:11,0:11:99:0,33,255\t./.:0,0:0\t1/1:0,1:1:66:36,3,0\t0/0:8,0:8:99:0,24,255\t0/0:1,0:1:66:0,3,36\t0/0:7,0:7:99:0,21,252\t0/0:1,0:1:66:0,3,36\t0/0:3,0:3:88:0,9,108\t0/0:5,0:5:96:0,15,180\t0/0:6,0:6:98:0,18,216\r\n" ] } ], "source": [ "!head -n 12 resultados.vcf |grep -v \"#\" " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Filter genotypes with depth lower than 6 reads and discard SNPs are called by less than 50% of individuals in any population" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'YER1', 'YER3', 'YER2', 'YER5', 'YER4', 'SAL4', 'SAL5', 'MNT30', 'SAL2', 'CHI21', 'SAL3', 'CHI20', 'CHI23', 'SAL1', 'CHI22', 'CHI25', 'CHI24', 'CHI27', 'YER7', 'CHI26', 'YER6', 'YER9', 'CHI29', 'YER8', 'CHI28', 'SAL8', 'SAL9', 'SAL6', 'SAL7', 'CHI9', 'CHI8', 'SAL30', 'CHI7', 'CHI6', 'CHI5', 'CHI4', 'CHI30', 'CHI3', 'MNT20', 'SAL24', 'CHI2', 'SAL25', 'MNT22', 'CHI1', 'SAL26', 'MNT21', 'SAL27', 'MNT24', 'SAL28', 'MNT23', 'SAL29', 'MNT26', 'MNT25', 'MNT28', 'MNT27', 'MNT29', 'TUR8', 'TUR7', 'TUR6', 'TUR5', 'TUR4', 'TUR3', 'TUR2', 'TUR1', 'AYA9', 'TUR9', 'AYA7', 'AYA8', 'AYA5', 'MNT11', 'AYA6', 'MNT10', 'AYA3', 'MNT13', 'AYA4', 'MNT12', 'AYA1', 'MNT15', 'MNT14', 'AYA2', 'MNT17', 'MNT16', 'MNT19', 'MNT18', 'YER11', 'YER12', 'YER10', 'YER19', 'YER17', 'YER18', 'YER15', 'YER16', 'YER13', 'YER14', 'CHI10', 'CHI12', 'CHI11', 'CAM9', 'CHI14', 'CAM8', 'CHI13', 'CAM7', 'CHI16', 'CAM6', 'CAM5', 'CHI15', 'CAM4', 'CHI18', 'CHI17', 'CAM3', 'CAM2', 'CAM1', 'CHI19', 'YER22', 'YER23', 'YER20', 'YER21', 'RAS2', 'RAS3', 'YER28', 'RAS1', 'YER29', 'YER26', 'YER27', 'YER24', 'YER25', 'RAS8', 'RAS9', 'RAS6', 'RAS7', 'RAS4', 'RAS5', 'AYA30', 'YER30', 'AYA29', 'AYA26', 'AYA25', 'AYA28', 'AYA27', 'AYA22', 'AYA21', 'AYA24', 'AYA23', 'AYA20', 'TUR30', 'SAL20', 'SAL21', 'SAL22', 'SAL23', 'SAL13', 'SAL14', 'SAL15', 'SAL16', 'SAL17', 'SAL18', 'SAL19', 'SAL10', 'SAL11', 'SAL12', 'PET29', 'PET28', 'PET27', 'PET26', 'PET25', 'PET24', 'PET23', 'TUR17', 'TUR16', 'TUR15', 'TUR14', 'TUR13', 'TUR12', 'TUR11', 'TUR10', 'PET30', 'TUR19', 'TUR18', 'TUR20', 'TUR28', 'PET4', 'PET3', 'TUR27', 'TUR26', 'PET6', 'PET5', 'TUR25', 'TUR24', 'TUR23', 'TUR22', 'PET2', 'TUR21', 'PET1', 'PET8', 'PET7', 'TUR29', 'PET9', 'AYA19', 'AYA18', 'AYA15', 'AYA14', 'AYA17', 'AYA16', 'AYA11', 'AYA10', 'AYA13', 'AYA12', 'RAS10', 'CAM30', 'RAS13', 'RAS14', 'RAS11', 'RAS12', 'RAS17', 'RAS18', 'RAS15', 'RAS16', 'RAS19', 'MNT1', 'MNT2', 'CAM10', 'CAM11', 'RAS30', 'PET11', 'CAM18', 'PET10', 'CAM19', 'CAM16', 'CAM17', 'CAM14', 'CAM15', 'CAM12', 'CAM13', 'CAM21', 'PET19', 'RAS20', 'MNT7', 'MNT8', 'CAM22', 'RAS21', 'PET18', 'MNT9', 'PET17', 'CAM20', 'PET16', 'PET15', 'RAS24', 'MNT3', 'RAS25', 'PET14', 'MNT4', 'MNT5', 'PET13', 'RAS22', 'MNT6', 'PET12', 'RAS23', 'RAS28', 'RAS29', 'RAS26', 'RAS27', 'CAM29', 'PET22', 'PET21', 'CAM27', 'PET20', 'CAM28', 'CAM25', 'CAM26', 'CAM23', 'CAM24']\n" ] } ], "source": [ "#open vcf file\n", "import re\n", "import numpy as np\n", "file_filtrate = open('resultados.vcf')\n", "\n", "#create a new vcf file\n", "new = open('resultados_filtrados.vcf', 'w')\n", "\n", "num_line=0\n", "\n", "for line in file_filtrate:\n", " num_line+=1\n", " if num_line<12:\n", " new.write(line)\n", " if num_line==11:\n", " header=line\n", " header = re.sub('\\n', '', header)\n", " label_samples=header.split('\\t')\n", " print(label_samples)\n", "\n", " else:\n", " \n", " a=line.split('\\t')\n", "\n", " n=0\n", " genotiped=[0.0]*9\n", " not_genotiped=[0.0]*9\n", " fraction_genotiped=[0.0]*9\n", " \n", " for genotype in a:\n", " \n", " n=n+1\n", " if n<10:\n", " new.write(genotype+\"\\t\")\n", " else:\n", " #cambiar esta linea en f(x) num indiividuos!\n", " if n<279:\n", "\n", " b=genotype.split(':')\n", "\n", " if (int(b[2])>=6):\n", " new.write(genotype+\"\\t\")\n", " \n", " pop_asoc=(label_samples[n-1])[:3]\n", " if pop_asoc=='AYA':\n", " genotiped[0]+=1\n", " if pop_asoc=='YER':\n", " genotiped[1]+=1\n", " if pop_asoc=='CAM':\n", " genotiped[2]+=1\n", " if pop_asoc=='PET':\n", " genotiped[3]+=1\n", " if pop_asoc=='RAS':\n", " genotiped[4]+=1\n", " if pop_asoc=='TUR':\n", " genotiped[5]+=1\n", " if pop_asoc=='SAL':\n", " genotiped[6]+=1\n", " if pop_asoc=='CHI':\n", " genotiped[7]+=1\n", " if pop_asoc=='MNT':\n", " genotiped[8]+=1\n", " else:\n", "\n", " new.write('./.:0,0:0'+\"\\t\")\n", " \n", " pop_asoc=(label_samples[n-1])[:3]\n", " if pop_asoc=='AYA':\n", " not_genotiped[0]+=1\n", " if pop_asoc=='YER':\n", " not_genotiped[1]+=1\n", " if pop_asoc=='CAM':\n", " not_genotiped[2]+=1\n", " if pop_asoc=='PET':\n", " not_genotiped[3]+=1\n", " if pop_asoc=='RAS':\n", " not_genotiped[4]+=1\n", " if pop_asoc=='TUR':\n", " not_genotiped[5]+=1\n", " if pop_asoc=='SAL':\n", " not_genotiped[6]+=1\n", " if pop_asoc=='CHI':\n", " not_genotiped[7]+=1\n", " if pop_asoc=='MNT':\n", " not_genotiped[8]+=1\n", " \n", " else:\n", " if (int(b[2])>=6):\n", " end=genotype.split(\"\\n\")\n", " new.write(end[0])\n", " \n", " pop_asoc=(label_samples[n-1])[:3]\n", " if pop_asoc=='AYA':\n", " genotiped[0]+=1\n", " if pop_asoc=='YER':\n", " genotiped[1]+=1\n", " if pop_asoc=='CAM':\n", " genotiped[2]+=1\n", " if pop_asoc=='PET':\n", " genotiped[3]+=1\n", " if pop_asoc=='RAS':\n", " genotiped[4]+=1\n", " if pop_asoc=='TUR':\n", " genotiped[5]+=1\n", " if pop_asoc=='SAL':\n", " genotiped[6]+=1\n", " if pop_asoc=='CHI':\n", " genotiped[7]+=1\n", " if pop_asoc=='MNT':\n", " genotiped[8]+=1\n", " else:\n", " new.write('./.:0,0:0')\n", " pop_asoc=(label_samples[n-1])[:3]\n", " if pop_asoc=='AYA':\n", " not_genotiped[0]+=1\n", " if pop_asoc=='YER':\n", " not_genotiped[1]+=1\n", " if pop_asoc=='CAM':\n", " not_genotiped[2]+=1\n", " if pop_asoc=='PET':\n", " not_genotiped[3]+=1\n", " if pop_asoc=='RAS':\n", " not_genotiped[4]+=1\n", " if pop_asoc=='TUR':\n", " not_genotiped[5]+=1\n", " if pop_asoc=='SAL':\n", " not_genotiped[6]+=1\n", " if pop_asoc=='CHI':\n", " not_genotiped[7]+=1\n", " if pop_asoc=='MNT':\n", " not_genotiped[8]+=1\n", " \n", " \n", " fraction_genotiped=np.array(genotiped)/(np.array(genotiped)+np.array(not_genotiped))\n", " \n", " if any(i < 0.5 for i in fraction_genotiped):\n", " new.write('remove\\n')\n", " else:\n", " new.write('\\n')\n", " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now we have to eliminate the SNPs are called by less than 50% of individuals in any population (with the remove word in the line)" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!cat resultados_filtrados.vcf | grep -v \"remove\" > results_filtered_1_2.vcf" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "7477\r\n" ] } ], "source": [ "!cat results_filtered_1_2.vcf | grep -v \"#\" | wc -l" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "VCFtools - v0.1.11\n", "(C) Adam Auton 2009\n", "\n", "Parameters as interpreted:\n", "\t--vcf results_filtered_1_2.vcf\n", "\t--maf 0.01\n", "\t--max-alleles 2\n", "\t--max-meanDP 150\n", "\t--min-alleles 2\n", "\t--out results_filtered_1_2_3_4_5\n", "\t--recode\n", "\t--remove-indels\n", "\n", "Index file is older than variant file. Will regenerate.