Summary from DiagnosticSNPS Wed Nov 13 17:03:29 2013 The full .pheno file is Eco68_patho.pheno The phenotype subset file is Eco68_patho_50%.pheno The ppcs file written by GetSNPprobs is Eco68_patho_50%.ppcs The SNPs file written by GetSNPprobs is Eco68_patho_50%.SNPs The maximum PPV is 0.98 The maximum number of SNPS is 1000 Addition of SNPs is terminated when PPV declines below 0.97 * the highest PPV so far. Those SNPs that are absent only in phenotype positive or only in phenotype negative strains are excluded from this analysis. There are 68 strains in the .pheno file. The following strains were used by GetSNPprobs to calculate the chi-square probabilities and the posterior probabilities of the character states that are in the .ppcs file. Strain phenotype Eco536 1 Eco53638 1 EcoB_REL606 0 EcoBL21DE3 0 EcoCFT073 1 EcoED1a 0 EcoIAI1 0 EcoIAI39 1 EcoK12_MDS42 0 EcoK12_MG1655 0 EcoK12_W3110 0 EcoKO11FL 0 EcoLF82 1 EcoO7K1_CE10 1 EcoO26H11_str11368 1 EcoO55H7_RM12579 1 EcoO104H4_209EL-2071 1 EcoO157H7_EC4115 1 EcoO157H7_EDL933 1 EcoO157H7_Sakai 1 EcoO157H7_TW14588 1 EcoSMS35 0 EcoUM146 1 EcoUMNF18 1 EcoUMNK88 1 EcoW 0 EcoXUZhou21 1 Shidy_Sd197 1 Shifl_5_8401 1 Shiso_53G 1 Shiso_Ss046 1 The following 36 strains are used to calculate accuracy. Eco042 Eco55989 EcoABU83972 EcoAPEC01 EcoAPEC078 EcoATCC8739 EcoBL21-Gold EcoBW2952 EcoCloneDi2 EcoDH1 EcoDi14 EcoE24377A EcoETEC_H10407 EcoHS EcoIHE3034 EcoK12_DH10B EcoNA114 EcoO55H7_CB9615 EcoO83H1_NRG857C EcoO103H2_12009 EcoO104H4_2009EL-2050 EcoO104H4_2011C-3493 EcoO111H-_11128 EcoO127H6_E2348_69 EcoO157H7_TW14359 EcoS88 EcoSE11 EcoSE15 EcoUMN026 EcoUTI89 Shibo_CDC3083-94 Shibo_Sb277 Shifl_2a_245T Shifl_2a_301 Shifl_5a_M90T Shifl_2002017 Accuracy is estimated as SNPs are added starting with those with the lowest Chi-square probabilities until the estimated PPV is >= 0.98 or PPV is lower than 0.97 * the previous estimate. Addition of SNPs was terminated when PPV to less than 0.97 of its maximum. Cycle SNP Accuracy PPV NPV 1 258294 0.833333333333333 0.888888888888889 0.666666666666667 2 370125 0.833333333333333 0.888888888888889 0.666666666666667 3 344900 0.833333333333333 0.888888888888889 0.666666666666667 4 74791 0.852941176470588 0.92 0.666666666666667 5 168989 0.805555555555556 0.884615384615385 0.6 6 360001 0.833333333333333 0.888888888888889 0.666666666666667 7 128092 0.833333333333333 0.92 0.636363636363636 8 219438 0.833333333333333 0.92 0.636363636363636 9 408522 0.833333333333333 0.92 0.636363636363636 10 86206 0.805555555555556 0.884615384615385 0.6 11 114865 0.805555555555556 0.884615384615385 0.6 12 333663 0.777777777777778 0.88 0.545454545454545 13 415198 0.805555555555556 0.884615384615385 0.6 14 140900 0.833333333333333 0.92 0.636363636363636 15 109514 0.833333333333333 0.92 0.636363636363636 16 182377 0.833333333333333 0.92 0.636363636363636 17 247005 0.833333333333333 0.92 0.636363636363636 18 255253 0.861111111111111 0.923076923076923 0.7 19 383119 0.833333333333333 0.92 0.636363636363636 20 55972 0.861111111111111 0.923076923076923 0.7 21 59965 0.833333333333333 0.92 0.636363636363636 22 199272 0.861111111111111 0.923076923076923 0.7 23 325625 0.861111111111111 0.923076923076923 0.7 24 81165 0.888888888888889 0.925925925925926 0.777777777777778 25 