Mercurial > repos > nml > mykrobe_parser
comparison test-data/test-data.json @ 0:6eae14751768 draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
| author | nml |
|---|---|
| date | Fri, 28 Sep 2018 16:01:47 -0400 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:6eae14751768 |
|---|---|
| 1 { | |
| 2 "sample": { | |
| 3 "probe_sets": [ | |
| 4 "/Drives/P/Galaxies/main_nml/galaxy-common/deps/_conda/envs/__mykrobe@0.5.6/lib/python3.5/site-packages/mykrobe/data/panels/tb-species-170421.fasta.gz", | |
| 5 "/Drives/P/Galaxies/main_nml/galaxy-common/deps/_conda/envs/__mykrobe@0.5.6/lib/python3.5/site-packages/mykrobe/data/panels/tb-walker-probe-set-feb-09-2017.fasta.gz" | |
| 6 ], | |
| 7 "sequence_calls": {}, | |
| 8 "variant_calls": { | |
| 9 "rpoB_S450Q-TCG761154CAG": { | |
| 10 "info": { | |
| 11 "contamination_depths": [], | |
| 12 "coverage": { | |
| 13 "alternate": { | |
| 14 "median_depth": 0, | |
| 15 "min_non_zero_depth": 14, | |
| 16 "percent_coverage": 4.55, | |
| 17 "kmer_count": 14 | |
| 18 }, | |
| 19 "reference": { | |
| 20 "median_depth": 0, | |
| 21 "min_non_zero_depth": 14, | |
| 22 "percent_coverage": 4.55, | |
| 23 "kmer_count": 14 | |
| 24 } | |
| 25 }, | |
| 26 "expected_depths": [ | |
| 27 17.0 | |
| 28 ], | |
| 29 "filter": "LOW_GT_CONF", | |
| 30 "conf": 0 | |
| 31 }, | |
| 32 "genotype_likelihoods": [ | |
| 33 -99999999, | |
| 34 -99999999, | |
| 35 -99999999 | |
| 36 ], | |
| 37 "_cls": "Call.VariantCall", | |
| 38 "genotype": [ | |
| 39 0, | |
| 40 0 | |
| 41 ], | |
| 42 "variant": "ref-S450Q?var_name=TCG761154CAG&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450Q" | |
| 43 }, | |
| 44 "rpoB_Q436A-CAG761112GCC": { | |
| 45 "info": { | |
| 46 "contamination_depths": [], | |
| 47 "coverage": { | |
| 48 "alternate": { | |
| 49 "median_depth": 0, | |
| 50 "min_non_zero_depth": 17, | |
| 51 "percent_coverage": 22.73, | |
| 52 "kmer_count": 86 | |
| 53 }, | |
| 54 "reference": { | |
| 55 "median_depth": 19, | |
| 56 "min_non_zero_depth": 17, | |
| 57 "percent_coverage": 100.0, | |
| 58 "kmer_count": 413 | |
| 59 } | |
| 60 }, | |
| 61 "expected_depths": [ | |
| 62 17.0 | |
| 63 ], | |
| 64 "filter": "PASS", | |
| 65 "conf": 99999996 | |
| 66 }, | |
| 67 "genotype_likelihoods": [ | |
| 68 -2.79216398346472, | |
| 69 -99999999, | |
| 70 -99999999 | |
| 71 ], | |
| 72 "_cls": "Call.VariantCall", | |
| 73 "genotype": [ | |
| 74 0, | |
| 75 0 | |
| 76 ], | |
| 77 "variant": "ref-Q436A?var_name=CAG761112GCC&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436A" | |
| 78 }, | |
| 79 "rpoB_F433D-TTC761103GAT": { | |
| 80 "info": { | |
| 81 "contamination_depths": [], | |
| 82 "coverage": { | |
| 83 "alternate": { | |
| 84 "median_depth": 0, | |
| 85 "min_non_zero_depth": 17, | |
| 86 "percent_coverage": 22.73, | |
| 87 "kmer_count": 87 | |
| 88 }, | |
| 89 "reference": { | |
| 90 "median_depth": 19, | |
| 91 "min_non_zero_depth": 18, | |
| 92 "percent_coverage": 100.0, | |
| 93 "kmer_count": 421 | |
| 94 } | |
| 95 }, | |
| 96 "expected_depths": [ | |
| 97 17.0 | |
| 98 ], | |
| 99 "filter": "PASS", | |
| 100 "conf": 99999996 | |
| 101 }, | |
| 102 "genotype_likelihoods": [ | |
| 103 -2.79216398346472, | |
| 104 -99999999, | |
| 105 -99999999 | |
| 106 ], | |
| 107 "_cls": "Call.VariantCall", | |
| 108 "genotype": [ | |
| 109 0, | |
| 110 0 | |
| 111 ], | |
| 112 "variant": "ref-F433D?var_name=TTC761103GAT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=F433D" | |
| 113 }, | |
| 114 "katG_S315C-GCT2155167ACA": { | |
| 115 "info": { | |
| 116 "contamination_depths": [], | |
| 117 "coverage": { | |
| 118 "alternate": { | |
| 119 "median_depth": 0, | |
| 120 "min_non_zero_depth": 0, | |
| 121 "percent_coverage": 0.0, | |
| 122 "kmer_count": 0 | |
| 123 }, | |
| 124 "reference": { | |
| 125 "median_depth": 0, | |
| 126 "min_non_zero_depth": 17, | |
| 127 "percent_coverage": 4.55, | |
| 128 "kmer_count": 17 | |
| 129 } | |
| 130 }, | |
| 131 "expected_depths": [ | |
| 132 17.0 | |
| 133 ], | |
| 134 "filter": "LOW_GT_CONF", | |
| 135 "conf": 0 | |
| 136 }, | |
| 137 "genotype_likelihoods": [ | |
| 138 -99999999, | |
| 139 -99999999, | |
| 140 -99999999 | |
| 141 ], | |
| 142 "_cls": "Call.VariantCall", | |
| 143 "genotype": [ | |
| 144 0, | |
| 145 0 | |
| 146 ], | |
| 147 "variant": "ref-S315C?var_name=GCT2155167ACA&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315C" | |
| 148 }, | |
| 149 "rpoB_S428A-AGC761088GCA": { | |
| 150 "info": { | |
| 151 "contamination_depths": [], | |
| 152 "coverage": { | |
| 153 "alternate": { | |
| 154 "median_depth": 0, | |
| 155 "min_non_zero_depth": 0, | |
| 156 "percent_coverage": 0.0, | |
| 157 "kmer_count": 0 | |
| 158 }, | |
| 159 "reference": { | |
| 160 "median_depth": 18, | |
| 161 "min_non_zero_depth": 14, | |
| 162 "percent_coverage": 100.0, | |
| 163 "kmer_count": 382 | |
| 164 } | |
| 165 }, | |
| 166 "expected_depths": [ | |
| 167 17.0 | |
| 168 ], | |
| 169 "filter": "PASS", | |
| 170 "conf": 99999996 | |
| 171 }, | |
| 172 "genotype_likelihoods": [ | |
| 173 -2.6809383483544966, | |
| 174 -99999999, | |
| 175 -99999999 | |
| 176 ], | |
| 177 "_cls": "Call.VariantCall", | |
| 178 "genotype": [ | |
| 179 0, | |
| 180 0 | |
| 181 ], | |
| 182 "variant": "ref-S428A?var_name=AGC761088GCA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428A" | |
| 183 }, | |
| 184 "gyrA_P86L-CCG7557CTT": { | |
| 185 "info": { | |
| 186 "contamination_depths": [], | |
| 187 "coverage": { | |
| 188 "alternate": { | |
| 189 "median_depth": 0, | |
| 190 "min_non_zero_depth": 0, | |
| 191 "percent_coverage": 0.0, | |
| 192 "kmer_count": 0 | |
| 193 }, | |
| 194 "reference": { | |
| 195 "median_depth": 16, | |
| 196 "min_non_zero_depth": 13, | |
| 197 "percent_coverage": 100.0, | |
| 198 "kmer_count": 359 | |
| 199 } | |
| 200 }, | |
| 201 "expected_depths": [ | |
| 202 17.0 | |
| 203 ], | |
| 204 "filter": "PASS", | |
| 205 "conf": 99999996 | |
| 206 }, | |
| 207 "genotype_likelihoods": [ | |
| 208 -2.62377993451455, | |
| 209 -99999999, | |
| 210 -99999999 | |
| 211 ], | |
| 212 "_cls": "Call.VariantCall", | |
| 213 "genotype": [ | |
| 214 0, | |
| 215 0 | |
| 216 ], | |
| 217 "variant": "ref-P86L?var_name=CCG7557CTT&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86L" | |
| 218 }, | |
| 219 "katG_W328L-CCA2155128GAG": { | |
| 220 "info": { | |
| 221 "contamination_depths": [], | |
| 222 "coverage": { | |
| 223 "alternate": { | |
| 224 "median_depth": 0, | |
| 225 "min_non_zero_depth": 0, | |
| 226 "percent_coverage": 0.0, | |
| 227 "kmer_count": 0 | |
| 228 }, | |
| 229 "reference": { | |
| 230 "median_depth": 13, | |
| 231 "min_non_zero_depth": 12, | |
| 232 "percent_coverage": 100.0, | |
| 233 "kmer_count": 284 | |
| 234 } | |
| 235 }, | |
| 236 "expected_depths": [ | |
| 237 17.0 | |
| 238 ], | |
| 239 "filter": "PASS", | |
| 240 "conf": 99999996 | |
| 241 }, | |
| 242 "genotype_likelihoods": [ | |
| 243 -3.0037237137259485, | |
| 244 -99999999, | |
| 245 -99999999 | |
| 246 ], | |
| 247 "_cls": "Call.VariantCall", | |
| 248 "genotype": [ | |
| 249 0, | |
| 250 0 | |
| 251 ], | |
| 252 "variant": "ref-W328L?var_name=CCA2155128GAG&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W328L" | |
| 253 }, | |
| 254 "katG_S315M-GCT2155167CAT": { | |
| 255 "info": { | |
| 256 "contamination_depths": [], | |
| 257 "coverage": { | |
| 258 "alternate": { | |
| 259 "median_depth": 0, | |
| 260 "min_non_zero_depth": 17, | |
| 261 "percent_coverage": 4.55, | |
| 262 "kmer_count": 17 | |
| 263 }, | |
| 264 "reference": { | |
| 265 "median_depth": 0, | |
| 266 "min_non_zero_depth": 17, | |
| 267 "percent_coverage": 4.55, | |
| 268 "kmer_count": 17 | |
| 269 } | |
| 270 }, | |
| 271 "expected_depths": [ | |
| 272 17.0 | |
| 273 ], | |
| 274 "filter": "LOW_GT_CONF", | |
| 275 "conf": 0 | |
| 276 }, | |
| 277 "genotype_likelihoods": [ | |
| 278 -99999999, | |
| 279 -99999999, | |
| 280 -99999999 | |
| 281 ], | |
| 282 "_cls": "Call.VariantCall", | |
| 283 "genotype": [ | |
| 284 0, | |
| 285 0 | |
| 286 ], | |
| 287 "variant": "ref-S315M?var_name=GCT2155167CAT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315M" | |
| 288 }, | |
| 289 "gid_S136Y-TGA4407795GTA": { | |
| 290 "info": { | |
| 291 "contamination_depths": [], | |
| 292 "coverage": { | |
| 293 "alternate": { | |
| 294 "median_depth": 0, | |
| 295 "min_non_zero_depth": 15, | |
| 296 "percent_coverage": 4.55, | |
| 297 "kmer_count": 15 | |
| 298 }, | |
| 299 "reference": { | |
| 300 "median_depth": 15, | |
| 301 "min_non_zero_depth": 14, | |
| 302 "percent_coverage": 100.0, | |
| 303 "kmer_count": 327 | |
| 304 } | |
| 305 }, | |
| 306 "expected_depths": [ | |
| 307 17.0 | |
| 308 ], | |
| 309 "filter": "PASS", | |
| 310 "conf": 99999996 | |
| 311 }, | |
| 312 "genotype_likelihoods": [ | |
| 313 -2.6844045563309873, | |
| 314 -99999999, | |
| 315 -99999999 | |
| 316 ], | |
| 317 "_cls": "Call.VariantCall", | |
| 318 "genotype": [ | |
| 319 0, | |
| 320 0 | |
| 321 ], | |
| 322 "variant": "ref-S136Y?var_name=TGA4407795GTA&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136Y" | |
| 323 }, | |
| 324 "embB_M306V-ATG4247429GTG": { | |
| 325 "info": { | |
| 326 "contamination_depths": [], | |
| 327 "coverage": { | |
| 328 "alternate": { | |
| 329 "median_depth": 0, | |
| 330 "min_non_zero_depth": 16, | |
| 331 "percent_coverage": 9.09, | |
| 332 "kmer_count": 32 | |
| 333 }, | |
| 334 "reference": { | |
| 335 "median_depth": 14, | |
| 336 "min_non_zero_depth": 8, | |
| 337 "percent_coverage": 100.0, | |
| 338 "kmer_count": 293 | |
| 339 } | |
| 340 }, | |
| 341 "expected_depths": [ | |
| 342 17.0 | |
| 343 ], | |
| 344 "filter": "PASS", | |
| 345 "conf": 99999996 | |
| 346 }, | |
| 347 "genotype_likelihoods": [ | |
| 348 -2.8095676992849885, | |
| 349 -99999999, | |
| 350 -99999999 | |
| 351 ], | |
| 352 "_cls": "Call.VariantCall", | |
| 353 "genotype": [ | |
| 354 0, | |
| 355 0 | |
| 356 ], | |
| 357 "variant": "ref-M306V?var_name=ATG4247429GTG&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306V" | |
| 358 }, | |
| 359 "katG_W505I-CCA2154597TAT": { | |
| 360 "info": { | |
| 361 "contamination_depths": [], | |
| 362 "coverage": { | |
| 363 "alternate": { | |
| 364 "median_depth": 0, | |
| 365 "min_non_zero_depth": 0, | |
| 366 "percent_coverage": 0.0, | |
| 367 "kmer_count": 0 | |
| 368 }, | |
| 369 "reference": { | |
| 370 "median_depth": 18, | |
| 371 "min_non_zero_depth": 16, | |
| 372 "percent_coverage": 100.0, | |
| 373 "kmer_count": 385 | |
| 374 } | |
| 375 }, | |
| 376 "expected_depths": [ | |
| 377 17.0 | |
| 378 ], | |
| 379 "filter": "PASS", | |
| 380 "conf": 99999996 | |
| 381 }, | |
| 382 "genotype_likelihoods": [ | |
| 383 -2.6809383483544966, | |
| 384 -99999999, | |
| 385 -99999999 | |
| 386 ], | |
| 387 "_cls": "Call.VariantCall", | |
| 388 "genotype": [ | |
| 389 0, | |
| 390 0 | |
| 391 ], | |
| 392 "variant": "ref-W505I?var_name=CCA2154597TAT&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505I" | |
| 393 }, | |
| 394 "gid_A80P-CGC4407963GGG": { | |
| 395 "info": { | |
| 396 "contamination_depths": [], | |
| 397 "coverage": { | |
| 398 "alternate": { | |
| 399 "median_depth": 0, | |
| 400 "min_non_zero_depth": 0, | |
| 401 "percent_coverage": 0.0, | |
| 402 "kmer_count": 0 | |
| 403 }, | |
| 404 "reference": { | |
| 405 "median_depth": 23, | |
| 406 "min_non_zero_depth": 21, | |
| 407 "percent_coverage": 100.0, | |
| 408 "kmer_count": 509 | |
| 409 } | |
| 410 }, | |
| 411 "expected_depths": [ | |
| 412 17.0 | |
| 413 ], | |
| 414 "filter": "PASS", | |
| 415 "conf": 99999995 | |
| 416 }, | |
| 417 "genotype_likelihoods": [ | |
| 418 -3.726101987804734, | |
| 419 -99999999, | |
| 420 -99999999 | |
| 421 ], | |
| 422 "_cls": "Call.VariantCall", | |
| 423 "genotype": [ | |
| 424 0, | |
| 425 0 | |
| 426 ], | |
| 427 "variant": "ref-A80P?var_name=CGC4407963GGG&num_alts=43&ref=NC_000962.3&enum=0&gene=gid&mut=A80P" | |
| 428 }, | |
| 429 "gid_V88A-TAC4407939TGC": { | |
| 430 "info": { | |
| 431 "contamination_depths": [], | |
| 432 "coverage": { | |
| 433 "alternate": { | |
| 434 "median_depth": 0, | |
| 435 "min_non_zero_depth": 24, | |
| 436 "percent_coverage": 4.55, | |
| 437 "kmer_count": 24 | |
| 438 }, | |
| 439 "reference": { | |
| 440 "median_depth": 20, | |
| 441 "min_non_zero_depth": 16, | |
| 442 "percent_coverage": 100.0, | |
| 443 "kmer_count": 420 | |
| 444 } | |
| 445 }, | |
| 446 "expected_depths": [ | |
| 447 17.0 | |
| 448 ], | |
| 449 "filter": "PASS", | |
| 450 "conf": 99999996 | |
| 451 }, | |
| 452 "genotype_likelihoods": [ | |
| 453 -2.9546829129624985, | |
| 454 -99999999, | |
| 455 -99999999 | |
| 456 ], | |
| 457 "_cls": "Call.VariantCall", | |
| 458 "genotype": [ | |
| 459 0, | |
| 460 0 | |
| 461 ], | |
| 462 "variant": "ref-V88A?var_name=TAC4407939TGC&num_alts=21&ref=NC_000962.3&enum=0&gene=gid&mut=V88A" | |
| 463 }, | |
| 464 "rpoB_A451L-GCG761157TTG": { | |
| 465 "info": { | |
| 466 "contamination_depths": [], | |
| 467 "coverage": { | |
| 468 "alternate": { | |
| 469 "median_depth": 0, | |
| 470 "min_non_zero_depth": 15, | |
| 471 "percent_coverage": 4.55, | |
| 472 "kmer_count": 15 | |
| 473 }, | |
| 474 "reference": { | |
| 475 "median_depth": 14, | |
| 476 "min_non_zero_depth": 14, | |
| 477 "percent_coverage": 100.0, | |
| 478 "kmer_count": 319 | |
| 479 } | |
| 480 }, | |
| 481 "expected_depths": [ | |
| 482 17.0 | |
| 483 ], | |
| 484 "filter": "PASS", | |
| 485 "conf": 99999996 | |
| 486 }, | |
| 487 "genotype_likelihoods": [ | |
| 488 -2.8095676992849885, | |
| 489 -99999999, | |
| 490 -99999999 | |
| 491 ], | |
| 492 "_cls": "Call.VariantCall", | |
| 493 "genotype": [ | |
| 494 0, | |
| 495 0 | |
| 496 ], | |
| 497 "variant": "ref-A451L?var_name=GCG761157TTG&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451L" | |
| 498 }, | |
| 499 "gyrA_A90L-GCG7569TTG": { | |
| 500 "info": { | |
| 501 "contamination_depths": [], | |
| 502 "coverage": { | |
| 503 "alternate": { | |
| 504 "median_depth": 0, | |
| 505 "min_non_zero_depth": 20, | |
| 506 "percent_coverage": 4.55, | |
| 507 "kmer_count": 20 | |
| 508 }, | |
| 509 "reference": { | |
| 510 "median_depth": 19, | |
| 511 "min_non_zero_depth": 18, | |
| 512 "percent_coverage": 100.0, | |
| 513 "kmer_count": 410 | |
| 514 } | |
| 515 }, | |
| 516 "expected_depths": [ | |
| 517 17.0 | |
| 518 ], | |
| 519 "filter": "PASS", | |
| 520 "conf": 99999996 | |
| 521 }, | |
| 522 "genotype_likelihoods": [ | |
| 523 -2.79216398346472, | |
| 524 -99999999, | |
| 525 -99999999 | |
| 526 ], | |
| 527 "_cls": "Call.VariantCall", | |
| 528 "genotype": [ | |
| 529 0, | |
| 530 0 | |
| 531 ], | |
| 532 "variant": "ref-A90L?var_name=GCG7569TTG&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90L" | |
| 533 }, | |
| 534 "gyrA_D94S-GAC7581TCA": { | |
| 535 "info": { | |
| 536 "contamination_depths": [], | |
| 537 "coverage": { | |
| 538 "alternate": { | |
| 539 "median_depth": 0, | |
| 540 "min_non_zero_depth": 0, | |
| 541 "percent_coverage": 0.0, | |
| 542 "kmer_count": 0 | |
| 543 }, | |
| 544 "reference": { | |
| 545 "median_depth": 19, | |
| 546 "min_non_zero_depth": 17, | |
| 547 "percent_coverage": 100.0, | |
| 548 "kmer_count": 406 | |
| 549 } | |
| 550 }, | |
| 551 "expected_depths": [ | |
| 552 17.0 | |
| 553 ], | |
| 554 "filter": "PASS", | |
| 555 "conf": 99999996 | |
| 556 }, | |
| 557 "genotype_likelihoods": [ | |
| 558 -2.79216398346472, | |
| 559 -99999999, | |
| 560 -99999999 | |
| 561 ], | |
| 562 "_cls": "Call.VariantCall", | |
| 563 "genotype": [ | |
| 564 0, | |
| 565 0 | |
| 566 ], | |
| 567 "variant": "ref-D94S?var_name=GAC7581TCA&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94S" | |
| 568 }, | |
| 569 "rpoB_S431A-AGC761097GCT": { | |
| 570 "info": { | |
| 571 "contamination_depths": [], | |
| 572 "coverage": { | |
| 573 "alternate": { | |
| 574 "median_depth": 0, | |
| 575 "min_non_zero_depth": 19, | |
| 576 "percent_coverage": 22.73, | |
| 577 "kmer_count": 98 | |
| 578 }, | |
| 579 "reference": { | |
| 580 "median_depth": 19, | |
| 581 "min_non_zero_depth": 17, | |
| 582 "percent_coverage": 100.0, | |
| 583 "kmer_count": 411 | |
| 584 } | |
| 585 }, | |
| 586 "expected_depths": [ | |
| 587 17.0 | |
| 588 ], | |
| 589 "filter": "PASS", | |
| 590 "conf": 99999996 | |
| 591 }, | |
| 592 "genotype_likelihoods": [ | |
| 593 -2.79216398346472, | |
| 594 -99999999, | |
| 595 -99999999 | |
| 596 ], | |
| 597 "_cls": "Call.VariantCall", | |
| 598 "genotype": [ | |
| 599 0, | |
| 600 0 | |
| 601 ], | |
| 602 "variant": "ref-S431A?var_name=AGC761097GCT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431A" | |
| 603 }, | |
| 604 "rpoB_A451N-GCG761157AAT": { | |
| 605 "info": { | |
| 606 "contamination_depths": [], | |
| 607 "coverage": { | |
| 608 "alternate": { | |
| 609 "median_depth": 0, | |
| 610 "min_non_zero_depth": 0, | |
| 611 "percent_coverage": 0.0, | |
| 612 "kmer_count": 0 | |
| 613 }, | |
| 614 "reference": { | |
| 615 "median_depth": 14, | |
| 616 "min_non_zero_depth": 14, | |
| 617 "percent_coverage": 100.0, | |
| 618 "kmer_count": 319 | |
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| 620 }, | |
| 621 "expected_depths": [ | |
| 622 17.0 | |
| 623 ], | |
| 624 "filter": "PASS", | |
| 625 "conf": 99999996 | |
| 626 }, | |
| 627 "genotype_likelihoods": [ | |
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| 630 -99999999 | |
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| 632 "_cls": "Call.VariantCall", | |
| 633 "genotype": [ | |
| 634 0, | |
| 635 0 | |