\n", "Building new index file.\n", "\tScanning Chromosome: 22\n", "\tScanning Chromosome: 32\n", "\tScanning Chromosome: 61\n", "\tScanning Chromosome: 63\n", "\tScanning Chromosome: 64\n", "\tScanning Chromosome: 96\n", "\tScanning Chromosome: 102\n", "\tScanning Chromosome: 123\n", "\tScanning Chromosome: 138\n", "\tScanning Chromosome: 141\n", "\tScanning Chromosome: 147\n", "\tScanning Chromosome: 164\n", "\tScanning Chromosome: 197\n", "\tScanning Chromosome: 199\n", "\tScanning Chromosome: 202\n", "\tScanning Chromosome: 205\n", "\tScanning Chromosome: 276\n", "\tScanning Chromosome: 290\n", "\tScanning Chromosome: 311\n", "\tScanning Chromosome: 315\n", "\tScanning Chromosome: 329\n", "\tScanning Chromosome: 342\n", "\tScanning Chromosome: 378\n", "\tScanning Chromosome: 384\n", "\tScanning Chromosome: 399\n", "\tScanning Chromosome: 413\n", "\tScanning Chromosome: 425\n", "\tScanning Chromosome: 431\n", "\tScanning Chromosome: 438\n", "\tScanning Chromosome: 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"\tScanning Chromosome: 1024\n", "\tScanning Chromosome: 1028\n", "\tScanning Chromosome: 1062\n", "\tScanning Chromosome: 1081\n", "\tScanning Chromosome: 1087\n", "\tScanning Chromosome: 1092\n", "\tScanning Chromosome: 1099\n", "\tScanning Chromosome: 1126\n", "\tScanning Chromosome: 1147\n", "\tScanning Chromosome: 1152\n", "\tScanning Chromosome: 1174\n", "\tScanning Chromosome: 1175\n", "\tScanning Chromosome: 1180\n", "\tScanning Chromosome: 1187\n", "\tScanning Chromosome: 1189\n", "\tScanning Chromosome: 1255\n", "\tScanning Chromosome: 1264\n", "\tScanning Chromosome: 1273\n", "\tScanning Chromosome: 1281\n", "\tScanning Chromosome: 1295\n", "\tScanning Chromosome: 1300\n", "\tScanning Chromosome: 1316\n", "\tScanning Chromosome: 1319\n", "\tScanning Chromosome: 1321\n", "\tScanning Chromosome: 1322\n", "\tScanning Chromosome: 1331\n", "\tScanning Chromosome: 1359\n", "\tScanning Chromosome: 1371\n", "\tScanning Chromosome: 1401\n", "\tScanning Chromosome: 1403\n", "\tScanning Chromosome: 1419\n", "\tScanning Chromosome: 1433\n", "\tScanning Chromosome: 1465\n", "\tScanning Chromosome: 1479\n", "\tScanning Chromosome: 1511\n", "\tScanning Chromosome: 1522\n", "\tScanning Chromosome: 1526\n", "\tScanning Chromosome: 1529\n", "\tScanning Chromosome: 1532\n", "\tScanning Chromosome: 1540\n", "\tScanning Chromosome: 1569\n", "\tScanning Chromosome: 1670\n", "\tScanning Chromosome: 1706\n", "\tScanning Chromosome: 1721\n", "\tScanning Chromosome: 1728\n", "\tScanning Chromosome: 1755\n", "\tScanning Chromosome: 1776\n", "\tScanning Chromosome: 1777\n", "\tScanning Chromosome: 1784\n", "\tScanning Chromosome: 1788\n", "\tScanning Chromosome: 1804\n", "\tScanning Chromosome: 1807\n", "\tScanning Chromosome: 1810\n", "\tScanning Chromosome: 1817\n", "\tScanning Chromosome: 1819\n", "\tScanning Chromosome: 1820\n", "\tScanning Chromosome: 1885\n", "\tScanning Chromosome: 1889\n", "\tScanning Chromosome: 1891\n", "\tScanning Chromosome: 1995\n", "\tScanning Chromosome: 1996\n", "\tScanning Chromosome: 2001\n", "\tScanning Chromosome: 2004\n", "\tScanning Chromosome: 2011\n", "\tScanning Chromosome: 2031\n", "\tScanning Chromosome: 2067\n", "\tScanning Chromosome: 2089\n", "\tScanning Chromosome: 2122\n", "\tScanning Chromosome: 2134\n", "\tScanning Chromosome: 2138\n", "\tScanning Chromosome: 2159\n", "\tScanning Chromosome: 2162\n", "\tScanning Chromosome: 2171\n", "\tScanning Chromosome: 2172\n", "\tScanning Chromosome: 2232\n", "\tScanning Chromosome: 2287\n", "\tScanning Chromosome: 2313\n", "\tScanning Chromosome: 2321\n", "\tScanning Chromosome: 2327\n", "\tScanning Chromosome: 2345\n", "\tScanning Chromosome: 2347\n", "\tScanning Chromosome: 2363\n", "\tScanning Chromosome: 2371\n", "\tScanning Chromosome: 2384\n", "\tScanning Chromosome: 2389\n", "\tScanning Chromosome: 2415\n", "\tScanning Chromosome: 2434\n", "\tScanning Chromosome: 2438\n", "\tScanning Chromosome: 2449\n", "\tScanning Chromosome: 2454\n", 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"\tScanning Chromosome: 2990\n", "\tScanning Chromosome: 2994\n", "\tScanning Chromosome: 3012\n", "\tScanning Chromosome: 3013\n", "\tScanning Chromosome: 3040\n", "\tScanning Chromosome: 3059\n", "\tScanning Chromosome: 3098\n", "\tScanning Chromosome: 3107\n", "\tScanning Chromosome: 3113\n", "\tScanning Chromosome: 3147\n", "\tScanning Chromosome: 3162\n", "\tScanning Chromosome: 3166\n", "\tScanning Chromosome: 3184\n", "\tScanning Chromosome: 3199\n", "\tScanning Chromosome: 3208\n", "\tScanning Chromosome: 3213\n", "\tScanning Chromosome: 3243\n", "\tScanning Chromosome: 3254\n", "\tScanning Chromosome: 3260\n", "\tScanning Chromosome: 3272\n", "\tScanning Chromosome: 3306\n", "\tScanning Chromosome: 3312\n", "\tScanning Chromosome: 3316\n", "\tScanning Chromosome: 3317\n", "\tScanning Chromosome: 3320\n", "\tScanning Chromosome: 3326\n", "\tScanning Chromosome: 3356\n", "\tScanning Chromosome: 3361\n", "\tScanning Chromosome: 3363\n", "\tScanning Chromosome: 3384\n", 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"\tScanning Chromosome: 7957\n", "\tScanning Chromosome: 8056\n", "\tScanning Chromosome: 8075\n", "\tScanning Chromosome: 8098\n", "\tScanning Chromosome: 8100\n", "\tScanning Chromosome: 8198\n", "\tScanning Chromosome: 8210\n", "\tScanning Chromosome: 8225\n", "\tScanning Chromosome: 8235\n", "\tScanning Chromosome: 8254\n", "\tScanning Chromosome: 8314\n", "\tScanning Chromosome: 8350\n", "\tScanning Chromosome: 8360\n", "\tScanning Chromosome: 8364\n", "\tScanning Chromosome: 8385\n", "\tScanning Chromosome: 8386\n", "\tScanning Chromosome: 8438\n", "\tScanning Chromosome: 8458\n", "\tScanning Chromosome: 8514\n", "\tScanning Chromosome: 8523\n", "\tScanning Chromosome: 8549\n", "\tScanning Chromosome: 8610\n", "\tScanning Chromosome: 8619\n", "\tScanning Chromosome: 8658\n", "\tScanning Chromosome: 8674\n", "\tScanning Chromosome: 8678\n", "\tScanning Chromosome: 8680\n", "\tScanning Chromosome: 8709\n", "\tScanning Chromosome: 8715\n", "\tScanning Chromosome: 8719\n", "\tScanning Chromosome: 8744\n", "\tScanning Chromosome: 8747\n", "\tScanning Chromosome: 8748\n", "\tScanning Chromosome: 8801\n", "\tScanning Chromosome: 8847\n", "\tScanning Chromosome: 8852\n", "\tScanning Chromosome: 8856\n", "\tScanning Chromosome: 8863\n", "\tScanning Chromosome: 8880\n", "\tScanning Chromosome: 