142165 0.861111111111111 0.923076923076923 0.7 26 382723 0.888888888888889 0.925925925925926 0.777777777777778 27 131109 0.861111111111111 0.923076923076923 0.7 28 180103 0.861111111111111 0.923076923076923 0.7 29 228308 0.888888888888889 0.925925925925926 0.777777777777778 30 276140 0.861111111111111 0.923076923076923 0.7 31 391063 0.861111111111111 0.923076923076923 0.7 32 22888 0.861111111111111 0.923076923076923 0.7 33 235733 0.861111111111111 0.923076923076923 0.7 34 339653 0.861111111111111 0.923076923076923 0.7 35 412160 0.861111111111111 0.923076923076923 0.7 36 101071 0.861111111111111 0.923076923076923 0.7 37 272923 0.861111111111111 0.923076923076923 0.7 38 185287 0.861111111111111 0.923076923076923 0.7 39 21268 0.861111111111111 0.923076923076923 0.7 40 331528 0.861111111111111 0.923076923076923 0.7 41 229804 0.861111111111111 0.923076923076923 0.7 42 286072 0.861111111111111 0.923076923076923 0.7 43 398357 0.861111111111111 0.923076923076923 0.7 44 27458 0.861111111111111 0.923076923076923 0.7 45 73234 0.861111111111111 0.923076923076923 0.7 46 82330 0.861111111111111 0.923076923076923 0.7 47 93930 0.861111111111111 0.923076923076923 0.7 48 143250 0.861111111111111 0.923076923076923 0.7 49 272012 0.861111111111111 0.923076923076923 0.7 50 372694 0.861111111111111 0.923076923076923 0.7 51 382868 0.861111111111111 0.923076923076923 0.7 52 384487 0.861111111111111 0.923076923076923 0.7 53 389248 0.861111111111111 0.923076923076923 0.7 54 405120 0.861111111111111 0.923076923076923 0.7 55 68173 0.861111111111111 0.923076923076923 0.7 56 78007 0.861111111111111 0.923076923076923 0.7 57 158052 0.861111111111111 0.923076923076923 0.7 58 347745 0.861111111111111 0.923076923076923 0.7 59 90 0.861111111111111 0.923076923076923 0.7 60 142554 0.861111111111111 0.923076923076923 0.7 61 151025 0.861111111111111 0.923076923076923 0.7 62 246965 0.861111111111111 0.923076923076923 0.7 63 19403 0.861111111111111 0.923076923076923 0.7 64 187512 0.861111111111111 0.923076923076923 0.7 65 266704 0.861111111111111 0.923076923076923 0.7 66 388553 0.861111111111111 0.923076923076923 0.7 67 376499 0.861111111111111 0.923076923076923 0.7 68 1465 0.861111111111111 0.923076923076923 0.7 69 21149 0.916666666666667 0.928571428571429 0.875 70 66471 0.888888888888889 0.925925925925926 0.777777777777778 71 96964 0.916666666666667 0.928571428571429 0.875 72 133864 0.916666666666667 0.928571428571429 0.875 73 192172 0.916666666666667 0.928571428571429 0.875 74 210608 0.916666666666667 0.928571428571429 0.875 75 264753 0.916666666666667 0.928571428571429 0.875 76 307269 0.916666666666667 0.928571428571429 0.875 77 369145 0.916666666666667 0.928571428571429 0.875 78 371579 0.916666666666667 0.928571428571429 0.875 79 377128 0.916666666666667 0.928571428571429 0.875 80 49002 0.916666666666667 0.928571428571429 0.875 81 55502 0.916666666666667 0.928571428571429 0.875 82 354956 0.916666666666667 0.928571428571429 0.875 83 56929 0.916666666666667 0.928571428571429 0.875 84 123188 0.916666666666667 0.928571428571429 0.875 85 166191 0.916666666666667 0.928571428571429 0.875 86 386757 0.916666666666667 0.928571428571429 0.875 87 66418 0.916666666666667 0.928571428571429 0.875 88 78244 0.916666666666667 0.928571428571429 0.875 89 148445 