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| 637 "variant": "ref-A451N?var_name=GCG761157AAT&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451N" | |
| 638 }, | |
| 639 "rpoB_Q429S-CAG761091AGC": { | |
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| 651 "min_non_zero_depth": 15, | |
| 652 "percent_coverage": 100.0, | |
| 653 "kmer_count": 395 | |
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| 655 }, | |
| 656 "expected_depths": [ | |
| 657 17.0 | |
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| 661 }, | |
| 662 "genotype_likelihoods": [ | |
| 663 -2.6809383483544966, | |
| 664 -99999999, | |
| 665 -99999999 | |
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| 667 "_cls": "Call.VariantCall", | |
| 668 "genotype": [ | |
| 669 0, | |
| 670 0 | |
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| 672 "variant": "ref-Q429S?var_name=CAG761091AGC&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429S" | |
| 673 }, | |
| 674 "rpoB_L443W-TTG761133TGG": { | |
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| 677 "coverage": { | |
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| 691 "expected_depths": [ | |
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| 699 -99999999, | |
| 700 -99999999 | |
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| 702 "_cls": "Call.VariantCall", | |
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| 705 0 | |
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| 707 "variant": "ref-L443W?var_name=TTG761133TGG&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443W" | |
| 708 }, | |
| 709 "rpoB_L443H-TTG761133CAC": { | |
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| 712 "coverage": { | |
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| 722 "percent_coverage": 95.45, | |
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| 726 "expected_depths": [ | |
| 727 17.0 | |
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| 729 "filter": "LOW_GT_CONF", | |
| 730 "conf": 0 | |
| 731 }, | |
| 732 "genotype_likelihoods": [ | |
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| 734 -99999999, | |
| 735 -99999999 | |
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| 737 "_cls": "Call.VariantCall", | |
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| 739 0, | |
| 740 0 | |
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| 742 "variant": "ref-L443H?var_name=TTG761133CAC&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443H" | |
| 743 }, | |
| 744 "rpoB_R447Q-CGC761145CAG": { | |
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| 747 "coverage": { | |
| 748 "alternate": { | |
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| 754 "reference": { | |
| 755 "median_depth": 16, | |
| 756 "min_non_zero_depth": 14, | |
| 757 "percent_coverage": 100.0, | |
| 758 "kmer_count": 358 | |
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| 760 }, | |
| 761 "expected_depths": [ | |
| 762 17.0 | |
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| 766 }, | |
| 767 "genotype_likelihoods": [ | |
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| 769 -99999999, | |
| 770 -99999999 | |
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| 772 "_cls": "Call.VariantCall", | |
| 773 "genotype": [ | |
| 774 0, | |
| 775 0 | |
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| 777 "variant": "ref-R447Q?var_name=CGC761145CAG&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447Q" | |
| 778 }, | |
| 779 "rpoB_L440I-CTG761124ATT": { | |
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| 782 "coverage": { | |
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| 786 "percent_coverage": 13.64, | |
| 787 "kmer_count": 54 | |
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| 791 "min_non_zero_depth": 17, | |
| 792 "percent_coverage": 100.0, | |
| 793 "kmer_count": 385 | |
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| 795 }, | |
| 796 "expected_depths": [ | |
| 797 17.0 | |
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| 801 }, | |
| 802 "genotype_likelihoods": [ | |
| 803 -2.6237799345145465, | |
| 804 -99999999, | |
| 805 -99999999 | |
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| 807 "_cls": "Call.VariantCall", | |
| 808 "genotype": [ | |
| 809 0, | |
| 810 0 | |
| 811 ], | |
| 812 "variant": "ref-L440I?var_name=CTG761124ATT&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440I" | |
| 813 }, | |
| 814 "rpoB_F425R-TTC761079AGG": { | |
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| 817 "coverage": { | |
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| 824 "reference": { | |
| 825 "median_depth": 15, | |
| 826 "min_non_zero_depth": 14, | |
| 827 "percent_coverage": 100.0, | |
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| 830 }, | |
| 831 "expected_depths": [ | |
| 832 17.0 | |
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| 836 }, | |
| 837 "genotype_likelihoods": [ | |
| 838 -2.6844045563309873, | |
| 839 -99999999, | |
| 840 -99999999 | |
| 841 ], | |
| 842 "_cls": "Call.VariantCall", | |
| 843 "genotype": [ | |
| 844 0, | |
| 845 0 | |
| 846 ], | |
| 847 "variant": "ref-F425R?var_name=TTC761079AGG&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425R" | |
| 848 }, | |
| 849 "rpoB_S441D-TCG761127GAT": { | |
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| 852 "coverage": { | |
| 853 "alternate": { | |
| 854 "median_depth": 0, | |
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| 856 "percent_coverage": 0.0, | |
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| 861 "min_non_zero_depth": 17, | |
| 862 "percent_coverage": 100.0, | |
| 863 "kmer_count": 384 | |
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| 865 }, | |
| 866 "expected_depths": [ | |
| 867 17.0 | |
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| 871 }, | |
| 872 "genotype_likelihoods": [ | |
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| 877 "_cls": "Call.VariantCall", | |
| 878 "genotype": [ | |
| 879 0, | |
| 880 0 | |
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| 882 "variant": "ref-S441D?var_name=TCG761127GAT&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441D" | |
| 883 }, | |
| 884 "pncA_Q10L-CTG2289212TAG": { | |
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| 888 "alternate": { | |
| 889 "median_depth": 0, | |
| 890 "min_non_zero_depth": 16, | |
| 891 "percent_coverage": 4.55, | |
| 892 "kmer_count": 16 | |
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| 895 "median_depth": 15, | |
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| 901 "expected_depths": [ | |
| 902 17.0 | |
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| 906 }, | |
| 907 "genotype_likelihoods": [ | |
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| 912 "_cls": "Call.VariantCall", | |
| 913 "genotype": [ | |
| 914 0, | |
| 915 0 | |
| 916 ], | |
| 917 "variant": "ref-Q10L?var_name=CTG2289212TAG&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10L" | |
| 918 }, | |
| 919 "gid_A205E-TGC4407588CTC": { | |
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| 922 "coverage": { | |
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| 925 "min_non_zero_depth": 21, | |
| 926 "percent_coverage": 4.55, | |
| 927 "kmer_count": 21 | |
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| 929 "reference": { | |
| 930 "median_depth": 0, | |
| 931 "min_non_zero_depth": 21, | |
| 932 "percent_coverage": 9.09, | |
| 933 "kmer_count": 42 | |
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| 936 "expected_depths": [ | |
| 937 17.0 | |
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| 939 "filter": "LOW_GT_CONF", | |
| 940 "conf": 0 | |
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| 942 "genotype_likelihoods": [ | |
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| 944 -99999999, | |
| 945 -99999999 | |
| 946 ], | |
| 947 "_cls": "Call.VariantCall", | |
| 948 "genotype": [ | |
| 949 0, | |
| 950 0 | |
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| 952 "variant": "ref-A205E?var_name=TGC4407588CTC&num_alts=6&ref=NC_000962.3&enum=0&gene=gid&mut=A205E" | |
| 953 }, | |
| 954 "rpoB_N438Q-AAC761118CAA": { | |
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| 957 "coverage": { | |
| 958 "alternate": { | |
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| 961 "percent_coverage": 22.73, | |
| 962 "kmer_count": 86 | |
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| 964 "reference": { | |
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| 966 "min_non_zero_depth": 17, | |
| 967 "percent_coverage": 100.0, | |
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| 971 "expected_depths": [ | |
| 972 17.0 | |
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| 975 "conf": 99999996 | |
| 976 }, | |
| 977 "genotype_likelihoods": [ | |
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| 979 -99999999, | |
| 980 -99999999 | |
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| 982 "_cls": "Call.VariantCall", | |
| 983 "genotype": [ | |
| 984 0, | |
| 985 0 | |
| 986 ], | |
| 987 "variant": "ref-N438Q?var_name=AAC761118CAA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438Q" | |
| 988 }, | |
| 989 "rpoB_D435L-GAC761109CTC": { | |
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| 992 "coverage": { | |
| 993 "alternate": { | |
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| 995 "min_non_zero_depth": 18, | |
| 996 "percent_coverage": 4.55, | |
| 997 "kmer_count": 18 | |
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| 999 "reference": { | |
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| 1001 "min_non_zero_depth": 17, | |
| 1002 "percent_coverage": 100.0, | |
| 1003 "kmer_count": 416 | |
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| 1005 }, | |
| 1006 "expected_depths": [ | |
| 1007 17.0 | |
| 1008 ], | |
| 1009 "filter": "PASS", | |
| 1010 "conf": 99999996 | |
| 1011 }, | |
| 1012 "genotype_likelihoods": [ | |
| 1013 -2.79216398346472, | |
| 1014 -99999999, | |
| 1015 -99999999 | |
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| 1017 "_cls": "Call.VariantCall", | |
| 1018 "genotype": [ | |
| 1019 0, | |
| 1020 0 | |
| 1021 ], | |
| 1022 "variant": "ref-D435L?var_name=GAC761109CTC&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435L" | |
| 1023 }, | |
| 1024 "pncA_Q10G-CTG2289212CCC": { | |
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| 1027 "coverage": { | |
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| 1031 "percent_coverage": 0.0, | |
| 1032 "kmer_count": 0 | |
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| 1034 "reference": { | |
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| 1036 "min_non_zero_depth": 14, | |
| 1037 "percent_coverage": 100.0, | |
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| 1040 }, | |
| 1041 "expected_depths": [ | |
| 1042 17.0 | |
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| 1045 "conf": 99999996 | |
| 1046 }, | |
| 1047 "genotype_likelihoods": [ | |
| 1048 -2.6844045563309873, | |
| 1049 -99999999, | |
| 1050 -99999999 | |
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| 1052 "_cls": "Call.VariantCall", | |
| 1053 "genotype": [ | |
| 1054 0, | |
| 1055 0 | |
| 1056 ], | |
| 1057 "variant": "ref-Q10G?var_name=CTG2289212CCC&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10G" | |
| 1058 }, | |
| 1059 "gyrA_H87T-CAC7560ACC": { | |
| 1060 "info": { | |
| 1061 "contamination_depths": [], | |
| 1062 "coverage": { | |
| 1063 "alternate": { | |
| 1064 "median_depth": 0, | |
| 1065 "min_non_zero_depth": 19, | |
| 1066 "percent_coverage": 4.55, | |
| 1067 "kmer_count": 19 | |
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| 1069 "reference": { | |
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| 1071 "min_non_zero_depth": 15, | |
| 1072 "percent_coverage": 100.0, | |
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| 1075 }, | |
| 1076 "expected_depths": [ | |
| 1077 17.0 | |
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| 1081 }, | |
| 1082 "genotype_likelihoods": [ | |
| 1083 -2.6809383483544966, | |
| 1084 -99999999, | |
| 1085 -99999999 | |
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| 1087 "_cls": "Call.VariantCall", | |
| 1088 "genotype": [ | |
| 1089 0, | |
| 1090 0 | |
| 1091 ], | |
| 1092 "variant": "ref-H87T?var_name=CAC7560ACC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87T" | |
| 1093 }, | |
| 1094 "rpoB_G426L-GGC761082CTC": { | |
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| 1097 "coverage": { | |
| 1098 "alternate": { | |
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| 1100 "min_non_zero_depth": 18, | |
| 1101 "percent_coverage": 8.0, | |
| 1102 "kmer_count": 36 | |
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| 1104 "reference": { | |
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| 1106 "min_non_zero_depth": 14, | |
| 1107 "percent_coverage": 92.0, | |
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| 1110 }, | |
| 1111 "expected_depths": [ | |
| 1112 17.0 | |
| 1113 ], | |
| 1114 "filter": "LOW_GT_CONF", | |
| 1115 "conf": 0 | |
| 1116 }, | |
| 1117 "genotype_likelihoods": [ | |
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| 1119 -99999999, | |
| 1120 -99999999 | |
| 1121 ], | |
| 1122 "_cls": "Call.VariantCall", | |
| 1123 "genotype": [ | |
| 1124 0, | |
| 1125 0 | |
| 1126 ], | |
| 1127 "variant": "ref-G426L?var_name=GGC761082CTC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426L" | |
| 1128 }, | |
| 1129 "rpoB_S431R-AGC761097AGA": { | |
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| 1132 "coverage": { | |
| 1133 "alternate": { | |
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| 1136 "percent_coverage": 22.73, | |
| 1137 "kmer_count": 98 | |
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| 1141 "min_non_zero_depth": 17, | |
| 1142 "percent_coverage": 100.0, | |
| 1143 "kmer_count": 411 | |
| 1144 } | |
| 1145 }, | |
| 1146 "expected_depths": [ | |
| 1147 17.0 | |
| 1148 ], | |
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| 1150 "conf": 99999996 | |
| 1151 }, | |
| 1152 "genotype_likelihoods": [ | |
| 1153 -2.79216398346472, | |
| 1154 -99999999, | |
| 1155 -99999999 | |
| 1156 ], | |
| 1157 "_cls": "Call.VariantCall", | |
| 1158 "genotype": [ | |
| 1159 0, | |
| 1160 0 | |
| 1161 ], | |
| 1162 "variant": "ref-S431R?var_name=AGC761097AGA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431R" | |
| 1163 }, | |
| 1164 "rpoB_F425D-TTC761079GAC": { | |
| 1165 "info": { | |
| 1166 "contamination_depths": [], | |
| 1167 "coverage": { | |
| 1168 "alternate": { | |
| 1169 "median_depth": 0, | |
| 1170 "min_non_zero_depth": 16, | |
| 1171 "percent_coverage": 13.64, | |
| 1172 "kmer_count": 48 | |
| 1173 }, | |
| 1174 "reference": { | |
| 1175 "median_depth": 15, | |
| 1176 "min_non_zero_depth": 14, | |
| 1177 "percent_coverage": 100.0, | |
| 1178 "kmer_count": 344 | |
| 1179 } | |
| 1180 }, | |
| 1181 "expected_depths": [ | |
| 1182 17.0 | |
| 1183 ], | |
| 1184 "filter": "PASS", | |
| 1185 "conf": 99999996 | |
| 1186 }, | |
| 1187 "genotype_likelihoods": [ | |
| 1188 -2.6844045563309873, | |
| 1189 -99999999, | |
| 1190 -99999999 | |
| 1191 ], | |
| 1192 "_cls": "Call.VariantCall", | |
| 1193 "genotype": [ | |
| 1194 0, | |
| 1195 0 | |
| 1196 ], | |
| 1197 "variant": "ref-F425D?var_name=TTC761079GAC&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425D" | |
| 1198 }, | |
| 1199 "embB_G406A-GGC4247729GCT": { | |
| 1200 "info": { | |
| 1201 "contamination_depths": [], | |
| 1202 "coverage": { | |
| 1203 "alternate": { | |
| 1204 "median_depth": 0, | |
| 1205 "min_non_zero_depth": 0, | |
| 1206 "percent_coverage": 0.0, | |
| 1207 "kmer_count": 0 | |
| 1208 }, | |
| 1209 "reference": { | |
| 1210 "median_depth": 19, | |
| 1211 "min_non_zero_depth": 17, | |
| 1212 "percent_coverage": 100.0, | |
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| 1806 "min_non_zero_depth": 16, | |
| 1807 "percent_coverage": 100.0, | |
| 1808 "kmer_count": 385 | |
| 1809 } | |
| 1810 }, | |
| 1811 "expected_depths": [ | |
| 1812 17.0 | |
| 1813 ], | |
| 1814 "filter": "PASS", | |
| 1815 "conf": 99999996 | |
| 1816 }, | |
| 1817 "genotype_likelihoods": [ | |
| 1818 -2.6809383483544966, | |
| 1819 -99999999, | |
| 1820 -99999999 | |
| 1821 ], | |
| 1822 "_cls": "Call.VariantCall", | |
| 1823 "genotype": [ | |
| 1824 0, | |
| 1825 0 | |
| 1826 ], | |
| 1827 "variant": "ref-W505S?var_name=CCA2154597AGA&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505S" | |
| 1828 }, | |
| 1829 "rpoB_K446A-AAG761142GCA": { | |
| 1830 "info": { | |
| 1831 "contamination_depths": [], | |
| 1832 "coverage": { | |
| 1833 "alternate": { | |
| 1834 "median_depth": 0, | |
| 1835 "min_non_zero_depth": 0, | |
| 1836 "percent_coverage": 0.0, | |
| 1837 "kmer_count": 0 | |
| 1838 }, | |
| 1839 "reference": { | |
| 1840 "median_depth": 17, | |
| 1841 "min_non_zero_depth": 14, | |
| 1842 "percent_coverage": 100.0, | |
| 1843 "kmer_count": 368 | |
| 1844 } | |
| 1845 }, | |
| 1846 "expected_depths": [ | |
| 1847 17.0 | |
| 1848 ], | |
| 1849 "filter": "PASS", | |
| 1850 "conf": 99999996 | |
| 1851 }, | |
| 1852 "genotype_likelihoods": [ | |
| 1853 -2.6237799345145465, | |
| 1854 -99999999, | |
| 1855 -99999999 | |
| 1856 ], | |
| 1857 "_cls": "Call.VariantCall", | |
| 1858 "genotype": [ | |
| 1859 0, | |
| 1860 0 | |
| 1861 ], | |
| 1862 "variant": "ref-K446A?var_name=AAG761142GCA&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446A" | |