8899\n", "\tScanning Chromosome: 8914\n", "\tScanning Chromosome: 8934\n", "\tScanning Chromosome: 8948\n", "\tScanning Chromosome: 8960\n", "\tScanning Chromosome: 8974\n", "\tScanning Chromosome: 8980\n", "\tScanning Chromosome: 9027\n", "\tScanning Chromosome: 9033\n", "\tScanning Chromosome: 9060\n", "\tScanning Chromosome: 9074\n", "\tScanning Chromosome: 9109\n", "\tScanning Chromosome: 9116\n", "\tScanning Chromosome: 9159\n", "\tScanning Chromosome: 9166\n", "\tScanning Chromosome: 9183\n", "\tScanning Chromosome: 9200\n", "\tScanning Chromosome: 9212\n", "\tScanning Chromosome: 9228\n", "\tScanning Chromosome: 9266\n", "\tScanning Chromosome: 9267\n", "\tScanning Chromosome: 9268\n", "\tScanning Chromosome: 9277\n", "\tScanning Chromosome: 9299\n", "\tScanning Chromosome: 9307\n", "\tScanning Chromosome: 9331\n", "\tScanning Chromosome: 9332\n", "\tScanning Chromosome: 9340\n", "\tScanning Chromosome: 9375\n", "\tScanning Chromosome: 9382\n", "\tScanning Chromosome: 9389\n", "\tScanning Chromosome: 9404\n", "\tScanning Chromosome: 9416\n", "\tScanning Chromosome: 9421\n", "\tScanning Chromosome: 9433\n", "\tScanning Chromosome: 9448\n", "\tScanning Chromosome: 9522\n", "\tScanning Chromosome: 9554\n", "\tScanning Chromosome: 9598\n", "\tScanning Chromosome: 9628\n", "\tScanning Chromosome: 9631\n", "\tScanning Chromosome: 9636\n", "\tScanning Chromosome: 9660\n", "\tScanning Chromosome: 9681\n", "\tScanning Chromosome: 9682\n", "\tScanning Chromosome: 9727\n", "\tScanning Chromosome: 9741\n", "\tScanning Chromosome: 9775\n", "\tScanning Chromosome: 9850\n", "\tScanning Chromosome: 9852\n", "\tScanning Chromosome: 9916\n", "\tScanning Chromosome: 9949\n", "\tScanning Chromosome: 9995\n", "\tScanning Chromosome: 10009\n", "\tScanning Chromosome: 10036\n", "\tScanning Chromosome: 10054\n", "\tScanning Chromosome: 10059\n", "\tScanning Chromosome: 10060\n", "\tScanning Chromosome: 10086\n", "\tScanning Chromosome: 10094\n", "\tScanning Chromosome: 10118\n", "\tScanning Chromosome: 10147\n", "\tScanning Chromosome: 10151\n", "\tScanning Chromosome: 10187\n", "\tScanning Chromosome: 10188\n", "\tScanning Chromosome: 10235\n", "\tScanning Chromosome: 10261\n", "\tScanning Chromosome: 10298\n", "\tScanning Chromosome: 10353\n", "\tScanning Chromosome: 10358\n", "\tScanning Chromosome: 10378\n", "\tScanning Chromosome: 10380\n", "\tScanning Chromosome: 10472\n", "\tScanning Chromosome: 10481\n", "\tScanning Chromosome: 10521\n", "\tScanning Chromosome: 10534\n", "\tScanning Chromosome: 10538\n", "\tScanning Chromosome: 10551\n", "\tScanning Chromosome: 10563\n", "\tScanning Chromosome: 10614\n", "\tScanning Chromosome: 10637\n", "\tScanning Chromosome: 10660\n", "\tScanning Chromosome: 10670\n", "\tScanning Chromosome: 10675\n", "\tScanning Chromosome: 10677\n", "\tScanning Chromosome: 10680\n", "\tScanning Chromosome: 10758\n", "\tScanning Chromosome: 10770\n", "\tScanning Chromosome: 10791\n", "\tScanning Chromosome: 10820\n", "\tScanning Chromosome: 10840\n", "\tScanning Chromosome: 10865\n", "\tScanning Chromosome: 10887\n", "\tScanning Chromosome: 10914\n", "\tScanning Chromosome: 10959\n", "\tScanning Chromosome: 10968\n", "\tScanning Chromosome: 10981\n", "\tScanning Chromosome: 10987\n", "\tScanning Chromosome: 11088\n", "\tScanning Chromosome: 11140\n", "\tScanning Chromosome: 11141\n", "\tScanning Chromosome: 11147\n", "\tScanning Chromosome: 11189\n", "\tScanning Chromosome: 11268\n", "\tScanning Chromosome: 11285\n", "\tScanning Chromosome: 11291\n", "\tScanning Chromosome: 11302\n", "\tScanning Chromosome: 11329\n", "\tScanning Chromosome: 11350\n", "\tScanning Chromosome: 11370\n", "\tScanning Chromosome: 11393\n", "\tScanning Chromosome: 11428\n", "\tScanning Chromosome: 11519\n", "\tScanning Chromosome: 11529\n", "\tScanning Chromosome: 11541\n", "\tScanning Chromosome: 11606\n", "\tScanning Chromosome: 11624\n", "\tScanning Chromosome: 11634\n", "\tScanning Chromosome: 11657\n", "\tScanning Chromosome: 11659\n", "\tScanning Chromosome: 11668\n", "\tScanning Chromosome: 11687\n", "\tScanning Chromosome: 11701\n", "\tScanning Chromosome: 11703\n", "\tScanning Chromosome: 11712\n", "\tScanning Chromosome: 11829\n", "\tScanning Chromosome: 11877\n", "\tScanning Chromosome: 11885\n", "\tScanning Chromosome: 11939\n", "\tScanning Chromosome: 11984\n", "\tScanning Chromosome: 12018\n", "\tScanning Chromosome: 12031\n", "\tScanning Chromosome: 12062\n", "\tScanning Chromosome: 12070\n", "\tScanning Chromosome: 12089\n", "\tScanning Chromosome: 12104\n", "\tScanning Chromosome: 12118\n", "\tScanning Chromosome: 12134\n", "\tScanning Chromosome: 12145\n", "\tScanning Chromosome: 12176\n", "\tScanning Chromosome: 12216\n", "\tScanning Chromosome: 12226\n", "\tScanning Chromosome: 12277\n", "\tScanning Chromosome: 12285\n", "\tScanning Chromosome: 12299\n", "\tScanning Chromosome: 12338\n", "\tScanning Chromosome: 12340\n", "\tScanning Chromosome: 12347\n", "\tScanning Chromosome: 12374\n", "\tScanning Chromosome: 12376\n", "\tScanning Chromosome: 12378\n", "\tScanning Chromosome: 12414\n", "\tScanning Chromosome: 12439\n", "\tScanning Chromosome: 12447\n", "\tScanning Chromosome: 12455\n", "\tScanning Chromosome: 12563\n", "\tScanning Chromosome: 12582\n", "\tScanning Chromosome: 12614\n", "\tScanning Chromosome: 12632\n", "\tScanning Chromosome: 12644\n", "\tScanning Chromosome: 12658\n", "\tScanning Chromosome: 12674\n", "\tScanning Chromosome: 12703\n", "\tScanning Chromosome: 12730\n", "\tScanning Chromosome: 12742\n", "\tScanning Chromosome: 12758\n", "\tScanning Chromosome: 12763\n", "\tScanning Chromosome: 12779\n", "\tScanning Chromosome: 12863\n", "\tScanning Chromosome: 12867\n", "\tScanning Chromosome: 12873\n", "\tScanning Chromosome: 12874\n", "\tScanning Chromosome: 12875\n", "\tScanning Chromosome: 12907\n", "\tScanning Chromosome: 12938\n", "\tScanning Chromosome: 13045\n", "\tScanning Chromosome: 13060\n", "\tScanning Chromosome: 13082\n", "\tScanning Chromosome: 13145\n", "\tScanning Chromosome: 13155\n", "\tScanning Chromosome: 13175\n", "\tScanning Chromosome: 13225\n", "\tScanning Chromosome: 13243\n", "\tScanning Chromosome: 13253\n", "\tScanning Chromosome: 13277\n", "\tScanning Chromosome: 13308\n", "\tScanning Chromosome: 13325\n", "\tScanning Chromosome: 13396\n", "\tScanning Chromosome: 13418\n", "\tScanning Chromosome: 13444\n", "\tScanning Chromosome: 13463\n", "\tScanning Chromosome: 13471\n", "\tScanning Chromosome: 13532\n", "\tScanning Chromosome: 13568\n", "\tScanning Chromosome: 13679\n", "\tScanning Chromosome: 13698\n", "\tScanning Chromosome: 13725\n", "\tScanning Chromosome: 13744\n", "\tScanning Chromosome: 13764\n", "\tScanning Chromosome: 13804\n", "\tScanning