0.916666666666667 0.928571428571429 0.875 90 154944 0.916666666666667 0.928571428571429 0.875 91 197320 0.916666666666667 0.928571428571429 0.875 92 198753 0.916666666666667 0.928571428571429 0.875 93 241846 0.916666666666667 0.928571428571429 0.875 94 409886 0.916666666666667 0.928571428571429 0.875 95 269138 0.916666666666667 0.928571428571429 0.875 96 57008 0.916666666666667 0.928571428571429 0.875 97 82432 0.916666666666667 0.928571428571429 0.875 98 110385 0.916666666666667 0.928571428571429 0.875 99 122424 0.916666666666667 0.928571428571429 0.875 100 138159 0.916666666666667 0.928571428571429 0.875 101 144908 0.916666666666667 0.928571428571429 0.875 102 171596 0.916666666666667 0.928571428571429 0.875 103 180726 0.916666666666667 0.928571428571429 0.875 104 192434 0.916666666666667 0.928571428571429 0.875 105 196891 0.916666666666667 0.928571428571429 0.875 106 197292 0.916666666666667 0.928571428571429 0.875 107 212221 0.916666666666667 0.928571428571429 0.875 108 265080 0.916666666666667 0.928571428571429 0.875 109 314915 0.916666666666667 0.928571428571429 0.875 110 328258 0.916666666666667 0.928571428571429 0.875 111 330118 0.944444444444444 0.931034482758621 1 112 346951 0.944444444444444 0.931034482758621 1 113 372879 0.944444444444444 0.931034482758621 1 114 395419 0.944444444444444 0.931034482758621 1 115 396662 0.944444444444444 0.931034482758621 1 116 414808 0.944444444444444 0.931034482758621 1 117 105611 0.944444444444444 0.931034482758621 1 118 141612 0.944444444444444 0.931034482758621 1 119 85774 0.944444444444444 0.931034482758621 1 120 108842 0.944444444444444 0.931034482758621 1 121 131430 0.944444444444444 0.931034482758621 1 122 151656 0.944444444444444 0.931034482758621 1 123 186878 0.944444444444444 0.931034482758621 1 124 217092 0.944444444444444 0.931034482758621 1 125 217795 0.944444444444444 0.931034482758621 1 126 317358 0.944444444444444 0.931034482758621 1 127 341592 0.944444444444444 0.931034482758621 1 128 364323 0.944444444444444 0.931034482758621 1 129 403007 0.944444444444444 0.931034482758621 1 130 414980 0.944444444444444 0.931034482758621 1 131 232234 0.944444444444444 0.931034482758621 1 132 389938 0.944444444444444 0.931034482758621 1 133 395801 0.944444444444444 0.931034482758621 1 134 397623 0.944444444444444 0.931034482758621 1 135 298583 0.944444444444444 0.931034482758621 1 136 200910 0.944444444444444 0.931034482758621 1 137 297573 0.944444444444444 0.931034482758621 1 138 330226 0.944444444444444 0.931034482758621 1 139 59384 0.944444444444444 0.931034482758621 1 140 252670 0.944444444444444 0.931034482758621 1 141 398608 0.944444444444444 0.931034482758621 1 142 2671 0.944444444444444 0.931034482758621 1 143 34145 0.944444444444444 0.931034482758621 1 144 52587 0.944444444444444 0.931034482758621 1 145 325748 0.944444444444444 0.931034482758621 1 146 65376 0.944444444444444 0.931034482758621 1 147 219525 0.944444444444444 0.931034482758621 1 148 247702 0.944444444444444 0.931034482758621 1 149 347682 0.944444444444444 0.931034482758621 1 150 354918 0.944444444444444 0.931034482758621 1 151 177012 0.944444444444444 0.931034482758621 1 152 243632 0.944444444444444 0.931034482758621 1 153 372863 0.944444444444444 0.931034482758621 1 154 163100 0.944444444444444 