| 1863 }, | |
| 1864 "gyrA_I92Q-ATC7575CAA": { | |
| 1865 "info": { | |
| 1866 "contamination_depths": [], | |
| 1867 "coverage": { | |
| 1868 "alternate": { | |
| 1869 "median_depth": 0, | |
| 1870 "min_non_zero_depth": 0, | |
| 1871 "percent_coverage": 0.0, | |
| 1872 "kmer_count": 0 | |
| 1873 }, | |
| 1874 "reference": { | |
| 1875 "median_depth": 19, | |
| 1876 "min_non_zero_depth": 18, | |
| 1877 "percent_coverage": 100.0, | |
| 1878 "kmer_count": 414 | |
| 1879 } | |
| 1880 }, | |
| 1881 "expected_depths": [ | |
| 1882 17.0 | |
| 1883 ], | |
| 1884 "filter": "PASS", | |
| 1885 "conf": 99999996 | |
| 1886 }, | |
| 1887 "genotype_likelihoods": [ | |
| 1888 -2.79216398346472, | |
| 1889 -99999999, | |
| 1890 -99999999 | |
| 1891 ], | |
| 1892 "_cls": "Call.VariantCall", | |
| 1893 "genotype": [ | |
| 1894 0, | |
| 1895 0 | |
| 1896 ], | |
| 1897 "variant": "ref-I92Q?var_name=ATC7575CAA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92Q" | |
| 1898 }, | |
| 1899 "pncA_Q141F-CTG2288819GAA": { | |
| 1900 "info": { | |
| 1901 "contamination_depths": [], | |
| 1902 "coverage": { | |
| 1903 "alternate": { | |
| 1904 "median_depth": 0, | |
| 1905 "min_non_zero_depth": 0, | |
| 1906 "percent_coverage": 0.0, | |
| 1907 "kmer_count": 0 | |
| 1908 }, | |
| 1909 "reference": { | |
| 1910 "median_depth": 0, | |
| 1911 "min_non_zero_depth": 14, | |
| 1912 "percent_coverage": 4.55, | |
| 1913 "kmer_count": 14 | |
| 1914 } | |
| 1915 }, | |
| 1916 "expected_depths": [ | |
| 1917 17.0 | |
| 1918 ], | |
| 1919 "filter": "LOW_GT_CONF", | |
| 1920 "conf": 0 | |
| 1921 }, | |
| 1922 "genotype_likelihoods": [ | |
| 1923 -99999999, | |
| 1924 -99999999, | |
| 1925 -99999999 | |
| 1926 ], | |
| 1927 "_cls": "Call.VariantCall", | |
| 1928 "genotype": [ | |
| 1929 0, | |
| 1930 0 | |
| 1931 ], | |
| 1932 "variant": "ref-Q141F?var_name=CTG2288819GAA&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141F" | |
| 1933 }, | |
| 1934 "pncA_Q10I-CTG2289212AAT": { | |
| 1935 "info": { | |
| 1936 "contamination_depths": [], | |
| 1937 "coverage": { | |
| 1938 "alternate": { | |
| 1939 "median_depth": 0, | |
| 1940 "min_non_zero_depth": 0, | |
| 1941 "percent_coverage": 0.0, | |
| 1942 "kmer_count": 0 | |
| 1943 }, | |
| 1944 "reference": { | |
| 1945 "median_depth": 15, | |
| 1946 "min_non_zero_depth": 14, | |
| 1947 "percent_coverage": 100.0, | |
| 1948 "kmer_count": 333 | |
| 1949 } | |
| 1950 }, | |
| 1951 "expected_depths": [ | |
| 1952 17.0 | |
| 1953 ], | |
| 1954 "filter": "PASS", | |
| 1955 "conf": 99999996 | |
| 1956 }, | |
| 1957 "genotype_likelihoods": [ | |
| 1958 -2.6844045563309873, | |
| 1959 -99999999, | |
| 1960 -99999999 | |
| 1961 ], | |
| 1962 "_cls": "Call.VariantCall", | |
| 1963 "genotype": [ | |
| 1964 0, | |
| 1965 0 | |
| 1966 ], | |
| 1967 "variant": "ref-Q10I?var_name=CTG2289212AAT&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10I" | |
| 1968 }, | |
| 1969 "embB_M306R-ATG4247429CGC": { | |
| 1970 "info": { | |
| 1971 "contamination_depths": [], | |
| 1972 "coverage": { | |
| 1973 "alternate": { | |
| 1974 "median_depth": 0, | |
| 1975 "min_non_zero_depth": 0, | |
| 1976 "percent_coverage": 0.0, | |
| 1977 "kmer_count": 0 | |
| 1978 }, | |
| 1979 "reference": { | |
| 1980 "median_depth": 14, | |
| 1981 "min_non_zero_depth": 8, | |
| 1982 "percent_coverage": 100.0, | |
| 1983 "kmer_count": 293 | |
| 1984 } | |
| 1985 }, | |
| 1986 "expected_depths": [ | |
| 1987 17.0 | |
| 1988 ], | |
| 1989 "filter": "PASS", | |
| 1990 "conf": 99999996 | |
| 1991 }, | |
| 1992 "genotype_likelihoods": [ | |
| 1993 -2.8095676992849885, | |
| 1994 -99999999, | |
| 1995 -99999999 | |
| 1996 ], | |
| 1997 "_cls": "Call.VariantCall", | |
| 1998 "genotype": [ | |
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| 2000 0 | |
| 2001 ], | |
| 2002 "variant": "ref-M306R?var_name=ATG4247429CGC&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306R" | |
| 2003 }, | |
| 2004 "gyrA_D94L-GAC7581TTG": { | |
| 2005 "info": { | |
| 2006 "contamination_depths": [], | |
| 2007 "coverage": { | |
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| 2010 "min_non_zero_depth": 0, | |
| 2011 "percent_coverage": 0.0, | |
| 2012 "kmer_count": 0 | |
| 2013 }, | |
| 2014 "reference": { | |
| 2015 "median_depth": 19, | |
| 2016 "min_non_zero_depth": 17, | |
| 2017 "percent_coverage": 100.0, | |
| 2018 "kmer_count": 406 | |
| 2019 } | |
| 2020 }, | |
| 2021 "expected_depths": [ | |
| 2022 17.0 | |
| 2023 ], | |
| 2024 "filter": "PASS", | |
| 2025 "conf": 99999996 | |
| 2026 }, | |
| 2027 "genotype_likelihoods": [ | |
| 2028 -2.79216398346472, | |
| 2029 -99999999, | |
| 2030 -99999999 | |
| 2031 ], | |
| 2032 "_cls": "Call.VariantCall", | |
| 2033 "genotype": [ | |
| 2034 0, | |
| 2035 0 | |
| 2036 ], | |
| 2037 "variant": "ref-D94L?var_name=GAC7581TTG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94L" | |
| 2038 }, | |
| 2039 "gid_E173P-CTC4407684AGG": { | |
| 2040 "info": { | |
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| 2047 "kmer_count": 22 | |
| 2048 }, | |
| 2049 "reference": { | |
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| 2052 "percent_coverage": 100.0, | |
| 2053 "kmer_count": 484 | |
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| 2055 }, | |
| 2056 "expected_depths": [ | |
| 2057 17.0 | |
| 2058 ], | |
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| 2060 "conf": 99999996 | |
| 2061 }, | |
| 2062 "genotype_likelihoods": [ | |
| 2063 -3.423821115931803, | |
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| 2067 "_cls": "Call.VariantCall", | |
| 2068 "genotype": [ | |
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| 2070 0 | |
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| 2072 "variant": "ref-E173P?var_name=CTC4407684AGG&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173P" | |
| 2073 }, | |
| 2074 "gyrA_I92C-ATC7575TGT": { | |
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| 2086 "min_non_zero_depth": 18, | |
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| 2090 }, | |
| 2091 "expected_depths": [ | |
| 2092 17.0 | |
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| 2095 "conf": 99999996 | |
| 2096 }, | |
| 2097 "genotype_likelihoods": [ | |
| 2098 -2.79216398346472, | |
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| 2100 -99999999 | |
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| 2102 "_cls": "Call.VariantCall", | |
| 2103 "genotype": [ | |
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| 2105 0 | |
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| 2107 "variant": "ref-I92C?var_name=ATC7575TGT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92C" | |
| 2108 }, | |
| 2109 "pncA_P54L-CGG2289080TAG": { | |
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| 2119 "reference": { | |
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| 2121 "min_non_zero_depth": 13, | |
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| 2125 }, | |
| 2126 "expected_depths": [ | |
| 2127 17.0 | |
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| 2131 }, | |
| 2132 "genotype_likelihoods": [ | |
| 2133 -2.8095676992849885, | |
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| 2137 "_cls": "Call.VariantCall", | |
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| 2140 0 | |
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| 2142 "variant": "ref-P54L?var_name=CGG2289080TAG&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=P54L" | |
| 2143 }, | |
| 2144 "rpoB_R448V-CGA761148GTA": { | |
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| 2154 "reference": { | |
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| 2160 }, | |
| 2161 "expected_depths": [ | |
| 2162 17.0 | |
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| 2166 }, | |
| 2167 "genotype_likelihoods": [ | |
| 2168 -2.62377993451455, | |
| 2169 -99999999, | |
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| 2172 "_cls": "Call.VariantCall", | |
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| 2175 0 | |
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| 2177 "variant": "ref-R448V?var_name=CGA761148GTA&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448V" | |
| 2178 }, | |
| 2179 "rpoB_R447S-CGC761145TCA": { | |
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| 2191 "min_non_zero_depth": 14, | |
| 2192 "percent_coverage": 100.0, | |
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| 2195 }, | |
| 2196 "expected_depths": [ | |
| 2197 17.0 | |
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| 2200 "conf": 99999996 | |
| 2201 }, | |
| 2202 "genotype_likelihoods": [ | |
| 2203 -2.62377993451455, | |
| 2204 -99999999, | |
| 2205 -99999999 | |
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| 2207 "_cls": "Call.VariantCall", | |
| 2208 "genotype": [ | |
| 2209 0, | |
| 2210 0 | |
| 2211 ], | |
| 2212 "variant": "ref-R447S?var_name=CGC761145TCA&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447S" | |
| 2213 }, | |
| 2214 "gyrA_D89W-GAC7566TGG": { | |
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| 2216 "contamination_depths": [], | |
| 2217 "coverage": { | |
| 2218 "alternate": { | |
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| 2224 "reference": { | |
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| 2226 "min_non_zero_depth": 16, | |
| 2227 "percent_coverage": 100.0, | |
| 2228 "kmer_count": 400 | |
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| 2230 }, | |
| 2231 "expected_depths": [ | |
| 2232 17.0 | |
| 2233 ], | |
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| 2235 "conf": 99999996 | |
| 2236 }, | |
| 2237 "genotype_likelihoods": [ | |
| 2238 -2.6809383483544966, | |
| 2239 -99999999, | |
| 2240 -99999999 | |
| 2241 ], | |
| 2242 "_cls": "Call.VariantCall", | |
| 2243 "genotype": [ | |
| 2244 0, | |
| 2245 0 | |
| 2246 ], | |
| 2247 "variant": "ref-D89W?var_name=GAC7566TGG&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89W" | |
| 2248 }, | |
| 2249 "rpoB_L430E-CTG761094GAA": { | |
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| 2251 "contamination_depths": [], | |
| 2252 "coverage": { | |
| 2253 "alternate": { | |
| 2254 "median_depth": 0, | |
| 2255 "min_non_zero_depth": 20, | |
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| 2257 "kmer_count": 100 | |
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| 2259 "reference": { | |
| 2260 "median_depth": 18, | |
| 2261 "min_non_zero_depth": 17, | |
| 2262 "percent_coverage": 100.0, | |
| 2263 "kmer_count": 404 | |
| 2264 } | |
| 2265 }, | |
| 2266 "expected_depths": [ | |
| 2267 17.0 | |
| 2268 ], | |
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| 2271 }, | |
| 2272 "genotype_likelihoods": [ | |
| 2273 -2.6809383483544966, | |
| 2274 -99999999, | |
| 2275 -99999999 | |
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| 2277 "_cls": "Call.VariantCall", | |
| 2278 "genotype": [ | |
| 2279 0, | |
| 2280 0 | |
| 2281 ], | |
| 2282 "variant": "ref-L430E?var_name=CTG761094GAA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430E" | |
| 2283 }, | |
| 2284 "rpoB_Q432T-CAA761100ACA": { | |
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| 2286 "contamination_depths": [], | |
| 2287 "coverage": { | |
| 2288 "alternate": { | |
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| 2292 "kmer_count": 113 | |
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| 2296 "min_non_zero_depth": 17, | |
| 2297 "percent_coverage": 100.0, | |
| 2298 "kmer_count": 417 | |
| 2299 } | |
| 2300 }, | |
| 2301 "expected_depths": [ | |
| 2302 17.0 | |
| 2303 ], | |
| 2304 "filter": "PASS", | |
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| 2306 }, | |
| 2307 "genotype_likelihoods": [ | |
| 2308 -2.79216398346472, | |
| 2309 -99999999, | |
| 2310 -99999999 | |
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| 2312 "_cls": "Call.VariantCall", | |
| 2313 "genotype": [ | |
| 2314 0, | |
| 2315 0 | |
| 2316 ], | |
| 2317 "variant": "ref-Q432T?var_name=CAA761100ACA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432T" | |
| 2318 }, | |
| 2319 "rpoB_N438I-AAC761118ATA": { | |
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| 2321 "contamination_depths": [], | |
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| 2323 "alternate": { | |
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| 2325 "min_non_zero_depth": 17, | |
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| 2327 "kmer_count": 86 | |
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| 2329 "reference": { | |
| 2330 "median_depth": 18, | |
| 2331 "min_non_zero_depth": 17, | |
| 2332 "percent_coverage": 100.0, | |
| 2333 "kmer_count": 399 | |
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| 2335 }, | |
| 2336 "expected_depths": [ | |
| 2337 17.0 | |
| 2338 ], | |
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| 2340 "conf": 99999996 | |
| 2341 }, | |
| 2342 "genotype_likelihoods": [ | |
| 2343 -2.6809383483544966, | |
| 2344 -99999999, | |
| 2345 -99999999 | |
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| 2347 "_cls": "Call.VariantCall", | |
| 2348 "genotype": [ | |
| 2349 0, | |
| 2350 0 | |
| 2351 ], | |
| 2352 "variant": "ref-N438I?var_name=AAC761118ATA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438I" | |
| 2353 }, | |
| 2354 "embB_M306V-ATG4247429GTT": { | |
| 2355 "info": { | |
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| 2358 "alternate": { | |
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| 2362 "kmer_count": 0 | |
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| 2364 "reference": { | |
| 2365 "median_depth": 14, | |
| 2366 "min_non_zero_depth": 8, | |
| 2367 "percent_coverage": 100.0, | |
| 2368 "kmer_count": 293 | |
| 2369 } | |
| 2370 }, | |
| 2371 "expected_depths": [ | |
| 2372 17.0 | |
| 2373 ], | |
| 2374 "filter": "PASS", | |
| 2375 "conf": 99999996 | |
| 2376 }, | |
| 2377 "genotype_likelihoods": [ | |
| 2378 -2.8095676992849885, | |
| 2379 -99999999, | |
| 2380 -99999999 | |
| 2381 ], | |
| 2382 "_cls": "Call.VariantCall", | |
| 2383 "genotype": [ | |
| 2384 0, | |
| 2385 0 | |
| 2386 ], | |
| 2387 "variant": "ref-M306V?var_name=ATG4247429GTT&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306V" | |
| 2388 }, | |
| 2389 "rpoB_Q432P-CAA761100CCA": { | |
| 2390 "info": { | |
| 2391 "contamination_depths": [], | |
| 2392 "coverage": { | |
| 2393 "alternate": { | |
| 2394 "median_depth": 0, | |
| 2395 "min_non_zero_depth": 17, | |
| 2396 "percent_coverage": 27.27, | |
| 2397 "kmer_count": 113 | |
| 2398 }, | |
| 2399 "reference": { | |
| 2400 "median_depth": 19, | |
| 2401 "min_non_zero_depth": 17, | |
| 2402 "percent_coverage": 100.0, | |
| 2403 "kmer_count": 417 | |
| 2404 } | |
| 2405 }, | |
| 2406 "expected_depths": [ | |
| 2407 17.0 | |
| 2408 ], | |
| 2409 "filter": "PASS", | |
| 2410 "conf": 99999996 | |
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| 2948 }, | |
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| 3006 }, | |
| 3007 "genotype_likelihoods": [ | |
| 3008 -2.6809383483544966, | |
| 3009 -99999999, | |
| 3010 -99999999 | |
| 3011 ], | |
| 3012 "_cls": "Call.VariantCall", | |
| 3013 "genotype": [ | |
| 3014 0, | |
| 3015 0 | |
| 3016 ], | |
| 3017 "variant": "ref-L430R?var_name=CTG761094CGT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430R" | |
| 3018 }, | |
| 3019 "embB_G406S-GGC4247729TCA": { | |
| 3020 "info": { | |
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| 3024 "median_depth": 0, | |
| 3025 "min_non_zero_depth": 0, | |
| 3026 "percent_coverage": 0.0, | |
| 3027 "kmer_count": 0 | |
| 3028 }, | |
| 3029 "reference": { | |
| 3030 "median_depth": 19, | |
| 3031 "min_non_zero_depth": 17, | |
| 3032 "percent_coverage": 100.0, | |
| 3033 "kmer_count": 408 | |
| 3034 } | |
| 3035 }, | |
| 3036 "expected_depths": [ | |
| 3037 17.0 | |
| 3038 ], | |
| 3039 "filter": "PASS", | |
| 3040 "conf": 99999996 | |
| 3041 }, | |
| 3042 "genotype_likelihoods": [ | |
| 3043 -2.79216398346472, | |
| 3044 -99999999, | |
| 3045 -99999999 | |
| 3046 ], | |
| 3047 "_cls": "Call.VariantCall", | |
| 3048 "genotype": [ | |
| 3049 0, | |
| 3050 0 | |
| 3051 ], | |
| 3052 "variant": "ref-G406S?var_name=GGC4247729TCA&num_alts=2&ref=NC_000962.3&enum=0&gene=embB&mut=G406S" | |
| 3053 }, | |
| 3054 "rpoB_T427A-ACC761085GCT": { | |
| 3055 "info": { | |
| 3056 "contamination_depths": [], | |
| 3057 "coverage": { | |
| 3058 "alternate": { | |
| 3059 "median_depth": 0, | |
| 3060 "min_non_zero_depth": 0, | |
| 3061 "percent_coverage": 0.0, | |
| 3062 "kmer_count": 0 | |
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| 3064 "reference": { | |
| 3065 "median_depth": 17, | |
| 3066 "min_non_zero_depth": 14, | |
| 3067 "percent_coverage": 100.0, | |
| 3068 "kmer_count": 367 | |
| 3069 } | |
| 3070 }, | |
| 3071 "expected_depths": [ | |
| 3072 17.0 | |
| 3073 ], | |
| 3074 "filter": "PASS", | |
| 3075 "conf": 99999996 | |
| 3076 }, | |
| 3077 "genotype_likelihoods": [ | |
| 3078 -2.6237799345145465, | |
| 3079 -99999999, | |
| 3080 -99999999 | |
| 3081 ], | |
| 3082 "_cls": "Call.VariantCall", | |
| 3083 "genotype": [ | |
| 3084 0, | |
| 3085 0 | |
| 3086 ], | |
| 3087 "variant": "ref-T427A?var_name=ACC761085GCT&num_alts=32&ref=NC_000962.3&enum=0&gene=rpoB&mut=T427A" | |
| 3088 }, | |
| 3089 "rpoB_M434G-ATG761106GGT": { | |
| 3090 "info": { | |
| 3091 "contamination_depths": [], | |
| 3092 "coverage": { | |
| 3093 "alternate": { | |
| 3094 "median_depth": 0, | |