Chromosome: 13811\n", "\tScanning Chromosome: 13818\n", "\tScanning Chromosome: 13834\n", "\tScanning Chromosome: 13837\n", "\tScanning Chromosome: 13874\n", "\tScanning Chromosome: 13932\n", "\tScanning Chromosome: 13935\n", "\tScanning Chromosome: 13979\n", "\tScanning Chromosome: 13982\n", "\tScanning Chromosome: 14100\n", "\tScanning Chromosome: 14139\n", "\tScanning Chromosome: 14188\n", "\tScanning Chromosome: 14200\n", "\tScanning Chromosome: 14216\n", "\tScanning Chromosome: 14280\n", "\tScanning Chromosome: 14316\n", "\tScanning Chromosome: 14317\n", "\tScanning Chromosome: 14427\n", "\tScanning Chromosome: 14435\n", "\tScanning Chromosome: 14450\n", "\tScanning Chromosome: 14472\n", "\tScanning Chromosome: 14485\n", "\tScanning Chromosome: 14524\n", "\tScanning Chromosome: 14533\n", "\tScanning Chromosome: 14558\n", "\tScanning Chromosome: 14566\n", "\tScanning Chromosome: 14583\n", "\tScanning Chromosome: 14598\n", "\tScanning Chromosome: 14614\n", "\tScanning Chromosome: 14627\n", "\tScanning Chromosome: 14652\n", "\tScanning Chromosome: 14759\n", "\tScanning Chromosome: 14806\n", "\tScanning Chromosome: 14832\n", "\tScanning Chromosome: 14848\n", "\tScanning Chromosome: 14863\n", "\tScanning Chromosome: 14875\n", "\tScanning Chromosome: 14956\n", "\tScanning Chromosome: 14960\n", "\tScanning Chromosome: 14980\n", "\tScanning Chromosome: 15062\n", "\tScanning Chromosome: 15084\n", "\tScanning Chromosome: 15113\n", "\tScanning Chromosome: 15118\n", "\tScanning Chromosome: 15133\n", "\tScanning Chromosome: 15141\n", "\tScanning Chromosome: 15268\n", "\tScanning Chromosome: 15283\n", "\tScanning Chromosome: 15317\n", "\tScanning Chromosome: 15359\n", "\tScanning Chromosome: 15377\n", "\tScanning Chromosome: 15398\n", "\tScanning Chromosome: 15401\n", "\tScanning Chromosome: 15410\n", "\tScanning Chromosome: 15460\n", "\tScanning Chromosome: 15495\n", "\tScanning Chromosome: 15502\n", "\tScanning Chromosome: 15525\n", "\tScanning Chromosome: 15545\n", "\tScanning Chromosome: 15660\n", "\tScanning Chromosome: 15699\n", "\tScanning Chromosome: 15712\n", "\tScanning Chromosome: 15746\n", "\tScanning Chromosome: 15809\n", "\tScanning Chromosome: 15819\n", "\tScanning Chromosome: 15893\n", "\tScanning Chromosome: 15955\n", "\tScanning Chromosome: 16012\n", "\tScanning Chromosome: 16020\n", "\tScanning Chromosome: 16050\n", "\tScanning Chromosome: 16067\n", "\tScanning Chromosome: 16172\n", "\tScanning Chromosome: 16201\n", "\tScanning Chromosome: 16213\n", "\tScanning Chromosome: 16215\n", "\tScanning Chromosome: 16247\n", "\tScanning Chromosome: 16270\n", "\tScanning Chromosome: 16273\n", "\tScanning Chromosome: 16296\n", "\tScanning Chromosome: 16372\n", "\tScanning Chromosome: 16374\n", "\tScanning Chromosome: 16380\n", "\tScanning Chromosome: 16429\n", "\tScanning Chromosome: 16449\n", "\tScanning Chromosome: 16469\n", "\tScanning Chromosome: 16506\n", "\tScanning Chromosome: 16513\n", "\tScanning Chromosome: 16537\n", "\tScanning Chromosome: 16564\n", "\tScanning Chromosome: 16628\n", "\tScanning Chromosome: 16630\n", "\tScanning Chromosome: 16670\n", "\tScanning Chromosome: 16697\n", "\tScanning Chromosome: 16698\n", "\tScanning Chromosome: 16716\n", "\tScanning Chromosome: 16727\n", "\tScanning Chromosome: 16734\n", "\tScanning Chromosome: 16770\n", "\tScanning Chromosome: 16798\n", "\tScanning Chromosome: 16800\n", "\tScanning Chromosome: 16877\n", "\tScanning Chromosome: 17035\n", "\tScanning Chromosome: 17072\n", "\tScanning Chromosome: 17139\n", "\tScanning Chromosome: 17291\n", "\tScanning Chromosome: 17296\n", "\tScanning Chromosome: 17299\n", "\tScanning Chromosome: 17308\n", "\tScanning Chromosome: 17357\n", "\tScanning Chromosome: 17393\n", "\tScanning Chromosome: 17398\n", "\tScanning Chromosome: 17429\n", "\tScanning Chromosome: 17519\n", "\tScanning Chromosome: 17549\n", "\tScanning Chromosome: 17619\n", "\tScanning Chromosome: 17677\n", "\tScanning Chromosome: 17768\n", "\tScanning Chromosome: 17788\n", "\tScanning Chromosome: 17842\n", "\tScanning Chromosome: 17888\n", "\tScanning Chromosome: 17892\n", "\tScanning Chromosome: 17900\n", "\tScanning Chromosome: 17932\n", "\tScanning Chromosome: 18015\n", "\tScanning Chromosome: 18029\n", "\tScanning Chromosome: 18037\n", "\tScanning Chromosome: 18065\n", "\tScanning Chromosome: 18111\n", "\tScanning Chromosome: 18158\n", "\tScanning Chromosome: 18162\n", "\tScanning Chromosome: 18165\n", "\tScanning Chromosome: 18168\n", "\tScanning Chromosome: 18173\n", "\tScanning Chromosome: 18289\n", "\tScanning Chromosome: 18446\n", "\tScanning Chromosome: 18532\n", "\tScanning Chromosome: 18620\n", "\tScanning Chromosome: 18809\n", "\tScanning Chromosome: 18817\n", "\tScanning Chromosome: 18822\n", "\tScanning Chromosome: 18827\n", "\tScanning Chromosome: 18838\n", "\tScanning Chromosome: 18844\n", "\tScanning Chromosome: 18850\n", "\tScanning Chromosome: 18977\n", "\tScanning Chromosome: 19004\n", "\tScanning Chromosome: 19094\n", "\tScanning Chromosome: 19157\n", "\tScanning Chromosome: 19225\n", "\tScanning Chromosome: 19240\n", "\tScanning Chromosome: 19377\n", "\tScanning Chromosome: 19405\n", "\tScanning Chromosome: 19479\n", "\tScanning Chromosome: 19591\n", "\tScanning Chromosome: 19616\n", "\tScanning Chromosome: 19623\n", "\tScanning Chromosome: 19662\n", "\tScanning Chromosome: 19692\n", "\tScanning Chromosome: 19706\n", "\tScanning Chromosome: 19739\n", "\tScanning Chromosome: 19805\n", "\tScanning Chromosome: 19854\n", "\tScanning Chromosome: 19865\n", "\tScanning Chromosome: 19915\n", "\tScanning Chromosome: 19960\n", "\tScanning Chromosome: 20000\n", "\tScanning Chromosome: 20036\n", "\tScanning Chromosome: 20049\n", "\tScanning Chromosome: 20077\n", "\tScanning Chromosome: 20102\n", "\tScanning Chromosome: 20133\n", "\tScanning Chromosome: 20193\n", "\tScanning Chromosome: 20203\n", "\tScanning Chromosome: 20236\n", "\tScanning Chromosome: 20275\n", "\tScanning Chromosome: 20298\n", "\tScanning Chromosome: 20304\n", "\tScanning Chromosome: 20309\n", "\tScanning Chromosome: 20310\n", "\tScanning Chromosome: 20334\n", "\tScanning Chromosome: 20483\n", "\tScanning Chromosome: 20552\n", "\tScanning Chromosome: 20674\n", "\tScanning Chromosome: 20864\n", "\tScanning Chromosome: 20867\n", "\tScanning Chromosome: 20993\n", "\tScanning Chromosome: 20994\n", "\tScanning Chromosome: 21150\n", "\tScanning Chromosome: 21205\n", "\tScanning Chromosome: 21237\n", "\tScanning Chromosome: 21305\n", "\tScanning Chromosome: 21351\n", "\tScanning Chromosome: 21373\n", "\tScanning Chromosome: 21377\n", "\tScanning Chromosome: 21380\n", "\tScanning Chromosome: 21397\n", "\tScanning Chromosome: 21418\n", "\tScanning Chromosome: 21426\n", "\tScanning