0.931034482758621 1 155 257445 0.944444444444444 0.931034482758621 1 156 380820 0.944444444444444 0.931034482758621 1 157 355984 0.944444444444444 0.931034482758621 1 158 7228 0.944444444444444 0.931034482758621 1 159 198640 0.944444444444444 0.931034482758621 1 160 288919 0.944444444444444 0.931034482758621 1 161 381916 0.944444444444444 0.931034482758621 1 162 397838 0.944444444444444 0.931034482758621 1 163 399887 0.944444444444444 0.931034482758621 1 164 177929 0.944444444444444 0.931034482758621 1 165 155465 0.944444444444444 0.931034482758621 1 166 114757 0.944444444444444 0.931034482758621 1 167 394566 0.944444444444444 0.931034482758621 1 168 160978 0.944444444444444 0.931034482758621 1 169 189673 0.944444444444444 0.931034482758621 1 170 378077 0.944444444444444 0.931034482758621 1 171 220609 0.944444444444444 0.931034482758621 1 172 39591 0.944444444444444 0.931034482758621 1 173 190749 0.944444444444444 0.931034482758621 1 174 273897 0.944444444444444 0.931034482758621 1 175 82037 0.944444444444444 0.931034482758621 1 176 117733 0.944444444444444 0.931034482758621 1 177 155342 0.944444444444444 0.931034482758621 1 178 147569 0.944444444444444 0.931034482758621 1 179 392058 0.944444444444444 0.931034482758621 1 180 100233 0.944444444444444 0.931034482758621 1 181 110554 0.944444444444444 0.931034482758621 1 182 328440 0.944444444444444 0.931034482758621 1 183 156903 0.944444444444444 0.931034482758621 1 184 211446 0.944444444444444 0.931034482758621 1 185 312746 0.944444444444444 0.931034482758621 1 186 30492 0.944444444444444 0.931034482758621 1 187 236866 0.944444444444444 0.931034482758621 1 188 265391 0.944444444444444 0.931034482758621 1 189 330831 0.944444444444444 0.931034482758621 1 190 113557 0.944444444444444 0.931034482758621 1 191 26400 0.944444444444444 0.931034482758621 1 192 80471 0.944444444444444 0.931034482758621 1 193 144534 0.944444444444444 0.931034482758621 1 194 219025 0.944444444444444 0.931034482758621 1 195 324529 0.944444444444444 0.931034482758621 1 196 351059 0.944444444444444 0.931034482758621 1 197 378550 0.944444444444444 0.931034482758621 1 198 388866 0.944444444444444 0.931034482758621 1 199 51832 0.944444444444444 0.931034482758621 1 200 97205 0.944444444444444 0.931034482758621 1 201 97752 0.944444444444444 0.931034482758621 1 202 106818 0.944444444444444 0.931034482758621 1 203 142277 0.944444444444444 0.931034482758621 1 204 183856 0.944444444444444 0.931034482758621 1 205 213393 0.944444444444444 0.931034482758621 1 206 215643 0.944444444444444 0.931034482758621 1 207 226044 0.944444444444444 0.931034482758621 1 207 SNPs were used to predict phenotypes For the strains used to calculate accuracy, after the last SNP was added, accuracy = 0.944444444444444, PPV = 0.931034482758621, and NPV = 1 For all strains whose phenotype is known accuracy = 0.970149253731343, PPV = 0.96 and NPV = 1 mean mean known probability probability predicted Strain phenotype positive negative phenotype Eco042 1 0.80373682955386 0.181770416822953 1 Eco536 1 0.885181346849546 0.114818653150455 1 Eco53638 1 0.869742453122861 0.13025754687714 1 Eco55989 1 0.882940924218312 0.117059075781689 1 EcoABU83972 1 0.875997907305016 0.124002092694985 1 EcoAPEC01 1 0.867768101838373 0.132231898161627 