| 3095 "min_non_zero_depth": 0, | |
| 3096 "percent_coverage": 0.0, | |
| 3097 "kmer_count": 0 | |
| 3098 }, | |
| 3099 "reference": { | |
| 3100 "median_depth": 19, | |
| 3101 "min_non_zero_depth": 17, | |
| 3102 "percent_coverage": 100.0, | |
| 3103 "kmer_count": 420 | |
| 3104 } | |
| 3105 }, | |
| 3106 "expected_depths": [ | |
| 3107 17.0 | |
| 3108 ], | |
| 3109 "filter": "PASS", | |
| 3110 "conf": 99999996 | |
| 3111 }, | |
| 3112 "genotype_likelihoods": [ | |
| 3113 -2.79216398346472, | |
| 3114 -99999999, | |
| 3115 -99999999 | |
| 3116 ], | |
| 3117 "_cls": "Call.VariantCall", | |
| 3118 "genotype": [ | |
| 3119 0, | |
| 3120 0 | |
| 3121 ], | |
| 3122 "variant": "ref-M434G?var_name=ATG761106GGT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434G" | |
| 3123 }, | |
| 3124 "pncA_Q141L-CTG2288819TAG": { | |
| 3125 "info": { | |
| 3126 "contamination_depths": [], | |
| 3127 "coverage": { | |
| 3128 "alternate": { | |
| 3129 "median_depth": 0, | |
| 3130 "min_non_zero_depth": 14, | |
| 3131 "percent_coverage": 4.55, | |
| 3132 "kmer_count": 14 | |
| 3133 }, | |
| 3134 "reference": { | |
| 3135 "median_depth": 0, | |
| 3136 "min_non_zero_depth": 14, | |
| 3137 "percent_coverage": 4.55, | |
| 3138 "kmer_count": 14 | |
| 3139 } | |
| 3140 }, | |
| 3141 "expected_depths": [ | |
| 3142 17.0 | |
| 3143 ], | |
| 3144 "filter": "LOW_GT_CONF", | |
| 3145 "conf": 0 | |
| 3146 }, | |
| 3147 "genotype_likelihoods": [ | |
| 3148 -99999999, | |
| 3149 -99999999, | |
| 3150 -99999999 | |
| 3151 ], | |
| 3152 "_cls": "Call.VariantCall", | |
| 3153 "genotype": [ | |
| 3154 0, | |
| 3155 0 | |
| 3156 ], | |
| 3157 "variant": "ref-Q141L?var_name=CTG2288819TAG&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141L" | |
| 3158 }, | |
| 3159 "rpoB_F425P-TTC761079CCT": { | |
| 3160 "info": { | |
| 3161 "contamination_depths": [], | |
| 3162 "coverage": { | |
| 3163 "alternate": { | |
| 3164 "median_depth": 0, | |
| 3165 "min_non_zero_depth": 16, | |
| 3166 "percent_coverage": 13.64, | |
| 3167 "kmer_count": 48 | |
| 3168 }, | |
| 3169 "reference": { | |
| 3170 "median_depth": 15, | |
| 3171 "min_non_zero_depth": 14, | |
| 3172 "percent_coverage": 100.0, | |
| 3173 "kmer_count": 344 | |
| 3174 } | |
| 3175 }, | |
| 3176 "expected_depths": [ | |
| 3177 17.0 | |
| 3178 ], | |
| 3179 "filter": "PASS", | |
| 3180 "conf": 99999996 | |
| 3181 }, | |
| 3182 "genotype_likelihoods": [ | |
| 3183 -2.6844045563309873, | |
| 3184 -99999999, | |
| 3185 -99999999 | |
| 3186 ], | |
| 3187 "_cls": "Call.VariantCall", | |
| 3188 "genotype": [ | |
| 3189 0, | |
| 3190 0 | |
| 3191 ], | |
| 3192 "variant": "ref-F425P?var_name=TTC761079CCT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425P" | |
| 3193 }, | |
| 3194 "rpoB_K446E-AAG761142GAA": { | |
| 3195 "info": { | |
| 3196 "contamination_depths": [], | |
| 3197 "coverage": { | |
| 3198 "alternate": { | |
| 3199 "median_depth": 0, | |
| 3200 "min_non_zero_depth": 0, | |
| 3201 "percent_coverage": 0.0, | |
| 3202 "kmer_count": 0 | |
| 3203 }, | |
| 3204 "reference": { | |
| 3205 "median_depth": 17, | |
| 3206 "min_non_zero_depth": 14, | |
| 3207 "percent_coverage": 100.0, | |
| 3208 "kmer_count": 368 | |
| 3209 } | |
| 3210 }, | |
| 3211 "expected_depths": [ | |
| 3212 17.0 | |
| 3213 ], | |
| 3214 "filter": "PASS", | |
| 3215 "conf": 99999996 | |
| 3216 }, | |
| 3217 "genotype_likelihoods": [ | |
| 3218 -2.6237799345145465, | |
| 3219 -99999999, | |
| 3220 -99999999 | |
| 3221 ], | |
| 3222 "_cls": "Call.VariantCall", | |
| 3223 "genotype": [ | |
| 3224 0, | |
| 3225 0 | |
| 3226 ], | |
| 3227 "variant": "ref-K446E?var_name=AAG761142GAA&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446E" | |
| 3228 }, | |
| 3229 "pncA_Q141E-CTG2288819CTC": { | |
| 3230 "info": { | |
| 3231 "contamination_depths": [], | |
| 3232 "coverage": { | |
| 3233 "alternate": { | |
| 3234 "median_depth": 0, | |
| 3235 "min_non_zero_depth": 0, | |
| 3236 "percent_coverage": 0.0, | |
| 3237 "kmer_count": 0 | |
| 3238 }, | |
| 3239 "reference": { | |
| 3240 "median_depth": 0, | |
| 3241 "min_non_zero_depth": 14, | |
| 3242 "percent_coverage": 4.55, | |
| 3243 "kmer_count": 14 | |
| 3244 } | |
| 3245 }, | |
| 3246 "expected_depths": [ | |
| 3247 17.0 | |
| 3248 ], | |
| 3249 "filter": "LOW_GT_CONF", | |
| 3250 "conf": 0 | |
| 3251 }, | |
| 3252 "genotype_likelihoods": [ | |
| 3253 -99999999, | |
| 3254 -99999999, | |
| 3255 -99999999 | |
| 3256 ], | |
| 3257 "_cls": "Call.VariantCall", | |
| 3258 "genotype": [ | |
| 3259 0, | |
| 3260 0 | |
| 3261 ], | |
| 3262 "variant": "ref-Q141E?var_name=CTG2288819CTC&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141E" | |
| 3263 }, | |
| 3264 "rpoB_K446A-AAG761142GCG": { | |
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| 3266 "contamination_depths": [], | |
| 3267 "coverage": { | |
| 3268 "alternate": { | |
| 3269 "median_depth": 0, | |
| 3270 "min_non_zero_depth": 14, | |
| 3271 "percent_coverage": 4.55, | |
| 3272 "kmer_count": 14 | |
| 3273 }, | |
| 3274 "reference": { | |
| 3275 "median_depth": 17, | |
| 3276 "min_non_zero_depth": 14, | |
| 3277 "percent_coverage": 100.0, | |
| 3278 "kmer_count": 368 | |
| 3279 } | |
| 3280 }, | |
| 3281 "expected_depths": [ | |
| 3282 17.0 | |
| 3283 ], | |
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| 3285 "conf": 99999996 | |
| 3286 }, | |
| 3287 "genotype_likelihoods": [ | |
| 3288 -2.6237799345145465, | |
| 3289 -99999999, | |
| 3290 -99999999 | |
| 3291 ], | |
| 3292 "_cls": "Call.VariantCall", | |
| 3293 "genotype": [ | |
| 3294 0, | |
| 3295 0 | |
| 3296 ], | |
| 3297 "variant": "ref-K446A?var_name=AAG761142GCG&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446A" | |
| 3298 }, | |
| 3299 "katG_S315R-GCT2155167ACG": { | |
| 3300 "info": { | |
| 3301 "contamination_depths": [], | |
| 3302 "coverage": { | |
| 3303 "alternate": { | |
| 3304 "median_depth": 0, | |
| 3305 "min_non_zero_depth": 0, | |
| 3306 "percent_coverage": 0.0, | |
| 3307 "kmer_count": 0 | |
| 3308 }, | |
| 3309 "reference": { | |
| 3310 "median_depth": 0, | |
| 3311 "min_non_zero_depth": 17, | |
| 3312 "percent_coverage": 4.55, | |
| 3313 "kmer_count": 17 | |
| 3314 } | |
| 3315 }, | |
| 3316 "expected_depths": [ | |
| 3317 17.0 | |
| 3318 ], | |
| 3319 "filter": "LOW_GT_CONF", | |
| 3320 "conf": 0 | |
| 3321 }, | |
| 3322 "genotype_likelihoods": [ | |
| 3323 -99999999, | |
| 3324 -99999999, | |
| 3325 -99999999 | |
| 3326 ], | |
| 3327 "_cls": "Call.VariantCall", | |
| 3328 "genotype": [ | |
| 3329 0, | |
| 3330 0 | |
| 3331 ], | |
| 3332 "variant": "ref-S315R?var_name=GCT2155167ACG&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315R" | |
| 3333 }, | |
| 3334 "gid_S136K-TGA4407795CTT": { | |
| 3335 "info": { | |
| 3336 "contamination_depths": [], | |
| 3337 "coverage": { | |
| 3338 "alternate": { | |
| 3339 "median_depth": 0, | |
| 3340 "min_non_zero_depth": 0, | |
| 3341 "percent_coverage": 0.0, | |
| 3342 "kmer_count": 0 | |
| 3343 }, | |
| 3344 "reference": { | |
| 3345 "median_depth": 15, | |
| 3346 "min_non_zero_depth": 14, | |
| 3347 "percent_coverage": 100.0, | |
| 3348 "kmer_count": 327 | |
| 3349 } | |
| 3350 }, | |
| 3351 "expected_depths": [ | |
| 3352 17.0 | |
| 3353 ], | |
| 3354 "filter": "PASS", | |
| 3355 "conf": 99999996 | |
| 3356 }, | |
| 3357 "genotype_likelihoods": [ | |
| 3358 -2.6844045563309873, | |
| 3359 -99999999, | |
| 3360 -99999999 | |
| 3361 ], | |
| 3362 "_cls": "Call.VariantCall", | |
| 3363 "genotype": [ | |
| 3364 0, | |
| 3365 0 | |
| 3366 ], | |
| 3367 "variant": "ref-S136K?var_name=TGA4407795CTT&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136K" | |
| 3368 }, | |
| 3369 "pncA_Q10R-CTG2289212TCG": { | |
| 3370 "info": { | |
| 3371 "contamination_depths": [], | |
| 3372 "coverage": { | |
| 3373 "alternate": { | |
| 3374 "median_depth": 0, | |
| 3375 "min_non_zero_depth": 16, | |
| 3376 "percent_coverage": 4.55, | |
| 3377 "kmer_count": 16 | |
| 3378 }, | |
| 3379 "reference": { | |
| 3380 "median_depth": 15, | |
| 3381 "min_non_zero_depth": 14, | |
| 3382 "percent_coverage": 100.0, | |
| 3383 "kmer_count": 333 | |
| 3384 } | |
| 3385 }, | |
| 3386 "expected_depths": [ | |
| 3387 17.0 | |
| 3388 ], | |
| 3389 "filter": "PASS", | |
| 3390 "conf": 99999996 | |
| 3391 }, | |
| 3392 "genotype_likelihoods": [ | |
| 3393 -2.6844045563309873, | |
| 3394 -99999999, | |
| 3395 -99999999 | |
| 3396 ], | |
| 3397 "_cls": "Call.VariantCall", | |
| 3398 "genotype": [ | |
| 3399 0, | |
| 3400 0 | |
| 3401 ], | |
| 3402 "variant": "ref-Q10R?var_name=CTG2289212TCG&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10R" | |
| 3403 }, | |
| 3404 "rpsL_K43R-AAG781686CGG": { | |
| 3405 "info": { | |
| 3406 "contamination_depths": [], | |
| 3407 "coverage": { | |
| 3408 "alternate": { | |
| 3409 "median_depth": 0, | |
| 3410 "min_non_zero_depth": 24, | |
| 3411 "percent_coverage": 9.09, | |
| 3412 "kmer_count": 48 | |
| 3413 }, | |
| 3414 "reference": { | |
| 3415 "median_depth": 0, | |
| 3416 "min_non_zero_depth": 24, | |
| 3417 "percent_coverage": 4.55, | |
| 3418 "kmer_count": 24 | |
| 3419 } | |
| 3420 }, | |
| 3421 "expected_depths": [ | |
| 3422 17.0 | |
| 3423 ], | |
| 3424 "filter": "LOW_GT_CONF", | |
| 3425 "conf": 0 | |
| 3426 }, | |
| 3427 "genotype_likelihoods": [ | |
| 3428 -99999999, | |
| 3429 -99999999, | |
| 3430 -99999999 | |
| 3431 ], | |
| 3432 "_cls": "Call.VariantCall", | |
| 3433 "genotype": [ | |
| 3434 0, | |
| 3435 0 | |
| 3436 ], | |
| 3437 "variant": "ref-K43R?var_name=AAG781686CGG&num_alts=6&ref=NC_000962.3&enum=0&gene=rpsL&mut=K43R" | |
| 3438 }, | |
| 3439 "rpoB_S441K-TCG761127AAG": { | |
| 3440 "info": { | |
| 3441 "contamination_depths": [], | |
| 3442 "coverage": { | |
| 3443 "alternate": { | |
| 3444 "median_depth": 0, | |
| 3445 "min_non_zero_depth": 18, | |
| 3446 "percent_coverage": 4.55, | |
| 3447 "kmer_count": 18 | |
| 3448 }, | |
| 3449 "reference": { | |
| 3450 "median_depth": 17, | |
| 3451 "min_non_zero_depth": 17, | |
| 3452 "percent_coverage": 100.0, | |
| 3453 "kmer_count": 384 | |
| 3454 } | |
| 3455 }, | |
| 3456 "expected_depths": [ | |
| 3457 17.0 | |
| 3458 ], | |
| 3459 "filter": "PASS", | |
| 3460 "conf": 99999996 | |
| 3461 }, | |
| 3462 "genotype_likelihoods": [ | |
| 3463 -2.6237799345145465, | |
| 3464 -99999999, | |
| 3465 -99999999 | |
| 3466 ], | |
| 3467 "_cls": "Call.VariantCall", | |
| 3468 "genotype": [ | |
| 3469 0, | |
| 3470 0 | |
| 3471 ], | |
| 3472 "variant": "ref-S441K?var_name=TCG761127AAG&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441K" | |
| 3473 }, | |
| 3474 "rpoB_Q429K-CAG761091AAA": { | |
| 3475 "info": { | |
| 3476 "contamination_depths": [], | |
| 3477 "coverage": { | |
| 3478 "alternate": { | |
| 3479 "median_depth": 0, | |
| 3480 "min_non_zero_depth": 14, | |
| 3481 "percent_coverage": 13.64, | |
| 3482 "kmer_count": 43 | |
| 3483 }, | |
| 3484 "reference": { | |
| 3485 "median_depth": 18, | |
| 3486 "min_non_zero_depth": 15, | |
| 3487 "percent_coverage": 100.0, | |
| 3488 "kmer_count": 395 | |
| 3489 } | |
| 3490 }, | |
| 3491 "expected_depths": [ | |
| 3492 17.0 | |
| 3493 ], | |
| 3494 "filter": "PASS", | |
| 3495 "conf": 99999996 | |
| 3496 }, | |
| 3497 "genotype_likelihoods": [ | |
| 3498 -2.6809383483544966, | |
| 3499 -99999999, | |
| 3500 -99999999 | |
| 3501 ], | |
| 3502 "_cls": "Call.VariantCall", | |
| 3503 "genotype": [ | |
| 3504 0, | |
| 3505 0 | |
| 3506 ], | |
| 3507 "variant": "ref-Q429K?var_name=CAG761091AAA&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429K" | |
| 3508 }, | |
| 3509 "rpoB_G442D-GGG761130GAT": { | |
| 3510 "info": { | |
| 3511 "contamination_depths": [], | |
| 3512 "coverage": { | |
| 3513 "alternate": { | |
| 3514 "median_depth": 0, | |
| 3515 "min_non_zero_depth": 17, | |
| 3516 "percent_coverage": 4.55, | |
| 3517 "kmer_count": 17 | |
| 3518 }, | |
| 3519 "reference": { | |
| 3520 "median_depth": 18, | |
| 3521 "min_non_zero_depth": 17, | |
| 3522 "percent_coverage": 100.0, | |
| 3523 "kmer_count": 387 | |
| 3524 } | |
| 3525 }, | |
| 3526 "expected_depths": [ | |
| 3527 17.0 | |
| 3528 ], | |
| 3529 "filter": "PASS", | |
| 3530 "conf": 99999996 | |
| 3531 }, | |
| 3532 "genotype_likelihoods": [ | |
| 3533 -2.6809383483544966, | |
| 3534 -99999999, | |
| 3535 -99999999 | |
| 3536 ], | |
| 3537 "_cls": "Call.VariantCall", | |
| 3538 "genotype": [ | |
| 3539 0, | |
| 3540 0 | |
| 3541 ], | |
| 3542 "variant": "ref-G442D?var_name=GGG761130GAT&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442D" | |
| 3543 }, | |
| 3544 "gid_G73A-CCC4407984TGC": { | |
| 3545 "info": { | |
| 3546 "contamination_depths": [], | |
| 3547 "coverage": { | |
| 3548 "alternate": { | |
| 3549 "median_depth": 0, | |
| 3550 "min_non_zero_depth": 17, | |
| 3551 "percent_coverage": 4.55, | |
| 3552 "kmer_count": 17 | |
| 3553 }, | |
| 3554 "reference": { | |
| 3555 "median_depth": 18, | |
| 3556 "min_non_zero_depth": 17, | |
| 3557 "percent_coverage": 100.0, | |
| 3558 "kmer_count": 412 | |
| 3559 } | |
| 3560 }, | |
| 3561 "expected_depths": [ | |
| 3562 17.0 | |
| 3563 ], | |
| 3564 "filter": "PASS", | |
| 3565 "conf": 99999996 | |
| 3566 }, | |
| 3567 "genotype_likelihoods": [ | |
| 3568 -2.6809383483544966, | |
| 3569 -99999999, | |
| 3570 -99999999 | |
| 3571 ], | |
| 3572 "_cls": "Call.VariantCall", | |
| 3573 "genotype": [ | |
| 3574 0, | |
| 3575 0 | |
| 3576 ], | |
| 3577 "variant": "ref-G73A?var_name=CCC4407984TGC&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=G73A" | |
| 3578 }, | |
| 3579 "rpoB_Q432G-CAA761100GGC": { | |
| 3580 "info": { | |
| 3581 "contamination_depths": [], | |
| 3582 "coverage": { | |
| 3583 "alternate": { | |
| 3584 "median_depth": 0, | |
| 3585 "min_non_zero_depth": 17, | |
| 3586 "percent_coverage": 22.73, | |
| 3587 "kmer_count": 93 | |
| 3588 }, | |
| 3589 "reference": { | |
| 3590 "median_depth": 19, | |
| 3591 "min_non_zero_depth": 17, | |
| 3592 "percent_coverage": 100.0, | |
| 3593 "kmer_count": 417 | |
| 3594 } | |
| 3595 }, | |
| 3596 "expected_depths": [ | |
| 3597 17.0 | |
| 3598 ], | |
| 3599 "filter": "PASS", | |
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| 3601 }, | |
| 3602 "genotype_likelihoods": [ | |
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| 3604 -99999999, | |
| 3605 -99999999 | |
| 3606 ], | |
| 3607 "_cls": "Call.VariantCall", | |
| 3608 "genotype": [ | |
| 3609 0, | |
| 3610 0 | |
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| 3613 }, | |
| 3614 "embB_Q497R-CAG4248002AGG": { | |
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| 3622 "kmer_count": 19 | |
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| 3625 "median_depth": 20, | |
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| 3627 "percent_coverage": 100.0, | |
| 3628 "kmer_count": 441 | |
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| 3630 }, | |
| 3631 "expected_depths": [ | |
| 3632 17.0 | |
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| 3635 "conf": 99999996 | |
| 3636 }, | |
| 3637 "genotype_likelihoods": [ | |
| 3638 -2.9546829129624985, | |
| 3639 -99999999, | |
| 3640 -99999999 | |
| 3641 ], | |
| 3642 "_cls": "Call.VariantCall", | |
| 3643 "genotype": [ | |
| 3644 0, | |
| 3645 0 | |
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| 3647 "variant": "ref-Q497R?var_name=CAG4248002AGG&num_alts=3&ref=NC_000962.3&enum=0&gene=embB&mut=Q497R" | |
| 3648 }, | |
| 3649 "pncA_C14R-GCA2289200CCT": { | |
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| 3661 "min_non_zero_depth": 14, | |
| 3662 "percent_coverage": 100.0, | |
| 3663 "kmer_count": 337 | |
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| 3665 }, | |
| 3666 "expected_depths": [ | |
| 3667 17.0 | |
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| 3671 }, | |
| 3672 "genotype_likelihoods": [ | |
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| 3674 -99999999, | |
| 3675 -99999999 | |
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| 3677 "_cls": "Call.VariantCall", | |
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| 3679 0, | |
| 3680 0 | |
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| 3682 "variant": "ref-C14R?var_name=GCA2289200CCT&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=C14R" | |
| 3683 }, | |
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| 3696 "min_non_zero_depth": 18, | |
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| 3700 }, | |
| 3701 "expected_depths": [ | |
| 3702 17.0 | |
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| 3705 "conf": 99999996 | |
| 3706 }, | |
| 3707 "genotype_likelihoods": [ | |
| 3708 -2.9546829129624985, | |
| 3709 -99999999, | |
| 3710 -99999999 | |
| 3711 ], | |
| 3712 "_cls": "Call.VariantCall", | |
| 3713 "genotype": [ | |
| 3714 0, | |
| 3715 0 | |
| 3716 ], | |
| 3717 "variant": "ref-P75R?var_name=CGG4407978CCG&num_alts=29&ref=NC_000962.3&enum=0&gene=gid&mut=P75R" | |
| 3718 }, | |
| 3719 "rpoB_L430Q-CTG761094CAA": { | |
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| 3725 "min_non_zero_depth": 20, | |
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| 3727 "kmer_count": 100 | |
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| 3729 "reference": { | |
| 3730 "median_depth": 18, | |
| 3731 "min_non_zero_depth": 17, | |
| 3732 "percent_coverage": 100.0, | |
| 3733 "kmer_count": 404 | |
| 3734 } | |
| 3735 }, | |
| 3736 "expected_depths": [ | |
| 3737 17.0 | |
| 3738 ], | |
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| 3740 "conf": 99999996 | |
| 3741 }, | |