Chromosome: 21455\n", "\tScanning Chromosome: 21491\n", "\tScanning Chromosome: 21508\n", "\tScanning Chromosome: 21541\n", "\tScanning Chromosome: 21583\n", "\tScanning Chromosome: 21592\n", "\tScanning Chromosome: 21617\n", "\tScanning Chromosome: 21732\n", "\tScanning Chromosome: 21807\n", "\tScanning Chromosome: 21815\n", "\tScanning Chromosome: 21838\n", "\tScanning Chromosome: 21858\n", "\tScanning Chromosome: 21867\n", "\tScanning Chromosome: 21920\n", "\tScanning Chromosome: 22040\n", "\tScanning Chromosome: 22152\n", "\tScanning Chromosome: 22157\n", "\tScanning Chromosome: 22206\n", "\tScanning Chromosome: 22220\n", "\tScanning Chromosome: 22228\n", "\tScanning Chromosome: 22275\n", "\tScanning Chromosome: 22430\n", "\tScanning Chromosome: 22481\n", "\tScanning Chromosome: 22521\n", "\tScanning Chromosome: 22538\n", "\tScanning Chromosome: 22577\n", "\tScanning Chromosome: 22581\n", "\tScanning Chromosome: 22661\n", "\tScanning Chromosome: 22662\n", "\tScanning Chromosome: 22663\n", "\tScanning Chromosome: 22716\n", "\tScanning Chromosome: 22745\n", "\tScanning Chromosome: 22785\n", "\tScanning Chromosome: 22875\n", "\tScanning Chromosome: 22890\n", "\tScanning Chromosome: 22892\n", "\tScanning Chromosome: 22895\n", "\tScanning Chromosome: 22920\n", "\tScanning Chromosome: 23070\n", "\tScanning Chromosome: 23077\n", "\tScanning Chromosome: 23115\n", "\tScanning Chromosome: 23116\n", "\tScanning Chromosome: 23120\n", "\tScanning Chromosome: 23128\n", "\tScanning Chromosome: 23210\n", "\tScanning Chromosome: 23267\n", "\tScanning Chromosome: 23284\n", "\tScanning Chromosome: 23307\n", "\tScanning Chromosome: 23363\n", "\tScanning Chromosome: 23370\n", "\tScanning Chromosome: 23450\n", "\tScanning Chromosome: 23459\n", "\tScanning Chromosome: 23515\n", "\tScanning Chromosome: 23526\n", "\tScanning Chromosome: 23664\n", "\tScanning Chromosome: 23677\n", "\tScanning Chromosome: 23691\n", "\tScanning Chromosome: 23741\n", "\tScanning Chromosome: 23808\n", "\tScanning Chromosome: 23809\n", "\tScanning Chromosome: 23824\n", "\tScanning Chromosome: 23844\n", "\tScanning Chromosome: 23857\n", "\tScanning Chromosome: 23980\n", "\tScanning Chromosome: 24015\n", "\tScanning Chromosome: 24021\n", "\tScanning Chromosome: 24063\n", "\tScanning Chromosome: 24125\n", "\tScanning Chromosome: 24131\n", "\tScanning Chromosome: 24245\n", "\tScanning Chromosome: 24299\n", "\tScanning Chromosome: 24456\n", "\tScanning Chromosome: 24525\n", "\tScanning Chromosome: 24556\n", "\tScanning Chromosome: 24716\n", "\tScanning Chromosome: 24758\n", "\tScanning Chromosome: 24799\n", "\tScanning Chromosome: 24909\n", "\tScanning Chromosome: 24929\n", "\tScanning Chromosome: 24968\n", "\tScanning Chromosome: 25019\n", "\tScanning Chromosome: 25060\n", "\tScanning Chromosome: 25092\n", "\tScanning Chromosome: 25123\n", "\tScanning Chromosome: 25124\n", "\tScanning Chromosome: 25162\n", "\tScanning Chromosome: 25209\n", "\tScanning Chromosome: 25230\n", "\tScanning Chromosome: 25339\n", "\tScanning Chromosome: 25361\n", "\tScanning Chromosome: 25468\n", "\tScanning Chromosome: 25516\n", "\tScanning Chromosome: 25552\n", "\tScanning Chromosome: 25654\n", "\tScanning Chromosome: 25658\n", "\tScanning Chromosome: 25705\n", "\tScanning Chromosome: 25714\n", "\tScanning Chromosome: 25751\n", "\tScanning Chromosome: 25791\n", "\tScanning Chromosome: 25795\n", "\tScanning Chromosome: 25813\n", "\tScanning Chromosome: 25835\n", "\tScanning Chromosome: 25879\n", "\tScanning Chromosome: 25987\n", "\tScanning Chromosome: 25989\n", "\tScanning Chromosome: 26045\n", "\tScanning Chromosome: 26070\n", "\tScanning Chromosome: 26218\n", "\tScanning Chromosome: 26325\n", "\tScanning Chromosome: 26327\n", "\tScanning Chromosome: 26369\n", "\tScanning Chromosome: 26398\n", "\tScanning Chromosome: 26412\n", "\tScanning Chromosome: 26414\n", "\tScanning Chromosome: 26415\n", "\tScanning Chromosome: 26432\n", "\tScanning Chromosome: 26439\n", "\tScanning Chromosome: 26462\n", "\tScanning Chromosome: 26526\n", "\tScanning Chromosome: 26575\n", "\tScanning Chromosome: 26640\n", "\tScanning Chromosome: 26740\n", "\tScanning Chromosome: 26799\n", "\tScanning Chromosome: 26807\n", "\tScanning Chromosome: 26873\n", "\tScanning Chromosome: 26921\n", "\tScanning Chromosome: 26943\n", "\tScanning Chromosome: 27001\n", "\tScanning Chromosome: 27036\n", "\tScanning Chromosome: 27184\n", "\tScanning Chromosome: 27242\n", "\tScanning Chromosome: 27292\n", "\tScanning Chromosome: 27407\n", "\tScanning Chromosome: 27476\n", "\tScanning Chromosome: 27547\n", "\tScanning Chromosome: 27568\n", "\tScanning Chromosome: 27615\n", "\tScanning Chromosome: 27662\n", "\tScanning Chromosome: 27709\n", "\tScanning Chromosome: 27749\n", "\tScanning Chromosome: 27765\n", "\tScanning Chromosome: 27865\n", "\tScanning Chromosome: 27926\n", "\tScanning Chromosome: 27944\n", "\tScanning Chromosome: 28004\n", "\tScanning Chromosome: 28017\n", "\tScanning Chromosome: 28252\n", "\tScanning Chromosome: 28282\n", "\tScanning Chromosome: 28357\n", "\tScanning Chromosome: 28574\n", "\tScanning Chromosome: 28618\n", "\tScanning Chromosome: 28757\n", "\tScanning Chromosome: 28833\n", "\tScanning Chromosome: 28851\n", "\tScanning Chromosome: 28930\n", "\tScanning Chromosome: 28984\n", "\tScanning Chromosome: 29045\n", "\tScanning Chromosome: 29107\n", "\tScanning Chromosome: 29140\n", "\tScanning Chromosome: 29266\n", "\tScanning Chromosome: 29272\n", "\tScanning Chromosome: 29306\n", "\tScanning Chromosome: 29364\n", "\tScanning Chromosome: 29577\n", "\tScanning Chromosome: 29587\n", "\tScanning Chromosome: 29626\n", "\tScanning Chromosome: 29658\n", "\tScanning Chromosome: 29685\n", "\tScanning Chromosome: 29817\n", "\tScanning Chromosome: 29831\n", "\tScanning Chromosome: 29864\n", "\tScanning Chromosome: 29906\n", "\tScanning Chromosome: 29978\n", "\tScanning Chromosome: 29981\n", "\tScanning Chromosome: 30003\n", "\tScanning Chromosome: 30019\n", "\tScanning Chromosome: 30085\n", "\tScanning Chromosome: 30086\n", "\tScanning Chromosome: 30087\n", "\tScanning Chromosome: 30138\n", "\tScanning Chromosome: 30142\n", "\tScanning Chromosome: 30145\n", "\tScanning Chromosome: 30183\n", "\tScanning Chromosome: 30210\n", "\tScanning Chromosome: 30218\n", "\tScanning Chromosome: 30427\n", "\tScanning Chromosome: 30433\n", "\tScanning Chromosome: 30434\n", "\tScanning Chromosome: 30467\n", "\tScanning Chromosome: 30502\n", "\tScanning Chromosome: 30593\n", "\tScanning Chromosome: 30600\n", "\tScanning Chromosome: 30615\n", "\tScanning Chromosome: 30620\n", "\tScanning Chromosome: 30667\n", "\tScanning Chromosome: 30709\n", "\tScanning Chromosome: 30854\n", "\tScanning Chromosome: 