1 EcoAPEC078 0 0.493785678298341 0.506214321701659 0 EcoATCC8739 0 0.595423231129093 0.404576768870908 1 EcoB_REL606 0 0.151738492318202 0.848261507681797 0 EcoBL21-Gold 0 0.139224059914041 0.860775940085958 0 EcoBL21DE3 0 0.149542620557113 0.850457379442886 0 EcoBW2952 0 0.155997234696038 0.844002765303961 0 EcoCFT073 1 0.907162586906004 0.0928374130939967 1 EcoCloneDi2 1 0.903931701905477 0.0960682980945232 1 EcoDH1 0 0.139278224750815 0.860721775249184 0 EcoDi14 1 0.899873730890985 0.100126269109016 1 EcoE24377A 1 0.549209682513763 0.450790317486237 1 EcoED1a 0 0.444058096677951 0.555941903322049 0 EcoETEC_H10407 1 0.726615610739307 0.273384389260695 1 EcoHS 0 0.499784021681434 0.500215978318566 0 EcoIAI1 0 0.410271577525816 0.589728422474183 0 EcoIAI39 1 0.9065955150006 0.0934044849994 1 EcoIHE3034 1 0.876906358840856 0.123093641159144 1 EcoK12_DH10B 0 0.200173809617822 0.799826190382178 0 EcoK12_MDS42 0 0.284615531235144 0.715384468764855 0 EcoK12_MG1655 0 0.139278224750815 0.860721775249184 0 EcoK12_W3110 0 0.139278224750815 0.860721775249184 0 EcoKO11FL 0 0.252531225201626 0.747468774798373 0 EcoLF82 1 0.855451396310379 0.144548603689622 1 EcoNA114 1 0.818018813376227 0.181981186623774 1 EcoO7K1_CE10 1 0.906410025212086 0.0935899747879144 1 EcoO26H11_str11368 1 0.869202477908187 0.130797522091813 1 EcoO55H7_CB9615 1 0.912108052173522 0.0878919478264779 1 EcoO55H7_RM12579 1 0.923968687512418 0.0760313124875816 1 EcoO83H1_NRG857C 1 0.864865492680997 0.135134507319004 1 EcoO103H2_12009 1 0.541437177647457 0.458562822352543 1 EcoO104H4_209EL-2071 1 0.886605688981475 0.113394311018526 1 EcoO104H4_2009EL-2050 1 0.883970642868168 0.116029357131833 1 EcoO104H4_2011C-3493 1 0.887601150846502 0.112398849153498 1 EcoO111H-_11128 1 0.607714756202909 0.392285243797092 1 EcoO127H6_E2348_69 1 0.832575631465861 0.16742436853414 1 EcoO157H7_EC4115 1 0.925793700931635 0.0742062990683652 1 EcoO157H7_EDL933 1 0.933124427102941 0.0668755728970594 1 EcoO157H7_Sakai 1 0.930261593690908 0.0697384063090919 1 EcoO157H7_TW14359 1 0.925793700931635 0.0742062990683652 1 EcoO157H7_TW14588 1 0.933630523261211 0.0663694767387893 1 EcoP12b ? 0.517990095663696 0.482009904336304 1 EcoS88 1 0.885021711030781 0.11497828896922 1 EcoSE11 0 0.422399964132569 0.57760003586743 0 EcoSE15 0 0.797032719732306 0.202967280267696 1 EcoSMS35 0 0.441269912754986 0.558730087245013 0 EcoUM146 1 0.906659393895188 0.0933406061048126 1 EcoUMN026 1 0.676414101221253 0.323585898778748 1 EcoUMNF18 1 0.755621458084398 0.244378541915603 1 EcoUMNK88 1 0.846038007293409 0.153961992706591 1 EcoUTI89 1 0.919524145890375 0.0804758541096257 1 EcoW 0 0.252531225201626 0.747468774798373 0 EcoXUZhou21 1 0.925793700931635 0.0742062990683652 1 Shibo_CDC3083-94 1 0.675515014711428 0.324484985288573 1 Shibo_Sb277 1 0.684632696798593 0.315367303201408 1 Shidy_Sd197 1 0.784993453084679 0.215006546915322 1 Shifl_2a_245T 1 0.87460388845239 0.125396111547612 1 Shifl_2a_301 1 0.864307689750394 0.135692310249607 1 Shifl_5_8401 1 0.867166817514175 0.132833182485827 1 Shifl_5a_M90T 1 0.867166817514175 0.132833182485827 1 Shifl_2002017 1 0.867312200001281 0.13268779999872 1 Shiso_53G 1 0.756825861148971 0.24317413885103 1 Shiso_Ss046 1 0.758655754283212 0.241344245716789 1