| 3742 "genotype_likelihoods": [ | |
| 3743 -2.6809383483544966, | |
| 3744 -99999999, | |
| 3745 -99999999 | |
| 3746 ], | |
| 3747 "_cls": "Call.VariantCall", | |
| 3748 "genotype": [ | |
| 3749 0, | |
| 3750 0 | |
| 3751 ], | |
| 3752 "variant": "ref-L430Q?var_name=CTG761094CAA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430Q" | |
| 3753 }, | |
| 3754 "gyrA_G88Q-GGC7563CAG": { | |
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| 3770 }, | |
| 3771 "expected_depths": [ | |
| 3772 17.0 | |
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| 3774 "filter": "LOW_GT_CONF", | |
| 3775 "conf": 0 | |
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| 3777 "genotype_likelihoods": [ | |
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| 3779 -99999999, | |
| 3780 -99999999 | |
| 3781 ], | |
| 3782 "_cls": "Call.VariantCall", | |
| 3783 "genotype": [ | |
| 3784 0, | |
| 3785 0 | |
| 3786 ], | |
| 3787 "variant": "ref-G88Q?var_name=GGC7563CAG&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88Q" | |
| 3788 }, | |
| 3789 "rpoB_Q432S-CAA761100TCA": { | |
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| 3797 "kmer_count": 113 | |
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| 3801 "min_non_zero_depth": 17, | |
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| 3803 "kmer_count": 417 | |
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| 3805 }, | |
| 3806 "expected_depths": [ | |
| 3807 17.0 | |
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| 3810 "conf": 99999996 | |
| 3811 }, | |
| 3812 "genotype_likelihoods": [ | |
| 3813 -2.79216398346472, | |
| 3814 -99999999, | |
| 3815 -99999999 | |
| 3816 ], | |
| 3817 "_cls": "Call.VariantCall", | |
| 3818 "genotype": [ | |
| 3819 0, | |
| 3820 0 | |
| 3821 ], | |
| 3822 "variant": "ref-Q432S?var_name=CAA761100TCA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432S" | |
| 3823 }, | |
| 3824 "rpoB_N437W-AAC761115TGG": { | |
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| 3827 "coverage": { | |
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| 3832 "kmer_count": 85 | |
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| 3834 "reference": { | |
| 3835 "median_depth": 18, | |
| 3836 "min_non_zero_depth": 17, | |
| 3837 "percent_coverage": 100.0, | |
| 3838 "kmer_count": 408 | |
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| 3840 }, | |
| 3841 "expected_depths": [ | |
| 3842 17.0 | |
| 3843 ], | |
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| 3845 "conf": 99999996 | |
| 3846 }, | |
| 3847 "genotype_likelihoods": [ | |
| 3848 -2.6809383483544966, | |
| 3849 -99999999, | |
| 3850 -99999999 | |
| 3851 ], | |
| 3852 "_cls": "Call.VariantCall", | |
| 3853 "genotype": [ | |
| 3854 0, | |
| 3855 0 | |
| 3856 ], | |
| 3857 "variant": "ref-N437W?var_name=AAC761115TGG&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437W" | |
| 3858 }, | |
| 3859 "rpoB_F433V-TTC761103GTT": { | |
| 3860 "info": { | |
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| 3864 "median_depth": 0, | |
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| 3867 "kmer_count": 87 | |
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| 3870 "median_depth": 19, | |
| 3871 "min_non_zero_depth": 18, | |
| 3872 "percent_coverage": 100.0, | |
| 3873 "kmer_count": 421 | |
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| 3875 }, | |
| 3876 "expected_depths": [ | |
| 3877 17.0 | |
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| 3880 "conf": 99999996 | |
| 3881 }, | |
| 3882 "genotype_likelihoods": [ | |
| 3883 -2.79216398346472, | |
| 3884 -99999999, | |
| 3885 -99999999 | |
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| 3887 "_cls": "Call.VariantCall", | |
| 3888 "genotype": [ | |
| 3889 0, | |
| 3890 0 | |
| 3891 ], | |
| 3892 "variant": "ref-F433V?var_name=TTC761103GTT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=F433V" | |
| 3893 }, | |
| 3894 "gyrA_D89P-GAC7566CCT": { | |
| 3895 "info": { | |
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| 3897 "coverage": { | |
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| 3899 "median_depth": 0, | |
| 3900 "min_non_zero_depth": 0, | |
| 3901 "percent_coverage": 0.0, | |
| 3902 "kmer_count": 0 | |
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| 3904 "reference": { | |
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| 3906 "min_non_zero_depth": 16, | |
| 3907 "percent_coverage": 100.0, | |
| 3908 "kmer_count": 400 | |
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| 3910 }, | |
| 3911 "expected_depths": [ | |
| 3912 17.0 | |
| 3913 ], | |
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| 3915 "conf": 99999996 | |
| 3916 }, | |
| 3917 "genotype_likelihoods": [ | |
| 3918 -2.6809383483544966, | |
| 3919 -99999999, | |
| 3920 -99999999 | |
| 3921 ], | |
| 3922 "_cls": "Call.VariantCall", | |
| 3923 "genotype": [ | |
| 3924 0, | |
| 3925 0 | |
| 3926 ], | |
| 3927 "variant": "ref-D89P?var_name=GAC7566CCT&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89P" | |
| 3928 }, | |
| 3929 "gyrA_A90C-GCG7569TGT": { | |
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| 3932 "coverage": { | |
| 3933 "alternate": { | |
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| 3937 "kmer_count": 0 | |
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| 3941 "min_non_zero_depth": 18, | |
| 3942 "percent_coverage": 100.0, | |
| 3943 "kmer_count": 410 | |
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| 3945 }, | |
| 3946 "expected_depths": [ | |
| 3947 17.0 | |
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| 3950 "conf": 99999996 | |
| 3951 }, | |
| 3952 "genotype_likelihoods": [ | |
| 3953 -2.79216398346472, | |
| 3954 -99999999, | |
| 3955 -99999999 | |
| 3956 ], | |
| 3957 "_cls": "Call.VariantCall", | |
| 3958 "genotype": [ | |
| 3959 0, | |
| 3960 0 | |
| 3961 ], | |
| 3962 "variant": "ref-A90C?var_name=GCG7569TGT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90C" | |
| 3963 }, | |
| 3964 "gyrA_A90S-GCG7569AGC": { | |
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| 3967 "coverage": { | |
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| 3974 "reference": { | |
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| 3976 "min_non_zero_depth": 18, | |
| 3977 "percent_coverage": 100.0, | |
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| 3980 }, | |
| 3981 "expected_depths": [ | |
| 3982 17.0 | |
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| 3985 "conf": 99999996 | |
| 3986 }, | |
| 3987 "genotype_likelihoods": [ | |
| 3988 -2.79216398346472, | |
| 3989 -99999999, | |
| 3990 -99999999 | |
| 3991 ], | |
| 3992 "_cls": "Call.VariantCall", | |
| 3993 "genotype": [ | |
| 3994 0, | |
| 3995 0 | |
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| 3997 "variant": "ref-A90S?var_name=GCG7569AGC&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90S" | |
| 3998 }, | |
| 3999 "rpoB_L443G-TTG761133GGC": { | |
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| 4002 "coverage": { | |
| 4003 "alternate": { | |
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| 4007 "kmer_count": 0 | |
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| 4011 "min_non_zero_depth": 17, | |
| 4012 "percent_coverage": 95.45, | |
| 4013 "kmer_count": 369 | |
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| 4016 "expected_depths": [ | |
| 4017 17.0 | |
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| 4019 "filter": "LOW_GT_CONF", | |
| 4020 "conf": 0 | |
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| 4022 "genotype_likelihoods": [ | |
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| 4024 -99999999, | |
| 4025 -99999999 | |
| 4026 ], | |
| 4027 "_cls": "Call.VariantCall", | |
| 4028 "genotype": [ | |
| 4029 0, | |
| 4030 0 | |
| 4031 ], | |
| 4032 "variant": "ref-L443G?var_name=TTG761133GGC&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443G" | |
| 4033 }, | |
| 4034 "pncA_D8G-GTC2289218CCC": { | |
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| 4036 "contamination_depths": [], | |
| 4037 "coverage": { | |
| 4038 "alternate": { | |
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| 4040 "min_non_zero_depth": 14, | |
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| 4042 "kmer_count": 14 | |
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| 4044 "reference": { | |
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| 4046 "min_non_zero_depth": 14, | |
| 4047 "percent_coverage": 100.0, | |
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| 4050 }, | |
| 4051 "expected_depths": [ | |
| 4052 17.0 | |
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| 4055 "conf": 99999996 | |
| 4056 }, | |
| 4057 "genotype_likelihoods": [ | |
| 4058 -2.6844045563309873, | |
| 4059 -99999999, | |
| 4060 -99999999 | |
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| 4062 "_cls": "Call.VariantCall", | |
| 4063 "genotype": [ | |
| 4064 0, | |
| 4065 0 | |
| 4066 ], | |
| 4067 "variant": "ref-D8G?var_name=GTC2289218CCC&num_alts=10&ref=NC_000962.3&enum=0&gene=pncA&mut=D8G" | |
| 4068 }, | |
| 4069 "katG_L159P-GAG2155635CGG": { | |
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| 4075 "min_non_zero_depth": 20, | |
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| 4077 "kmer_count": 20 | |
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| 4086 "expected_depths": [ | |
| 4087 17.0 | |
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| 4091 }, | |
| 4092 "genotype_likelihoods": [ | |
| 4093 -2.79216398346472, | |
| 4094 -99999999, | |
| 4095 -99999999 | |
| 4096 ], | |
| 4097 "_cls": "Call.VariantCall", | |
| 4098 "genotype": [ | |
| 4099 0, | |
| 4100 0 | |
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| 4102 "variant": "ref-L159P?var_name=GAG2155635CGG&num_alts=5&ref=NC_000962.3&enum=0&gene=katG&mut=L159P" | |
| 4103 }, | |
| 4104 "rpoB_T444P-ACC761136CCT": { | |
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| 4108 "alternate": { | |
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| 4111 "percent_coverage": 0.0, | |
| 4112 "kmer_count": 0 | |
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| 4116 "min_non_zero_depth": 16, | |
| 4117 "percent_coverage": 100.0, | |
| 4118 "kmer_count": 380 | |
| 4119 } | |
| 4120 }, | |
| 4121 "expected_depths": [ | |
| 4122 17.0 | |
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| 4125 "conf": 99999996 | |
| 4126 }, | |
| 4127 "genotype_likelihoods": [ | |
| 4128 -2.6237799345145465, | |
| 4129 -99999999, | |
| 4130 -99999999 | |
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| 4132 "_cls": "Call.VariantCall", | |
| 4133 "genotype": [ | |
| 4134 0, | |
| 4135 0 | |
| 4136 ], | |
| 4137 "variant": "ref-T444P?var_name=ACC761136CCT&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444P" | |
| 4138 }, | |
| 4139 "katG_W328L-CCA2155128TAG": { | |
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| 4141 "contamination_depths": [], | |
| 4142 "coverage": { | |
| 4143 "alternate": { | |
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| 4147 "kmer_count": 0 | |
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| 4149 "reference": { | |
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| 4151 "min_non_zero_depth": 12, | |
| 4152 "percent_coverage": 100.0, | |
| 4153 "kmer_count": 284 | |
| 4154 } | |
| 4155 }, | |
| 4156 "expected_depths": [ | |
| 4157 17.0 | |
| 4158 ], | |
| 4159 "filter": "PASS", | |
| 4160 "conf": 99999996 | |
| 4161 }, | |
| 4162 "genotype_likelihoods": [ | |
| 4163 -3.0037237137259485, | |
| 4164 -99999999, | |
| 4165 -99999999 | |
| 4166 ], | |
| 4167 "_cls": "Call.VariantCall", | |
| 4168 "genotype": [ | |
| 4169 0, | |
| 4170 0 | |
| 4171 ], | |
| 4172 "variant": "ref-W328L?var_name=CCA2155128TAG&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W328L" | |
| 4173 }, | |
| 4174 "rpoB_H445Y-CAC761139TAC": { | |
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| 4176 "contamination_depths": [], | |
| 4177 "coverage": { | |
| 4178 "alternate": { | |
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| 4180 "min_non_zero_depth": 15, | |
| 4181 "percent_coverage": 9.09, | |
| 4182 "kmer_count": 31 | |
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| 4184 "reference": { | |
| 4185 "median_depth": 17, | |
| 4186 "min_non_zero_depth": 15, | |
| 4187 "percent_coverage": 100.0, | |
| 4188 "kmer_count": 377 | |
| 4189 } | |
| 4190 }, | |
| 4191 "expected_depths": [ | |
| 4192 17.0 | |
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| 6553 }, | |
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| 6759 0, | |
| 6760 0 | |
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| 6795 0 | |
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| 6904 "katG_S315W-GCT2155167CCA": { | |
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| 6938 }, | |
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| 7009 "rpoB_S431G-AGC761097GGC": { | |
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| 7114 "rpoB_L452E-CTG761160GAA": { | |
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| 7149 "rpoB_Q429R-CAG761091AGA": { | |
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| 8347 "kmer_count": 0 | |
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| 8349 "reference": { | |
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| 8351 "min_non_zero_depth": 15, | |
| 8352 "percent_coverage": 100.0, | |
| 8353 "kmer_count": 377 | |
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| 8355 }, | |
| 8356 "expected_depths": [ | |
| 8357 17.0 | |
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| 8360 "conf": 99999996 | |
| 8361 }, | |
| 8362 "genotype_likelihoods": [ | |
| 8363 -2.6237799345145465, | |
| 8364 -99999999, | |
| 8365 -99999999 | |
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| 8367 "_cls": "Call.VariantCall", | |
| 8368 "genotype": [ | |
| 8369 0, | |
| 8370 0 | |
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| 8372 "variant": "ref-H445A?var_name=CAC761139GCT&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445A" | |
| 8373 }, | |
| 8374 "rpoB_P439T-CCG761121ACC": { | |
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| 8387 "percent_coverage": 100.0, | |
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| 8390 }, | |
| 8391 "expected_depths": [ | |
| 8392 17.0 | |
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| 8396 }, | |
| 8397 "genotype_likelihoods": [ | |
| 8398 -2.6237799345145465, | |
| 8399 -99999999, | |
| 8400 -99999999 | |
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| 8404 0, | |
| 8405 0 | |
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| 8407 "variant": "ref-P439T?var_name=CCG761121ACC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439T" | |
| 8408 }, | |
| 8409 "pncA_L4S-CAA2289230TGA": { | |
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| 8421 "min_non_zero_depth": 13, | |
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| 8423 "kmer_count": 320 | |
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| 8426 "expected_depths": [ | |
| 8427 17.0 | |
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| 8431 }, | |
| 8432 "genotype_likelihoods": [ | |
| 8433 -2.8095676992849885, | |
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| 8435 -99999999 | |
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| 8437 "_cls": "Call.VariantCall", | |
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| 8439 0, | |
| 8440 0 | |
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| 8443 }, | |
| 8444 "inhA_S94A-TCG1674481GCA": { | |
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| 8460 }, | |
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| 8462 17.0 | |
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| 8467 "genotype_likelihoods": [ | |
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| 8472 "_cls": "Call.VariantCall", | |
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| 8474 0, | |
| 8475 0 | |
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| 8477 "variant": "ref-S94A?var_name=TCG1674481GCA&num_alts=4&ref=NC_000962.3&enum=0&gene=inhA&mut=S94A" | |
| 8478 }, | |
| 8479 "rpoB_S431P-AGC761097CCT": { | |
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| 8502 "genotype_likelihoods": [ | |
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| 8508 "genotype": [ | |
| 8509 0, | |
| 8510 0 | |
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| 8512 "variant": "ref-S431P?var_name=AGC761097CCT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431P" | |
| 8513 }, | |
| 8514 "rpoB_F425T-TTC761079ACT": { | |
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| 8532 17.0 | |
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| 8536 }, | |
| 8537 "genotype_likelihoods": [ | |
| 8538 -2.6844045563309873, | |
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| 8542 "_cls": "Call.VariantCall", | |
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| 8545 0 | |
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| 8547 "variant": "ref-F425T?var_name=TTC761079ACT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425T" | |
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| 8571 }, | |
| 8572 "genotype_likelihoods": [ | |
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| 8580 0 | |
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| 8582 "variant": "ref-N437F?var_name=AAC761115TTC&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437F" | |