30924\n", "\tScanning Chromosome: 31069\n", "\tScanning Chromosome: 31076\n", "\tScanning Chromosome: 31183\n", "\tScanning Chromosome: 31186\n", "\tScanning Chromosome: 31365\n", "\tScanning Chromosome: 31401\n", "\tScanning Chromosome: 31415\n", "\tScanning Chromosome: 31498\n", "\tScanning Chromosome: 31613\n", "\tScanning Chromosome: 31621\n", "\tScanning Chromosome: 31688\n", "\tScanning Chromosome: 31692\n", "\tScanning Chromosome: 31721\n", "\tScanning Chromosome: 31752\n", "\tScanning Chromosome: 31779\n", "\tScanning Chromosome: 31900\n", "\tScanning Chromosome: 32010\n", "\tScanning Chromosome: 32168\n", "\tScanning Chromosome: 32244\n", "\tScanning Chromosome: 32254\n", "\tScanning Chromosome: 32367\n", "\tScanning Chromosome: 32394\n", "\tScanning Chromosome: 32521\n", "\tScanning Chromosome: 32615\n", "\tScanning Chromosome: 32831\n", "\tScanning Chromosome: 32890\n", "\tScanning Chromosome: 32986\n", "\tScanning Chromosome: 33111\n", "\tScanning Chromosome: 33291\n", "\tScanning Chromosome: 33361\n", "\tScanning Chromosome: 33406\n", "\tScanning Chromosome: 33540\n", "\tScanning Chromosome: 33605\n", "\tScanning Chromosome: 33620\n", "\tScanning Chromosome: 33691\n", "\tScanning Chromosome: 33929\n", "\tScanning Chromosome: 34146\n", "\tScanning Chromosome: 34209\n", "\tScanning Chromosome: 34222\n", "\tScanning Chromosome: 34279\n", "\tScanning Chromosome: 34354\n", "\tScanning Chromosome: 34457\n", "\tScanning Chromosome: 34622\n", "\tScanning Chromosome: 34681\n", "\tScanning Chromosome: 34687\n", "\tScanning Chromosome: 34823\n", "\tScanning Chromosome: 34844\n", "\tScanning Chromosome: 34924\n", "\tScanning Chromosome: 34945\n", "\tScanning Chromosome: 34960\n", "\tScanning Chromosome: 34971\n", "\tScanning Chromosome: 35048\n", "\tScanning Chromosome: 35191\n", "\tScanning Chromosome: 35337\n", "\tScanning Chromosome: 35402\n", "\tScanning Chromosome: 35565\n", "\tScanning Chromosome: 35608\n", "\tScanning Chromosome: 35633\n", "\tScanning Chromosome: 35746\n", "\tScanning Chromosome: 35765\n", "\tScanning Chromosome: 35876\n", "\tScanning Chromosome: 35977\n", "\tScanning Chromosome: 35995\n", "\tScanning Chromosome: 36097\n", "\tScanning Chromosome: 36140\n", "\tScanning Chromosome: 36217\n", "\tScanning Chromosome: 36344\n", "\tScanning Chromosome: 36429\n", "\tScanning Chromosome: 36587\n", "\tScanning Chromosome: 36641\n", "\tScanning Chromosome: 36844\n", "\tScanning Chromosome: 36994\n", "\tScanning Chromosome: 37196\n", "\tScanning Chromosome: 37412\n", "\tScanning Chromosome: 37438\n", "\tScanning Chromosome: 37447\n", "\tScanning Chromosome: 37561\n", "\tScanning Chromosome: 37630\n", "\tScanning Chromosome: 37676\n", "\tScanning Chromosome: 38000\n", "\tScanning Chromosome: 38144\n", "\tScanning Chromosome: 38252\n", "\tScanning Chromosome: 38322\n", "\tScanning Chromosome: 38664\n", "\tScanning Chromosome: 38755\n", "\tScanning Chromosome: 38847\n", "\tScanning Chromosome: 38912\n", "\tScanning Chromosome: 38917\n", "\tScanning Chromosome: 38957\n", "\tScanning Chromosome: 39291\n", "\tScanning Chromosome: 39330\n", "\tScanning Chromosome: 39332\n", "\tScanning Chromosome: 39453\n", "\tScanning Chromosome: 39615\n", "\tScanning Chromosome: 39642\n", "\tScanning Chromosome: 39644\n", "\tScanning Chromosome: 39951\n", "\tScanning Chromosome: 40007\n", "\tScanning Chromosome: 40025\n", "\tScanning Chromosome: 40134\n", "\tScanning Chromosome: 40150\n", "\tScanning Chromosome: 40252\n", "\tScanning Chromosome: 40388\n", "\tScanning Chromosome: 40412\n", "\tScanning Chromosome: 40662\n", "\tScanning Chromosome: 40756\n", "\tScanning Chromosome: 40833\n", "\tScanning Chromosome: 40852\n", "\tScanning Chromosome: 41143\n", "\tScanning Chromosome: 41175\n", "\tScanning Chromosome: 41511\n", "\tScanning Chromosome: 41820\n", "\tScanning Chromosome: 42075\n", "\tScanning Chromosome: 42102\n", "\tScanning Chromosome: 42196\n", "\tScanning Chromosome: 42301\n", "\tScanning Chromosome: 42338\n", "\tScanning Chromosome: 42471\n", "\tScanning Chromosome: 42553\n", "\tScanning Chromosome: 42670\n", "\tScanning Chromosome: 42671\n", "\tScanning Chromosome: 42802\n", "\tScanning Chromosome: 43179\n", "\tScanning Chromosome: 43218\n", "\tScanning Chromosome: 43257\n", "\tScanning Chromosome: 43306\n", "\tScanning Chromosome: 43706\n", "\tScanning Chromosome: 43809\n", "\tScanning Chromosome: 43816\n", "\tScanning Chromosome: 43892\n", "\tScanning Chromosome: 44145\n", "\tScanning Chromosome: 44330\n", "\tScanning Chromosome: 44384\n", "\tScanning Chromosome: 44519\n", "\tScanning Chromosome: 44551\n", "\tScanning Chromosome: 44717\n", "\tScanning Chromosome: 44720\n", "\tScanning Chromosome: 44870\n", "\tScanning Chromosome: 44875\n", "\tScanning Chromosome: 44909\n", "\tScanning Chromosome: 45099\n", "\tScanning Chromosome: 45162\n", "\tScanning Chromosome: 45288\n", "\tScanning Chromosome: 45309\n", "\tScanning Chromosome: 45423\n", "\tScanning Chromosome: 45965\n", "\tScanning Chromosome: 46177\n", "\tScanning Chromosome: 46310\n", "\tScanning Chromosome: 46341\n", "\tScanning Chromosome: 46409\n", "\tScanning Chromosome: 46493\n", "\tScanning Chromosome: 46590\n", "\tScanning Chromosome: 46616\n", "\tScanning Chromosome: 46659\n", "\tScanning Chromosome: 46669\n", "\tScanning Chromosome: 46913\n", "\tScanning Chromosome: 46918\n", "\tScanning Chromosome: 47105\n", "\tScanning Chromosome: 47123\n", "\tScanning Chromosome: 47287\n", "\tScanning Chromosome: 47299\n", "\tScanning Chromosome: 47359\n", "\tScanning Chromosome: 47654\n", "\tScanning Chromosome: 47715\n", "\tScanning Chromosome: 47933\n", "\tScanning Chromosome: 47940\n", "\tScanning Chromosome: 48090\n", "\tScanning Chromosome: 48157\n", "\tScanning Chromosome: 48206\n", "\tScanning Chromosome: 48208\n", "\tScanning Chromosome: 48464\n", "\tScanning Chromosome: 48592\n", "\tScanning Chromosome: 48826\n", "\tScanning Chromosome: 48910\n", "\tScanning Chromosome: 48936\n", "\tScanning Chromosome: 49256\n", "\tScanning Chromosome: 49335\n", "\tScanning Chromosome: 49506\n", "\tScanning Chromosome: 49622\n", "\tScanning Chromosome: 49644\n", "\tScanning Chromosome: 49724\n", "\tScanning Chromosome: 49786\n", "\tScanning Chromosome: 49843\n", "\tScanning Chromosome: 49875\n", "\tScanning Chromosome: 49881\n", "\tScanning Chromosome: 50193\n", "\tScanning Chromosome: 50195\n", "\tScanning Chromosome: 50483\n", "\tScanning Chromosome: 50540\n", "\tScanning Chromosome: 50749\n", "\tScanning Chromosome: 50856\n", "\tScanning Chromosome: 51073\n", "\tScanning Chromosome: 51108\n", "\tScanning Chromosome: 51231\n", "\tScanning Chromosome: 51472\n", "\tScanning Chromosome: 51524\n", "\tScanning Chromosome: 51924\n", "\tScanning Chromosome: 