| 8583 }, | |
| 8584 "gid_G117V-CCC4407852GAC": { | |
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| 8607 "genotype_likelihoods": [ | |
| 8608 -2.9546829129624985, | |
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| 8615 0 | |
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| 8617 "variant": "ref-G117V?var_name=CCC4407852GAC&num_alts=13&ref=NC_000962.3&enum=0&gene=gid&mut=G117V" | |
| 8618 }, | |
| 8619 "gyrA_D94G-GAC7581GGG": { | |
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| 8642 "genotype_likelihoods": [ | |
| 8643 -2.79216398346472, | |
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| 8645 -99999999 | |
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| 8647 "_cls": "Call.VariantCall", | |
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| 8650 0 | |
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| 8653 }, | |
| 8654 "rpoB_N438L-AAC761118CTG": { | |
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| 8677 "genotype_likelihoods": [ | |
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| 8682 "_cls": "Call.VariantCall", | |
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| 8684 0, | |
| 8685 0 | |
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| 8689 "embB_M306G-ATG4247429GGT": { | |
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| 8712 "genotype_likelihoods": [ | |
| 8713 -2.8095676992849885, | |
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| 8717 "_cls": "Call.VariantCall", | |
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| 8720 0 | |
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| 8722 "variant": "ref-M306G?var_name=ATG4247429GGT&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306G" | |
| 8723 }, | |
| 8724 "rpoB_K446D-AAG761142GAT": { | |
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| 8752 "_cls": "Call.VariantCall", | |
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| 8755 0 | |
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| 8757 "variant": "ref-K446D?var_name=AAG761142GAT&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446D" | |
| 8758 }, | |
| 8759 "gyrA_H85Q-CAC7554CAG": { | |
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| 8782 "genotype_likelihoods": [ | |
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| 8790 0 | |
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| 8792 "variant": "ref-H85Q?var_name=CAC7554CAG&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85Q" | |
| 8793 }, | |
| 8794 "gyrA_D89P-GAC7566CCG": { | |
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| 8817 "genotype_likelihoods": [ | |
| 8818 -2.6809383483544966, | |
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| 8825 0 | |
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| 8827 "variant": "ref-D89P?var_name=GAC7566CCG&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89P" | |
| 8828 }, | |
| 8829 "gid_Q125E-CTG4407828TTC": { | |
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| 8852 "genotype_likelihoods": [ | |
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| 8860 0 | |
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| 8862 "variant": "ref-Q125E?var_name=CTG4407828TTC&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125E" | |
| 8863 }, | |
| 8864 "gyrA_H85T-CAC7554ACA": { | |
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| 8887 "genotype_likelihoods": [ | |
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| 8892 "_cls": "Call.VariantCall", | |
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| 8894 0, | |
| 8895 0 | |
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| 8897 "variant": "ref-H85T?var_name=CAC7554ACA&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85T" | |
| 8898 }, | |
| 8899 "pncA_Y99S-GTA2288945ACT": { | |
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| 8911 "min_non_zero_depth": 16, | |
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| 8922 "genotype_likelihoods": [ | |
| 8923 -2.62377993451455, | |
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| 8927 "_cls": "Call.VariantCall", | |
| 8928 "genotype": [ | |
| 8929 0, | |
| 8930 0 | |
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| 8932 "variant": "ref-Y99S?var_name=GTA2288945ACT&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99S" | |
| 8933 }, | |
| 8934 "embB_M306H-ATG4247429CAT": { | |
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| 10543 }, | |
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| 10684 "embB_M306T-ATG4247429ACC": { | |
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| 11485 0 | |
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| 11520 0 | |
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| 11522 "variant": "ref-A90L?var_name=GCG7569CTT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90L" | |
| 11523 }, | |
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| 11557 "variant": "ref-P439K?var_name=CCG761121AAG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439K" | |
| 11558 }, | |
| 11559 "gyrA_D89S-GAC7566TCT": { | |
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| 11590 0 | |
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| 11592 "variant": "ref-D89S?var_name=GAC7566TCT&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89S" | |
| 11593 }, | |
| 11594 "gyrA_S91C-TCG7572TGT": { | |
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| 11625 0 | |
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| 11627 "variant": "ref-S91C?var_name=TCG7572TGT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91C" | |
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| 11629 "rpoB_S450D-TCG761154GAC": { | |
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| 11662 "variant": "ref-S450D?var_name=TCG761154GAC&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450D" | |
| 11663 }, | |
| 11664 "gid_Q125I-CTG4407828GAT": { | |
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| 11697 "variant": "ref-Q125I?var_name=CTG4407828GAT&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125I" | |
| 11698 }, | |
| 11699 "rpoB_S428G-AGC761088GGT": { | |
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| 11732 "variant": "ref-S428G?var_name=AGC761088GGT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428G" | |
| 11733 }, | |
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| 11767 "variant": "ref-Q10D?var_name=CTG2289212GTC&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10D" | |
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| 11802 "variant": "ref-D142G?var_name=GTC2155686TCC&num_alts=5&ref=NC_000962.3&enum=0&gene=katG&mut=D142G" | |
| 11803 }, | |
| 11804 "pncA_Q141G-CTG2288819ACC": { | |
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| 11838 }, | |
| 11839 "pncA_L27P-CAG2289161TGG": { | |
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| 11872 "variant": "ref-L27P?var_name=CAG2289161TGG&num_alts=5&ref=NC_000962.3&enum=0&gene=pncA&mut=L27P" | |
| 11873 }, | |
| 11874 "ahpC_C-72T-C2726121T": { | |
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| 12497 "_cls": "Call.VariantCall", | |
| 12498 "genotype": [ | |
| 12499 0, | |
| 12500 0 | |
| 12501 ], | |
| 12502 "variant": "ref-N437C?var_name=AAC761115TGT&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437C" | |
| 12503 }, | |
| 12504 "rpoB_L440S-CTG761124AGC": { | |
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| 12509 "median_depth": 0, | |
| 12510 "min_non_zero_depth": 18, | |
| 12511 "percent_coverage": 13.64, | |
| 12512 "kmer_count": 54 | |
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| 12514 "reference": { | |
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| 12516 "min_non_zero_depth": 17, | |
| 12517 "percent_coverage": 100.0, | |
| 12518 "kmer_count": 385 | |
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| 12520 }, | |
| 12521 "expected_depths": [ | |
| 12522 17.0 | |
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| 12526 }, | |
| 12527 "genotype_likelihoods": [ | |
| 12528 -2.6237799345145465, | |
| 12529 -99999999, | |
| 12530 -99999999 | |
| 12531 ], | |
| 12532 "_cls": "Call.VariantCall", | |
| 12533 "genotype": [ | |
| 12534 0, | |
| 12535 0 | |
| 12536 ], | |
| 12537 "variant": "ref-L440S?var_name=CTG761124AGC&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440S" | |
| 12538 }, | |
| 12539 "gyrA_D94E-GAC7581GAA": { | |
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| 12551 "min_non_zero_depth": 17, | |
| 12552 "percent_coverage": 100.0, | |
| 12553 "kmer_count": 406 | |
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| 12555 }, | |
| 12556 "expected_depths": [ | |
| 12557 17.0 | |
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| 12561 }, | |
| 12562 "genotype_likelihoods": [ | |
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| 12564 -99999999, | |
| 12565 -99999999 | |
| 12566 ], | |
| 12567 "_cls": "Call.VariantCall", | |
| 12568 "genotype": [ | |
| 12569 0, | |
| 12570 0 | |
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| 12572 "variant": "ref-D94E?var_name=GAC7581GAA&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94E" | |
| 12573 }, | |
| 12574 "rpoB_D435R-GAC761109CGC": { | |
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| 12580 "min_non_zero_depth": 1, | |
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| 12586 "min_non_zero_depth": 17, | |
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| 12590 }, | |
| 12591 "expected_depths": [ | |
| 12592 17.0 | |
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| 12596 }, | |
| 12597 "genotype_likelihoods": [ | |
| 12598 -2.79216398346472, | |
| 12599 -99999999, | |
| 12600 -99999999 | |
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| 12602 "_cls": "Call.VariantCall", | |
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| 12604 0, | |
| 12605 0 | |
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| 12607 "variant": "ref-D435R?var_name=GAC761109CGC&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435R" | |
| 12608 }, | |
| 12609 "katG_S315T-GCT2155167AGT": { | |
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| 12622 "percent_coverage": 4.55, | |
| 12623 "kmer_count": 17 | |
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| 12626 "expected_depths": [ | |
| 12627 17.0 | |
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| 12629 "filter": "LOW_GT_CONF", | |
| 12630 "conf": 0 | |
| 12631 }, | |
| 12632 "genotype_likelihoods": [ | |
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| 12634 -99999999, | |
| 12635 -99999999 | |
| 12636 ], | |
| 12637 "_cls": "Call.VariantCall", | |
| 12638 "genotype": [ | |
| 12639 0, | |
| 12640 0 | |
| 12641 ], | |
| 12642 "variant": "ref-S315T?var_name=GCT2155167AGT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315T" | |
| 12643 }, | |
| 12644 "rpoB_Q429R-CAG761091AGG": { | |
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| 12656 "min_non_zero_depth": 15, | |
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| 12660 }, | |
| 12661 "expected_depths": [ | |
| 12662 17.0 | |
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| 12666 }, | |
| 12667 "genotype_likelihoods": [ | |
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| 12669 -99999999, | |
| 12670 -99999999 | |
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| 12672 "_cls": "Call.VariantCall", | |
| 12673 "genotype": [ | |
| 12674 0, | |
| 12675 0 | |
| 12676 ], | |
| 12677 "variant": "ref-Q429R?var_name=CAG761091AGG&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429R" | |
| 12678 }, | |
| 12679 "gid_S136V-TGA4407795GAC": { | |
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| 12691 "min_non_zero_depth": 14, | |
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| 12693 "kmer_count": 327 | |
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| 12696 "expected_depths": [ | |
| 12697 17.0 | |
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| 12701 }, | |
| 12702 "genotype_likelihoods": [ | |
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| 12704 -99999999, | |
| 12705 -99999999 | |
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| 12707 "_cls": "Call.VariantCall", | |
| 12708 "genotype": [ | |
| 12709 0, | |
| 12710 0 | |
| 12711 ], | |
| 12712 "variant": "ref-S136V?var_name=TGA4407795GAC&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136V" | |
| 12713 }, | |
| 12714 "rpoB_Q429L-CAG761091TTA": { | |
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| 12726 "min_non_zero_depth": 15, | |
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| 12728 "kmer_count": 395 | |
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| 12730 }, | |
| 12731 "expected_depths": [ | |
| 12732 17.0 | |
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| 12736 }, | |
| 12737 "genotype_likelihoods": [ | |
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| 12739 -99999999, | |
| 12740 -99999999 | |
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| 12742 "_cls": "Call.VariantCall", | |
| 12743 "genotype": [ | |
| 12744 0, | |
| 12745 0 | |
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| 12747 "variant": "ref-Q429L?var_name=CAG761091TTA&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429L" | |
| 12748 }, | |
| 12749 "katG_W505G-CCA2154597ACC": { | |
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| 12761 "min_non_zero_depth": 16, | |
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| 12763 "kmer_count": 385 | |
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| 12766 "expected_depths": [ | |
| 12767 17.0 | |
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| 12771 }, | |
| 12772 "genotype_likelihoods": [ | |
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| 12775 -99999999 | |
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| 12777 "_cls": "Call.VariantCall", | |
| 12778 "genotype": [ | |
| 12779 0, | |
| 12780 0 | |
| 12781 ], | |
| 12782 "variant": "ref-W505G?var_name=CCA2154597ACC&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505G" | |
| 12783 }, | |
| 12784 "gyrA_S91I-TCG7572ATA": { | |
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| 12796 "min_non_zero_depth": 18, | |
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| 12798 "kmer_count": 413 | |
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| 12801 "expected_depths": [ | |
| 12802 17.0 | |
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| 12805 "conf": 99999996 | |
| 12806 }, | |
| 12807 "genotype_likelihoods": [ | |
| 12808 -2.79216398346472, | |
| 12809 -99999999, | |
| 12810 -99999999 | |
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| 12812 "_cls": "Call.VariantCall", | |
| 12813 "genotype": [ | |
| 12814 0, | |
| 12815 0 | |
| 12816 ], | |
| 12817 "variant": "ref-S91I?var_name=TCG7572ATA&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91I" | |
| 12818 }, | |
| 12819 "katG_S315G-GCT2155167CCC": { | |
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| 12827 "kmer_count": 0 | |
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| 12831 "min_non_zero_depth": 17, | |
| 12832 "percent_coverage": 4.55, | |
| 12833 "kmer_count": 17 | |
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| 12835 }, | |
| 12836 "expected_depths": [ | |
| 12837 17.0 | |
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| 12839 "filter": "LOW_GT_CONF", | |
| 12840 "conf": 0 | |
| 12841 }, | |
| 12842 "genotype_likelihoods": [ | |
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| 12844 -99999999, | |
| 12845 -99999999 | |
| 12846 ], | |
| 12847 "_cls": "Call.VariantCall", | |
| 12848 "genotype": [ | |
| 12849 0, | |
| 12850 0 | |
| 12851 ], | |
| 12852 "variant": "ref-S315G?var_name=GCT2155167CCC&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315G" | |
| 12853 }, | |
| 12854 "pncA_Y99R-GTA2288945TCT": { | |
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| 12860 "min_non_zero_depth": 16, | |
| 12861 "percent_coverage": 9.09, | |
| 12862 "kmer_count": 32 | |
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| 12864 "reference": { | |
| 12865 "median_depth": 16, | |
| 12866 "min_non_zero_depth": 16, | |
| 12867 "percent_coverage": 100.0, | |
| 12868 "kmer_count": 362 | |
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| 12870 }, | |
| 12871 "expected_depths": [ | |
| 12872 17.0 | |
| 12873 ], | |
| 12874 "filter": "PASS", | |
| 12875 "conf": 99999996 | |
| 12876 }, | |
| 12877 "genotype_likelihoods": [ | |
| 12878 -2.62377993451455, | |
| 12879 -99999999, | |
| 12880 -99999999 | |
| 12881 ], | |
| 12882 "_cls": "Call.VariantCall", | |
| 12883 "genotype": [ | |
| 12884 0, | |
| 12885 0 | |
| 12886 ], | |
| 12887 "variant": "ref-Y99R?var_name=GTA2288945TCT&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99R" | |
| 12888 }, | |
| 12889 "rpoB_M434R-ATG761106AGA": { | |
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| 12891 "contamination_depths": [], | |
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| 12901 "min_non_zero_depth": 17, | |
| 12902 "percent_coverage": 100.0, | |
| 12903 "kmer_count": 420 | |
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| 12905 }, | |
| 12906 "expected_depths": [ | |
| 12907 17.0 | |
| 12908 ], | |
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| 12910 "conf": 99999996 | |
| 12911 }, | |
| 12912 "genotype_likelihoods": [ | |
| 12913 -2.79216398346472, | |
| 12914 -99999999, | |
| 12915 -99999999 | |
| 12916 ], | |
| 12917 "_cls": "Call.VariantCall", | |
| 12918 "genotype": [ | |
| 12919 0, | |
| 12920 0 | |
| 12921 ], | |
| 12922 "variant": "ref-M434R?var_name=ATG761106AGA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434R" | |
| 12923 }, | |
| 12924 "pncA_S32I-GCT2289146AAT": { | |
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| 12930 "min_non_zero_depth": 17, | |
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| 12932 "kmer_count": 17 | |
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| 12936 "min_non_zero_depth": 17, | |
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| 12938 "kmer_count": 374 | |
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| 12941 "expected_depths": [ | |
| 12942 17.0 | |
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| 12946 }, | |
| 12947 "genotype_likelihoods": [ | |
| 12948 -2.6237799345145465, | |
| 12949 -99999999, | |
| 12950 -99999999 | |
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| 12952 "_cls": "Call.VariantCall", | |
| 12953 "genotype": [ | |
| 12954 0, | |
| 12955 0 | |
| 12956 ], | |
| 12957 "variant": "ref-S32I?var_name=GCT2289146AAT&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=S32I" | |
| 12958 }, | |
| 12959 "gid_I162S-GAT4407717GGA": { | |
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| 12971 "min_non_zero_depth": 14, | |
| 12972 "percent_coverage": 100.0, | |
| 12973 "kmer_count": 368 | |
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| 12976 "expected_depths": [ | |
| 12977 17.0 | |
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| 12981 }, | |
| 12982 "genotype_likelihoods": [ | |
| 12983 -2.6237799345145465, | |
| 12984 -99999999, | |
| 12985 -99999999 | |
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| 12987 "_cls": "Call.VariantCall", | |
| 12988 "genotype": [ | |
| 12989 0, | |
| 12990 0 | |
| 12991 ], | |
| 12992 "variant": "ref-I162S?var_name=GAT4407717GGA&num_alts=15&ref=NC_000962.3&enum=0&gene=gid&mut=I162S" | |
| 12993 }, | |
| 12994 "pncA_Y99A-GTA2288945CGC": { | |
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| 13000 "min_non_zero_depth": 16, | |
| 13001 "percent_coverage": 9.09, | |
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| 13004 "reference": { | |
| 13005 "median_depth": 16, | |
| 13006 "min_non_zero_depth": 16, | |
| 13007 "percent_coverage": 100.0, | |
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| 13011 "expected_depths": [ | |
| 13012 17.0 | |
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| 13016 }, | |
| 13017 "genotype_likelihoods": [ | |
| 13018 -2.62377993451455, | |
| 13019 -99999999, | |
| 13020 -99999999 | |
| 13021 ], | |
| 13022 "_cls": "Call.VariantCall", | |
| 13023 "genotype": [ | |
| 13024 0, | |
| 13025 0 | |
| 13026 ], | |
| 13027 "variant": "ref-Y99A?var_name=GTA2288945CGC&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99A" | |
| 13028 }, | |
| 13029 "gid_R118S-GCG4407849TGA": { | |
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| 13035 "min_non_zero_depth": 21, | |
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| 13037 "kmer_count": 21 | |
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| 13039 "reference": { | |
| 13040 "median_depth": 20, | |
| 13041 "min_non_zero_depth": 17, | |
| 13042 "percent_coverage": 100.0, | |
| 13043 "kmer_count": 428 | |
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| 13045 }, | |
| 13046 "expected_depths": [ | |
| 13047 17.0 | |
| 13048 ], | |
| 13049 "filter": "PASS", | |
| 13050 "conf": 99999996 | |
| 13051 }, | |
| 13052 "genotype_likelihoods": [ | |
| 13053 -2.9546829129624985, | |
| 13054 -99999999, | |
| 13055 -99999999 | |
| 13056 ], | |
| 13057 "_cls": "Call.VariantCall", | |
| 13058 "genotype": [ | |
| 13059 0, | |
| 13060 0 | |
| 13061 ], | |
| 13062 "variant": "ref-R118S?var_name=GCG4407849TGA&num_alts=14&ref=NC_000962.3&enum=0&gene=gid&mut=R118S" | |
| 13063 }, | |
| 13064 "rpoB_D435P-GAC761109CCG": { | |
| 13065 "info": { | |
| 13066 "contamination_depths": [], | |
| 13067 "coverage": { | |
| 13068 "alternate": { | |
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| 13072 "kmer_count": 0 | |
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| 13074 "reference": { | |
| 13075 "median_depth": 19, | |
| 13076 "min_non_zero_depth": 17, | |
| 13077 "percent_coverage": 100.0, | |
| 13078 "kmer_count": 416 | |
| 13079 } | |
| 13080 }, | |
| 13081 "expected_depths": [ | |
| 13082 17.0 | |
| 13083 ], | |
| 13084 "filter": "PASS", | |
| 13085 "conf": 99999996 | |
| 13086 }, | |
| 13087 "genotype_likelihoods": [ | |
| 13088 -2.79216398346472, | |
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| 13683 -2.9546829129624985, | |
| 13684 -99999999, | |
| 13685 -99999999 | |
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| 13687 "_cls": "Call.VariantCall", | |
| 13688 "genotype": [ | |
| 13689 0, | |
| 13690 0 | |
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| 13692 "variant": "ref-R118S?var_name=GCG4407849GGA&num_alts=14&ref=NC_000962.3&enum=0&gene=gid&mut=R118S" | |
| 13693 }, | |
| 13694 "rpoB_T444R-ACC761136AGG": { | |
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| 13707 "percent_coverage": 100.0, | |
| 13708 "kmer_count": 380 | |
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| 13710 }, | |
| 13711 "expected_depths": [ | |
| 13712 17.0 | |
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| 13715 "conf": 99999996 | |
| 13716 }, | |
| 13717 "genotype_likelihoods": [ | |
| 13718 -2.6237799345145465, | |
| 13719 -99999999, | |
| 13720 -99999999 | |
| 13721 ], | |
| 13722 "_cls": "Call.VariantCall", | |
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| 13724 0, | |
| 13725 0 | |
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| 13727 "variant": "ref-T444R?var_name=ACC761136AGG&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444R" | |
| 13728 }, | |
| 13729 "rpoB_D435S-GAC761109TCT": { | |
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| 13745 }, | |
| 13746 "expected_depths": [ | |
| 13747 17.0 | |
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| 13750 "conf": 99999996 | |
| 13751 }, | |
| 13752 "genotype_likelihoods": [ | |
| 13753 -2.79216398346472, | |
| 13754 -99999999, | |
| 13755 -99999999 | |
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| 13757 "_cls": "Call.VariantCall", | |
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| 13759 0, | |
| 13760 0 | |
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| 13762 "variant": "ref-D435S?var_name=GAC761109TCT&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435S" | |
| 13763 }, | |
| 13764 "rpoB_Q429L-CAG761091CTG": { | |
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| 13770 "min_non_zero_depth": 14, | |
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| 13776 "min_non_zero_depth": 15, | |
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| 13780 }, | |
| 13781 "expected_depths": [ | |
| 13782 17.0 | |
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| 13786 }, | |
| 13787 "genotype_likelihoods": [ | |
| 13788 -2.6809383483544966, | |
| 13789 -99999999, | |
| 13790 -99999999 | |
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| 13792 "_cls": "Call.VariantCall", | |
| 13793 "genotype": [ | |
| 13794 0, | |
| 13795 0 | |
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| 13797 "variant": "ref-Q429L?var_name=CAG761091CTG&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429L" | |
| 13798 }, | |
| 13799 "gyrA_I92Y-ATC7575TAC": { | |
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| 13805 "min_non_zero_depth": 18, | |
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| 13811 "min_non_zero_depth": 18, | |
| 13812 "percent_coverage": 100.0, | |
| 13813 "kmer_count": 414 | |
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| 13815 }, | |
| 13816 "expected_depths": [ | |
| 13817 17.0 | |
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| 13820 "conf": 99999996 | |
| 13821 }, | |
| 13822 "genotype_likelihoods": [ | |
| 13823 -2.79216398346472, | |
| 13824 -99999999, | |
| 13825 -99999999 | |
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| 13827 "_cls": "Call.VariantCall", | |
| 13828 "genotype": [ | |
| 13829 0, | |
| 13830 0 | |
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| 13832 "variant": "ref-I92Y?var_name=ATC7575TAC&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92Y" | |
| 13833 }, | |
| 13834 "rpoB_H445G-CAC761139GGG": { | |
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| 13846 "min_non_zero_depth": 15, | |
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| 13851 "expected_depths": [ | |
| 13852 17.0 | |
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| 13856 }, | |
| 13857 "genotype_likelihoods": [ | |
| 13858 -2.6237799345145465, | |
| 13859 -99999999, | |
| 13860 -99999999 | |
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| 13862 "_cls": "Call.VariantCall", | |
| 13863 "genotype": [ | |
| 13864 0, | |
| 13865 0 | |
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| 13867 "variant": "ref-H445G?var_name=CAC761139GGG&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445G" | |
| 13868 }, | |
| 13869 "rpoB_L440E-CTG761124GAA": { | |
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| 13887 17.0 | |
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| 13892 "genotype_likelihoods": [ | |
| 13893 -2.6237799345145465, | |
| 13894 -99999999, | |
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| 13897 "_cls": "Call.VariantCall", | |
| 13898 "genotype": [ | |
| 13899 0, | |
| 13900 0 | |
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| 13902 "variant": "ref-L440E?var_name=CTG761124GAA&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440E" | |
| 13903 }, | |
| 13904 "rpoB_L452N-CTG761160AAT": { | |
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| 13927 "genotype_likelihoods": [ | |
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| 13929 -99999999, | |
| 13930 -99999999 | |
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| 13932 "_cls": "Call.VariantCall", | |
| 13933 "genotype": [ | |
| 13934 0, | |
| 13935 0 | |
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| 13937 "variant": "ref-L452N?var_name=CTG761160AAT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452N" | |
| 13938 }, | |
| 13939 "katG_S315F-GCT2155167GAA": { | |
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| 13956 "expected_depths": [ | |
| 13957 17.0 | |
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| 13962 "genotype_likelihoods": [ | |
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| 13964 -99999999, | |
| 13965 -99999999 | |
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| 13967 "_cls": "Call.VariantCall", | |
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| 13969 0, | |
| 13970 0 | |
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| 13972 "variant": "ref-S315F?var_name=GCT2155167GAA&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315F" | |
| 13973 }, | |
| 13974 "pncA_Q10C-CTG2289212GCA": { | |
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| 13991 "expected_depths": [ | |
| 13992 17.0 | |
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| 13997 "genotype_likelihoods": [ | |
| 13998 -2.6844045563309873, | |
| 13999 -99999999, | |
| 14000 -99999999 | |
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| 14002 "_cls": "Call.VariantCall", | |
| 14003 "genotype": [ | |
| 14004 0, | |
| 14005 0 | |
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| 14007 "variant": "ref-Q10C?var_name=CTG2289212GCA&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10C" | |
| 14008 }, | |
| 14009 "rrs_C1402A-C1473247A": { | |
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| 14016 "percent_coverage": 9.09, | |
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| 14021 "min_non_zero_depth": 11, | |
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| 14026 "expected_depths": [ | |
| 14027 17.0 | |
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| 14032 "genotype_likelihoods": [ | |
| 14033 -2.6237799345145465, | |
| 14034 -99999999, | |
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| 14037 "_cls": "Call.VariantCall", | |
| 14038 "genotype": [ | |
| 14039 0, | |
| 14040 0 | |
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| 14042 "variant": "ref-C1402A?var_name=C1473247A&num_alts=4&ref=NC_000962.3&enum=0&gene=rrs&mut=C1402A" | |
| 14043 }, | |
| 14044 "gyrA_H85I-CAC7554ATT": { | |
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| 14048 "alternate": { | |
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| 14056 "min_non_zero_depth": 13, | |
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| 14061 "expected_depths": [ | |
| 14062 17.0 | |
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| 14067 "genotype_likelihoods": [ | |
| 14068 -2.6844045563309873, | |
| 14069 -99999999, | |
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| 14072 "_cls": "Call.VariantCall", | |
| 14073 "genotype": [ | |
| 14074 0, | |
| 14075 0 | |
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| 14077 "variant": "ref-H85I?var_name=CAC7554ATT&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85I" | |
| 14078 }, | |
| 14079 "gyrA_G88C-GGC7563TGC": { | |
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| 14083 "alternate": { | |
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| 14091 "min_non_zero_depth": 15, | |
| 14092 "percent_coverage": 95.45, | |
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| 14096 "expected_depths": [ | |
| 14097 17.0 | |
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| 14099 "filter": "LOW_GT_CONF", | |
| 14100 "conf": 0 | |
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| 14102 "genotype_likelihoods": [ | |
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| 14104 -99999999, | |
| 14105 -99999999 | |
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| 14107 "_cls": "Call.VariantCall", | |
| 14108 "genotype": [ | |
| 14109 0, | |
| 14110 0 | |
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| 14112 "variant": "ref-G88C?var_name=GGC7563TGC&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88C" | |
| 14113 }, | |
| 14114 "rpoB_Q432E-CAA761100GAA": { | |
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| 14118 "alternate": { | |
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| 14120 "min_non_zero_depth": 17, | |
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| 14126 "min_non_zero_depth": 17, | |
| 14127 "percent_coverage": 100.0, | |
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| 14131 "expected_depths": [ | |
| 14132 17.0 | |
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| 14137 "genotype_likelihoods": [ | |
| 14138 -2.79216398346472, | |
| 14139 -99999999, | |
| 14140 -99999999 | |
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| 14142 "_cls": "Call.VariantCall", | |
| 14143 "genotype": [ | |
| 14144 0, | |
| 14145 0 | |
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| 14147 "variant": "ref-Q432E?var_name=CAA761100GAA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432E" | |
| 14148 }, | |
| 14149 "rpoB_G981D-GGC762747GAT": { | |
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| 14161 "min_non_zero_depth": 6, | |
| 14162 "percent_coverage": 100.0, | |
| 14163 "kmer_count": 142 | |
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| 14166 "expected_depths": [ | |
| 14167 17.0 | |
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| 14170 "conf": 99999992 | |
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| 14172 "genotype_likelihoods": [ | |
| 14173 -6.863304481006136, | |
| 14174 -99999999, | |
| 14175 -99999999 | |
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| 14177 "_cls": "Call.VariantCall", | |
| 14178 "genotype": [ | |
| 14179 0, | |
| 14180 0 | |
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| 14182 "variant": "ref-G981D?var_name=GGC762747GAT&num_alts=2&ref=NC_000962.3&enum=0&gene=rpoB&mut=G981D" | |
| 14183 }, | |
| 14184 "gid_V41I-GAC4408080TAT": { | |
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| 14188 "alternate": { | |
| 14189 "median_depth": 0, | |
| 14190 "min_non_zero_depth": 17, | |
| 14191 "percent_coverage": 4.55, | |
| 14192 "kmer_count": 17 | |
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| 14194 "reference": { | |
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| 14196 "min_non_zero_depth": 17, | |
| 14197 "percent_coverage": 100.0, | |
| 14198 "kmer_count": 424 | |
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| 14200 }, | |
| 14201 "expected_depths": [ | |
| 14202 17.0 | |
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| 14206 }, | |
| 14207 "genotype_likelihoods": [ | |
| 14208 -2.6809383483544966, | |
| 14209 -99999999, | |
| 14210 -99999999 | |
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| 14212 "_cls": "Call.VariantCall", | |
| 14213 "genotype": [ | |
| 14214 0, | |
| 14215 0 | |
| 14216 ], | |
| 14217 "variant": "ref-V41I?var_name=GAC4408080TAT&num_alts=31&ref=NC_000962.3&enum=0&gene=gid&mut=V41I" | |
| 14218 }, | |
| 14219 "rpoB_A451S-GCG761157AGC": { | |
| 14220 "info": { | |
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| 14223 "alternate": { | |
| 14224 "median_depth": 0, | |
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| 14227 "kmer_count": 0 | |
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| 14229 "reference": { | |
| 14230 "median_depth": 14, | |
| 14231 "min_non_zero_depth": 14, | |
| 14232 "percent_coverage": 100.0, | |
| 14233 "kmer_count": 319 | |
| 14234 } | |
| 14235 }, | |