52064\n", "\tScanning Chromosome: 52376\n", "\tScanning Chromosome: 52734\n", "\tScanning Chromosome: 52958\n", "\tScanning Chromosome: 53407\n", "\tScanning Chromosome: 53411\n", "\tScanning Chromosome: 53433\n", "\tScanning Chromosome: 53576\n", "\tScanning Chromosome: 53578\n", "\tScanning Chromosome: 53686\n", "\tScanning Chromosome: 53697\n", "\tScanning Chromosome: 53776\n", "\tScanning Chromosome: 53797\n", "\tScanning Chromosome: 53955\n", "\tScanning Chromosome: 54168\n", "\tScanning Chromosome: 54264\n", "\tScanning Chromosome: 54377\n", "\tScanning Chromosome: 54540\n", "\tScanning Chromosome: 54564\n", "\tScanning Chromosome: 54621\n", "\tScanning Chromosome: 54782\n", "\tScanning Chromosome: 54924\n", "\tScanning Chromosome: 55090\n", "\tScanning Chromosome: 55511\n", "\tScanning Chromosome: 55666\n", "\tScanning Chromosome: 55695\n", "\tScanning Chromosome: 56231\n", "\tScanning Chromosome: 56321\n", "\tScanning Chromosome: 56713\n", "\tScanning Chromosome: 56791\n", "\tScanning Chromosome: 56802\n", "\tScanning Chromosome: 56872\n", "\tScanning Chromosome: 56894\n", "\tScanning Chromosome: 56901\n", "\tScanning Chromosome: 56935\n", "\tScanning Chromosome: 57049\n", "\tScanning Chromosome: 57470\n", "\tScanning Chromosome: 57544\n", "\tScanning Chromosome: 57691\n", "\tScanning Chromosome: 57745\n", "\tScanning Chromosome: 57910\n", "\tScanning Chromosome: 58091\n", "\tScanning Chromosome: 58266\n", "\tScanning Chromosome: 58786\n", "\tScanning Chromosome: 58809\n", "\tScanning Chromosome: 58871\n", "\tScanning Chromosome: 58919\n", "\tScanning Chromosome: 58989\n", "\tScanning Chromosome: 59432\n", "\tScanning Chromosome: 59567\n", "\tScanning Chromosome: 59768\n", "\tScanning Chromosome: 59888\n", "\tScanning Chromosome: 59945\n", "\tScanning Chromosome: 60122\n", "\tScanning Chromosome: 60223\n", "\tScanning Chromosome: 60310\n", "\tScanning Chromosome: 60321\n", "\tScanning Chromosome: 60591\n", "\tScanning Chromosome: 60599\n", "\tScanning Chromosome: 60642\n", "\tScanning Chromosome: 61025\n", "\tScanning Chromosome: 61182\n", "\tScanning Chromosome: 61256\n", "\tScanning Chromosome: 61417\n", "\tScanning Chromosome: 61733\n", "\tScanning Chromosome: 61927\n", "\tScanning Chromosome: 61967\n", "\tScanning Chromosome: 62207\n", "\tScanning Chromosome: 62274\n", "\tScanning Chromosome: 62587\n", "\tScanning Chromosome: 62702\n", "\tScanning Chromosome: 62865\n", "\tScanning Chromosome: 62868\n", "\tScanning Chromosome: 62987\n", "\tScanning Chromosome: 63233\n", "\tScanning Chromosome: 63477\n", "\tScanning Chromosome: 63489\n", "\tScanning Chromosome: 63527\n", "\tScanning Chromosome: 63734\n", "\tScanning Chromosome: 63942\n", "\tScanning Chromosome: 63954\n", "\tScanning Chromosome: 64226\n", "\tScanning Chromosome: 64393\n", "\tScanning Chromosome: 64412\n", "\tScanning Chromosome: 64882\n", "\tScanning Chromosome: 65190\n", "\tScanning Chromosome: 65693\n", "\tScanning Chromosome: 65803\n", "\tScanning Chromosome: 65900\n", "\tScanning Chromosome: 66145\n", "\tScanning Chromosome: 66358\n", "\tScanning Chromosome: 66404\n", "\tScanning Chromosome: 66879\n", "\tScanning Chromosome: 66880\n", "\tScanning Chromosome: 66916\n", "\tScanning Chromosome: 67075\n", "\tScanning Chromosome: 67188\n", "\tScanning Chromosome: 67221\n", "\tScanning Chromosome: 67270\n", "\tScanning Chromosome: 67357\n", "\tScanning Chromosome: 67385\n", "\tScanning Chromosome: 67465\n", "\tScanning Chromosome: 68224\n", "\tScanning Chromosome: 69084\n", "\tScanning Chromosome: 69152\n", "\tScanning Chromosome: 69684\n", "\tScanning Chromosome: 69786\n", "\tScanning Chromosome: 69848\n", "\tScanning Chromosome: 69934\n", "\tScanning Chromosome: 70109\n", "\tScanning Chromosome: 70268\n", "\tScanning Chromosome: 70385\n", "\tScanning Chromosome: 70851\n", "\tScanning Chromosome: 71819\n", "\tScanning Chromosome: 71917\n", "\tScanning Chromosome: 72392\n", "\tScanning Chromosome: 72604\n", "\tScanning Chromosome: 72710\n", "\tScanning Chromosome: 73225\n", "\tScanning Chromosome: 73571\n", "\tScanning Chromosome: 73832\n", "\tScanning Chromosome: 73860\n", "\tScanning Chromosome: 74219\n", "\tScanning Chromosome: 74258\n", "\tScanning Chromosome: 75375\n", "\tScanning Chromosome: 75499\n", "\tScanning Chromosome: 75598\n", "\tScanning Chromosome: 75741\n", "\tScanning Chromosome: 76719\n", "\tScanning Chromosome: 77236\n", "\tScanning Chromosome: 77279\n", "\tScanning Chromosome: 77683\n", "\tScanning Chromosome: 78061\n", "\tScanning Chromosome: 78148\n", "\tScanning Chromosome: 78197\n", "\tScanning Chromosome: 78315\n", "\tScanning Chromosome: 79689\n", "\tScanning Chromosome: 80323\n", "\tScanning Chromosome: 80634\n", "\tScanning Chromosome: 80968\n", "\tScanning Chromosome: 81332\n", "\tScanning Chromosome: 82034\n", "\tScanning Chromosome: 82816\n", "\tScanning Chromosome: 82913\n", "\tScanning Chromosome: 83018\n", "\tScanning Chromosome: 83195\n", "\tScanning Chromosome: 83588\n", "\tScanning Chromosome: 83996\n", "\tScanning Chromosome: 84059\n", "\tScanning Chromosome: 84076\n", "\tScanning Chromosome: 84682\n", "\tScanning Chromosome: 85069\n", "\tScanning Chromosome: 85519\n", "\tScanning Chromosome: 86224\n", "\tScanning Chromosome: 86465\n", "\tScanning Chromosome: 86466\n", "\tScanning Chromosome: 86468\n", "\tScanning Chromosome: 86574\n", "\tScanning Chromosome: 88881\n", "\tScanning Chromosome: 89576\n", "\tScanning Chromosome: 90570\n", "\tScanning Chromosome: 90700\n", "\tScanning Chromosome: 90840\n", "\tScanning Chromosome: 91157\n", "\tScanning Chromosome: 91786\n", "\tScanning Chromosome: 93177\n", "\tScanning Chromosome: 94219\n", "\tScanning Chromosome: 94864\n", "\tScanning Chromosome: 96144\n", "\tScanning Chromosome: 96294\n", "\tScanning Chromosome: 96397\n", "\tScanning Chromosome: 96480\n", "\tScanning Chromosome: 97070\n", "\tScanning Chromosome: 97398\n", "\tScanning Chromosome: 97921\n", "\tScanning Chromosome: 98027\n", "\tScanning Chromosome: 98605\n", "\tScanning Chromosome: 99911\n", "\tScanning Chromosome: 100239\n", "\tScanning Chromosome: 100649\n", "\tScanning Chromosome: 100881\n", "\tScanning Chromosome: 101093\n", "\tScanning Chromosome: 102644\n", "\tScanning Chromosome: 103325\n", "\tScanning Chromosome: 103491\n", "\tScanning Chromosome: 103512\n", "\tScanning Chromosome: 103514\n", "\tScanning Chromosome: 103517\n", "\tScanning Chromosome: 103518\n", "\tScanning Chromosome: 103521\n", "\tScanning Chromosome: 103525\n", "\tScanning Chromosome: 103526\n", "\tScanning Chromosome: 103532\n", "\tScanning Chromosome: 103537\n", "\tScanning Chromosome: 103539\n", "\tScanning Chromosome: 103540\n", "\tScanning Chromosome: 103550\n", "\tScanning Chromosome: 103551\n", "\tScanning Chromosome: 103554\n", "\tScanning Chromosome: 103564\n", "\tScanning Chromosome: 103568\n", "\tScanning Chromosome: 103574\n", "\tScanning Chromosome: 103579\n", "\tScanning Chromosome: 103581\n", "\tScanning Chromosome: 103585\n", "\tScanning Chromosome: 103592\n", "\tScanning Chromosome: 103601\n", "\tScanning Chromosome: 103608\n", "\tScanning Chromosome: 103609\n", "\tScanning Chromosome: 103614\n", "\tScanning Chromosome: 103641\n", "\tScanning Chromosome: 104092\n", "\tScanning Chromosome: 104104\n", "\tScanning Chromosome: 104109\n", "\tScanning Chromosome: 104277\n", "\tScanning Chromosome: 104469\n", "\tScanning Chromosome: 107034\n", "\tScanning Chromosome: 107145\n", "\tScanning Chromosome: 107285\n", "\tScanning Chromosome: 108241\n", "\tScanning Chromosome: 108388\n", "\tScanning Chromosome: 108900\n", "\tScanning Chromosome: 109116\n", "\tScanning Chromosome: 109688\n", "\tScanning Chromosome: 110360\n", "\tScanning Chromosome: 110483\n", "\tScanning Chromosome: 111234\n", "\tScanning Chromosome: 112644\n", "\tScanning Chromosome: 112929\n", "\tScanning Chromosome: 113150\n", "\tScanning Chromosome: 114743\n", "\tScanning Chromosome: 115293\n", "\tScanning Chromosome: 115723\n", "\tScanning Chromosome: 115957\n", "\tScanning Chromosome: 116110\n", "\tScanning Chromosome: 116692\n", "\tScanning Chromosome: 116957\n", "\tScanning Chromosome: 117958\n", "\tScanning Chromosome: 118004\n", "\tScanning Chromosome: 118367\n", "\tScanning Chromosome: 119396\n", "\tScanning Chromosome: 119978\n", "\tScanning Chromosome: 120927\n", "\tScanning Chromosome: 121231\n", "\tScanning Chromosome: 122274\n", "\tScanning Chromosome: 122774\n", "\tScanning Chromosome: 123182\n", "\tScanning Chromosome: 123882\n", "\tScanning Chromosome: 124255\n", "\tScanning Chromosome: 124735\n", "\tScanning Chromosome: 125170\n", "\tScanning Chromosome: 126331\n", "\tScanning Chromosome: 126679\n", "\tScanning Chromosome: 128983\n", "\tScanning Chromosome: 129304\n", "\tScanning Chromosome: 129576\n", "\tScanning Chromosome: 131004\n", "\tScanning Chromosome: 131464\n", "\tScanning Chromosome: 131809\n", "\tScanning Chromosome: 131895\n", "\tScanning Chromosome: 131940\n", "\tScanning Chromosome: 132483\n", "\tScanning Chromosome: 132582\n", "\tScanning Chromosome: 133835\n", "\tScanning Chromosome: 133870\n", "\tScanning Chromosome: 134414\n", "\tScanning Chromosome: 135064\n", "\tScanning Chromosome: 135123\n", "\tScanning Chromosome: 136403\n", "\tScanning Chromosome: 136452\n", "\tScanning Chromosome: 136519\n", "\tScanning Chromosome: 136974\n", "\tScanning Chromosome: 137580\n", "\tScanning Chromosome: 139470\n", "\tScanning Chromosome: 139492\n", "\tScanning Chromosome: 140168\n", "\tScanning Chromosome: 141291\n", "\tScanning Chromosome: 142257\n", "\tScanning Chromosome: 143270\n", "\tScanning Chromosome: 144146\n", "\tScanning Chromosome: 144394\n", "\tScanning Chromosome: 144513\n", "\tScanning Chromosome: 144635\n", "\tScanning Chromosome: 145111\n", "\tScanning Chromosome: 145265\n", "\tScanning Chromosome: 145886\n", "\tScanning Chromosome: 146924\n", "\tScanning Chromosome: 147401\n", "\tScanning Chromosome: 147530\n", "\tScanning Chromosome: 147656\n", "\tScanning Chromosome: 148333\n", "\tScanning Chromosome: 149127\n", "\tScanning Chromosome: 149200\n", "\tScanning Chromosome: 149586\n", "\tScanning Chromosome: 149996\n", "Writing Index file.\n", "File contains 7477 entries and 270 individuals.\n", "Applying Required Filters.\n", "Filtering sites by allele type\n", "Filtering sites by number of alleles\n", "Filtering sites by mean depth\n", "Filtering sites by allele frequency and call rate\n", "After filtering, kept 270 out of 270 Individuals\n", "After filtering, kept 4799 out of a possible 7477 Sites\n", "Outputting VCF file... Done\n", "Run Time = 3.00 seconds\n" ] } ], "source": [ "!vcftools --vcf results_filtered_1_2.vcf --max-meanDP 150 --maf 0.01 --min-alleles 2 --max-alleles 2 --remove-indels --out results_filtered_1_2_3_4_5 --recode" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "4799\r\n" ] } ], "source": [ "!cat results_filtered_1_2_3_4_5.recode.vcf | grep -v \"#\" |wc -l" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "256\r\n" ] } ], "source": [ "!less results_filtered_1_2_3_4_5.recode.vcf | grep \"#\" -v | perl -ne 'chomp; @a=split(\"\\t\"); $ID = $a[2]; shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); $count=0;$total=0 ; for (@a){ $total++; if (($_ =~ /0\\/1/) || ($_ =~ /1\\/0/)){ $count++} elsif($_ =~ /\\.\\/\\./){ $total--}} $prop = ($count/$total); print \"$prop\\t$.\\n\"'| sort -n | perl -ne 'chomp; @a=split(\"\\t\"); if ($a[0] >0.6) { print \"$_\\n\"}' | cut -f 2 |sort -n > snps_high_heterozigosity_0.6.txt\n", "!cat snps_high_heterozigosity_0.6.txt | wc -l" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [], "source": [ "new = open('results_filtered_1_2_3_4_5_6.vcf', 'w')\n", "lines_removed=open('lines_removed.txt', 'w')\n", "\n", "file_remove = open('snps_high_heterozigosity_0.6.txt', 'r')\n", "file_content= file_remove.read()\n", "lines_remove=file_content.split(\"\\n\")\n", "linea =0\n", "a =0\n", "with open ('results_filtered_1_2_3_4_5.recode.vcf') as f:\n", " for fila_vcf in f:\n", " linea=linea+1\n", " if linea>11:\n", " for snp in lines_remove:\n", " if snp != '': \n", " if linea == int(snp) + 11:\n", " new.write(\"remove\")\n", " lines_removed.write(str(linea) + \"\\t\" + str(snp) + \"\\n\")\n", " new.write(fila_vcf)" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "256\n", "256\n" ] } ], "source": [ "!cat results_filtered_1_2_3_4_5_6.vcf | grep \"remove\" | wc -l\n", "!cat snps_high_heterozigosity_0.6.txt | wc -l" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0\r\n" ] } ], "source": [ "!less results_filtered_1_2_3_4_5_6.vcf | grep -v \"remove\" | grep \"#\" -v | perl -ne 'chomp; @a=split(\"\\t\"); $ID = $a[2]; shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); shift(@a); $count=0;$total=0 ; for (@a){ $total++; if (($_ =~ /0\\/1/) || ($_ =~ /1\\/0/)){ $count++} elsif($_ =~ /\\.\\/\\./){ $total--}} $prop = ($count/$total); print \"$prop\\t$.\\n\"'| sort -n | perl -ne 'chomp; @a=split(\"\\t\"); if ($a[0] >0.6) { print \"$_\\n\"}' | cut -f 2 |sort -n > snps_high_heterozigosity_0.6_final.txt\n", "!cat snps_high_heterozigosity_0.6_final.txt | wc -l" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!less results_filtered_1_2_3_4_5_6.vcf | grep -v \"remove\" > 9pop270samples_final.vcf" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "4543\r\n" ] } ], "source": [ "!cat 9pop270samples_final.vcf | grep -v \"#\" | wc -l" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.4.3" } }, "nbformat": 4, "nbformat_minor": 0 }