| 14236 "expected_depths": [ | |
| 14237 17.0 | |
| 14238 ], | |
| 14239 "filter": "PASS", | |
| 14240 "conf": 99999996 | |
| 14241 }, | |
| 14242 "genotype_likelihoods": [ | |
| 14243 -2.8095676992849885, | |
| 14244 -99999999, | |
| 14245 -99999999 | |
| 14246 ], | |
| 14247 "_cls": "Call.VariantCall", | |
| 14248 "genotype": [ | |
| 14249 0, | |
| 14250 0 | |
| 14251 ], | |
| 14252 "variant": "ref-A451S?var_name=GCG761157AGC&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451S" | |
| 14253 }, | |
| 14254 "pncA_Y99D-GTA2288945GTC": { | |
| 14255 "info": { | |
| 14256 "contamination_depths": [], | |
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| 14258 "alternate": { | |
| 14259 "median_depth": 0, | |
| 14260 "min_non_zero_depth": 16, | |
| 14261 "percent_coverage": 9.09, | |
| 14262 "kmer_count": 32 | |
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| 14264 "reference": { | |
| 14265 "median_depth": 16, | |
| 14266 "min_non_zero_depth": 16, | |
| 14267 "percent_coverage": 100.0, | |
| 14268 "kmer_count": 362 | |
| 14269 } | |
| 14270 }, | |
| 14271 "expected_depths": [ | |
| 14272 17.0 | |
| 14273 ], | |
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| 14709 "gyrA_S91E-TCG7572GAG": { | |
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| 14779 "gyrA_H85V-CAC7554GTT": { | |
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| 21183 }, | |
| 21184 "gyrA_P86S-CCG7557AGT": { | |
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| 21289 "embB_D354A-GAC4247573GCA": { | |
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| 21359 "gyrA_D89R-GAC7566CGG": { | |
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| 23174 0, | |
| 23175 0 | |
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| 23178 }, | |
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| 23196 "expected_depths": [ | |
| 23197 17.0 | |
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| 23207 "_cls": "Call.VariantCall", | |
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| 23209 0, | |
| 23210 0 | |
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| 23244 0, | |
| 23245 0 | |
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| 23247 "variant": "ref-E173V?var_name=CTC4407684TAC&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173V" | |
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| 23267 17.0 | |
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| 23279 0, | |
| 23280 0 | |
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| 23282 "variant": "ref-S149R?var_name=GCT4407756ACG&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=S149R" | |
| 23283 }, | |
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| 23302 17.0 | |
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| 23307 "genotype_likelihoods": [ | |
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| 23312 "_cls": "Call.VariantCall", | |
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| 23314 0, | |
| 23315 0 | |
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| 23317 "variant": "ref-Y99C?var_name=GTA2288945GCA&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99C" | |
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| 23319 "gyrA_P86R-CCG7557AGA": { | |
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| 23337 17.0 | |
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| 23349 0, | |
| 23350 0 | |
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| 23352 "variant": "ref-P86R?var_name=CCG7557AGA&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86R" | |
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| 23385 0 | |
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| 23387 "variant": "ref-D12A?var_name=GTC2289206CGC&num_alts=13&ref=NC_000962.3&enum=0&gene=pncA&mut=D12A" | |
| 23388 }, | |
| 23389 "rpoB_N438E-AAC761118GAG": { | |
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| 23419 0, | |
| 23420 0 | |
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| 23422 "variant": "ref-N438E?var_name=AAC761118GAG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438E" | |
| 23423 }, | |
| 23424 "rpoB_P439C-CCG761121TGT": { | |
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| 23442 17.0 | |
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| 23454 0, | |
| 23455 0 | |
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| 23457 "variant": "ref-P439C?var_name=CCG761121TGT&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439C" | |
| 23458 }, | |
| 23459 "gyrA_Y93H-TAC7578CAC": { | |
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| 23487 "_cls": "Call.VariantCall", | |
| 23488 "genotype": [ | |
| 23489 0, | |
| 23490 0 | |
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| 23492 "variant": "ref-Y93H?var_name=TAC7578CAC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93H" | |
| 23493 }, | |
| 23494 "gid_S149R-GCT4407756CCG": { | |
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| 23518 -2.8095676992849885, | |
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| 23522 "_cls": "Call.VariantCall", | |
| 23523 "genotype": [ | |
| 23524 0, | |
| 23525 0 | |
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| 23527 "variant": "ref-S149R?var_name=GCT4407756CCG&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=S149R" | |
| 23528 }, | |
| 23529 "gyrA_G88N-GGC7563AAC": { | |
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| 23547 17.0 | |
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| 23550 "conf": 0 | |
| 23551 }, | |
| 23552 "genotype_likelihoods": [ | |
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| 23555 -99999999 | |
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| 23559 0, | |
| 23560 0 | |
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| 23562 "variant": "ref-G88N?var_name=GGC7563AAC&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88N" | |
| 23563 }, | |
| 23564 "katG_S315R-GCT2155167CCT": { | |
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| 23582 17.0 | |
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| 23587 "genotype_likelihoods": [ | |
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| 23590 -99999999 | |
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| 23592 "_cls": "Call.VariantCall", | |
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| 23594 0, | |
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| 23597 "variant": "ref-S315R?var_name=GCT2155167CCT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315R" | |
| 23598 }, | |
| 23599 "rpoB_N437K-AAC761115AAA": { | |
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| 23617 17.0 | |
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| 23622 "genotype_likelihoods": [ | |
| 23623 -2.6809383483544966, | |
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| 23627 "_cls": "Call.VariantCall", | |
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| 23629 0, | |
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| 23632 "variant": "ref-N437K?var_name=AAC761115AAA&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437K" | |
| 23633 }, | |
| 23634 "rpoB_K446T-AAG761142ACC": { | |
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| 23652 17.0 | |
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| 23657 "genotype_likelihoods": [ | |
| 23658 -2.6237799345145465, | |
| 23659 -99999999, | |
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| 23664 0, | |
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| 23667 "variant": "ref-K446T?var_name=AAG761142ACC&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446T" | |
| 23668 }, | |
| 23669 "rpoB_R448P-CGA761148CCC": { | |
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| 23687 17.0 | |
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| 23692 "genotype_likelihoods": [ | |
| 23693 -2.62377993451455, | |
| 23694 -99999999, | |
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| 23697 "_cls": "Call.VariantCall", | |
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| 23700 0 | |
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| 23702 "variant": "ref-R448P?var_name=CGA761148CCC&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448P" | |
| 23703 }, | |
| 23704 "rpoB_S450I-TCG761154ATT": { | |
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| 23727 "genotype_likelihoods": [ | |
| 23728 -99999999, | |
| 23729 -99999999, | |
| 23730 -99999999 | |
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| 23732 "_cls": "Call.VariantCall", | |
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| 23735 0 | |
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| 23737 "variant": "ref-S450I?var_name=TCG761154ATT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450I" | |
| 23738 }, | |
| 23739 "gyrA_H85R-CAC7554CGT": { | |
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| 23754 } | |
| 23755 }, | |
| 23756 "expected_depths": [ | |
| 23757 17.0 | |
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| 24947 17.0 | |
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| 24949 "filter": "LOW_GT_CONF", | |
| 24950 "conf": 0 | |
| 24951 }, | |
| 24952 "genotype_likelihoods": [ | |
| 24953 -99999999, | |
| 24954 -99999999, | |
| 24955 -99999999 | |
| 24956 ], | |
| 24957 "_cls": "Call.VariantCall", | |
| 24958 "genotype": [ | |
| 24959 0, | |
| 24960 0 | |
| 24961 ], | |
| 24962 "variant": "ref-Q141C?var_name=CTG2288819ACA&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141C" | |
| 24963 }, | |
| 24964 "gyrA_S91H-TCG7572CAC": { | |
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| 24967 "coverage": { | |
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| 24969 "median_depth": 0, | |
| 24970 "min_non_zero_depth": 0, | |
| 24971 "percent_coverage": 0.0, | |
| 24972 "kmer_count": 0 | |
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| 24974 "reference": { | |
| 24975 "median_depth": 19, | |
| 24976 "min_non_zero_depth": 18, | |
| 24977 "percent_coverage": 100.0, | |
| 24978 "kmer_count": 413 | |
| 24979 } | |
| 24980 }, | |
| 24981 "expected_depths": [ | |
| 24982 17.0 | |
| 24983 ], | |
| 24984 "filter": "PASS", | |
| 24985 "conf": 99999996 | |
| 24986 }, | |
| 24987 "genotype_likelihoods": [ | |
| 24988 -2.79216398346472, | |
| 24989 -99999999, | |
| 24990 -99999999 | |
| 24991 ], | |
| 24992 "_cls": "Call.VariantCall", | |
| 24993 "genotype": [ | |
| 24994 0, | |
| 24995 0 | |
| 24996 ], | |
| 24997 "variant": "ref-S91H?var_name=TCG7572CAC&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91H" | |
| 24998 }, | |
| 24999 "katG_W505E-CCA2154597CTC": { | |
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| 25004 "median_depth": 0, | |
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| 25006 "percent_coverage": 0.0, | |
| 25007 "kmer_count": 0 | |
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| 25009 "reference": { | |
| 25010 "median_depth": 18, | |
| 25011 "min_non_zero_depth": 16, | |
| 25012 "percent_coverage": 100.0, | |
| 25013 "kmer_count": 385 | |
| 25014 } | |
| 25015 }, | |
| 25016 "expected_depths": [ | |
| 25017 17.0 | |
| 25018 ], | |
| 25019 "filter": "PASS", | |
| 25020 "conf": 99999996 | |
| 25021 }, | |
| 25022 "genotype_likelihoods": [ | |
| 25023 -2.6809383483544966, | |
| 25024 -99999999, | |
| 25025 -99999999 | |
| 25026 ], | |
| 25027 "_cls": "Call.VariantCall", | |
| 25028 "genotype": [ | |
| 25029 0, | |
| 25030 0 | |
| 25031 ], | |
| 25032 "variant": "ref-W505E?var_name=CCA2154597CTC&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505E" | |
| 25033 }, | |
| 25034 "katG_W505D-CCA2154597GTC": { | |
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| 25044 "reference": { | |
| 25045 "median_depth": 18, | |
| 25046 "min_non_zero_depth": 16, | |
| 25047 "percent_coverage": 100.0, | |
| 25048 "kmer_count": 385 | |
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| 25050 }, | |
| 25051 "expected_depths": [ | |
| 25052 17.0 | |
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| 25055 "conf": 99999996 | |
| 25056 }, | |
| 25057 "genotype_likelihoods": [ | |
| 25058 -2.6809383483544966, | |
| 25059 -99999999, | |
| 25060 -99999999 | |
| 25061 ], | |
| 25062 "_cls": "Call.VariantCall", | |
| 25063 "genotype": [ | |
| 25064 0, | |
| 25065 0 | |
| 25066 ], | |
| 25067 "variant": "ref-W505D?var_name=CCA2154597GTC&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505D" | |
| 25068 }, | |
| 25069 "rpoB_Q429G-CAG761091GGC": { | |
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| 25072 "coverage": { | |
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| 25075 "min_non_zero_depth": 14, | |
| 25076 "percent_coverage": 13.64, | |
| 25077 "kmer_count": 43 | |
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| 25080 "median_depth": 18, | |
| 25081 "min_non_zero_depth": 15, | |
| 25082 "percent_coverage": 100.0, | |
| 25083 "kmer_count": 395 | |
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| 25085 }, | |
| 25086 "expected_depths": [ | |
| 25087 17.0 | |
| 25088 ], | |
| 25089 "filter": "PASS", | |
| 25090 "conf": 99999996 | |
| 25091 }, | |
| 25092 "genotype_likelihoods": [ | |
| 25093 -2.6809383483544966, | |
| 25094 -99999999, | |
| 25095 -99999999 | |
| 25096 ], | |
| 25097 "_cls": "Call.VariantCall", | |
| 25098 "genotype": [ | |
| 25099 0, | |
| 25100 0 | |
| 25101 ], | |
| 25102 "variant": "ref-Q429G?var_name=CAG761091GGC&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429G" | |
| 25103 }, | |
| 25104 "rpoB_S428G-AGC761088GGC": { | |
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| 25109 "median_depth": 0, | |
| 25110 "min_non_zero_depth": 19, | |
| 25111 "percent_coverage": 9.09, | |
| 25112 "kmer_count": 38 | |
| 25113 }, | |
| 25114 "reference": { | |
| 25115 "median_depth": 18, | |
| 25116 "min_non_zero_depth": 14, | |
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| 25118 "kmer_count": 382 | |
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| 25120 }, | |
| 25121 "expected_depths": [ | |
| 25122 17.0 | |
| 25123 ], | |
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| 25125 "conf": 99999996 | |
| 25126 }, | |
| 25127 "genotype_likelihoods": [ | |
| 25128 -2.6809383483544966, | |
| 25129 -99999999, | |
| 25130 -99999999 | |
| 25131 ], | |
| 25132 "_cls": "Call.VariantCall", | |
| 25133 "genotype": [ | |
| 25134 0, | |
| 25135 0 | |
| 25136 ], | |
| 25137 "variant": "ref-S428G?var_name=AGC761088GGC&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428G" | |
| 25138 }, | |
| 25139 "pncA_P54L-CGG2289080GAG": { | |
| 25140 "info": { | |
| 25141 "contamination_depths": [], | |
| 25142 "coverage": { | |
| 25143 "alternate": { | |
| 25144 "median_depth": 0, | |
| 25145 "min_non_zero_depth": 15, | |
| 25146 "percent_coverage": 18.18, | |
| 25147 "kmer_count": 60 | |
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| 25149 "reference": { | |
| 25150 "median_depth": 14, | |
| 25151 "min_non_zero_depth": 13, | |
| 25152 "percent_coverage": 100.0, | |
| 25153 "kmer_count": 315 | |
| 25154 } | |
| 25155 }, | |
| 25156 "expected_depths": [ | |
| 25157 17.0 | |
| 25158 ], | |
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| 25160 "conf": 99999996 | |
| 25161 }, | |
| 25162 "genotype_likelihoods": [ | |
| 25163 -2.8095676992849885, | |
| 25164 -99999999, | |
| 25165 -99999999 | |
| 25166 ], | |
| 25167 "_cls": "Call.VariantCall", | |
| 25168 "genotype": [ | |
| 25169 0, | |
| 25170 0 | |
| 25171 ], | |
| 25172 "variant": "ref-P54L?var_name=CGG2289080GAG&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=P54L" | |
| 25173 }, | |
| 25174 "gid_S136W-TGA4407795CCA": { | |
| 25175 "info": { | |
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| 25180 "min_non_zero_depth": 15, | |
| 25181 "percent_coverage": 4.55, | |
| 25182 "kmer_count": 15 | |
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| 25184 "reference": { | |
| 25185 "median_depth": 15, | |
| 25186 "min_non_zero_depth": 14, | |
| 25187 "percent_coverage": 100.0, | |
| 25188 "kmer_count": 327 | |
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| 25190 }, | |
| 25191 "expected_depths": [ | |
| 25192 17.0 | |
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| 25195 "conf": 99999996 | |
| 25196 }, | |
| 25197 "genotype_likelihoods": [ | |
| 25198 -2.6844045563309873, | |
| 25199 -99999999, | |
| 25200 -99999999 | |
| 25201 ], | |
| 25202 "_cls": "Call.VariantCall", | |
| 25203 "genotype": [ | |
| 25204 0, | |
| 25205 0 | |
| 25206 ], | |
| 25207 "variant": "ref-S136W?var_name=TGA4407795CCA&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136W" | |
| 25208 }, | |
| 25209 "rpoB_R447G-CGC761145GGT": { | |
| 25210 "info": { | |
| 25211 "contamination_depths": [], | |
| 25212 "coverage": { | |
| 25213 "alternate": { | |
| 25214 "median_depth": 0, | |
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| 25216 "percent_coverage": 0.0, | |
| 25217 "kmer_count": 0 | |
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| 25219 "reference": { | |
| 25220 "median_depth": 16, | |
| 25221 "min_non_zero_depth": 14, | |
| 25222 "percent_coverage": 100.0, | |
| 25223 "kmer_count": 358 | |
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| 25225 }, | |
| 25226 "expected_depths": [ | |
| 25227 17.0 | |
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| 25230 "conf": 99999996 | |
| 25231 }, | |
| 25232 "genotype_likelihoods": [ | |
| 25233 -2.62377993451455, | |
| 25234 -99999999, | |
| 25235 -99999999 | |
| 25236 ], | |
| 25237 "_cls": "Call.VariantCall", | |
| 25238 "genotype": [ | |
| 25239 0, | |
| 25240 0 | |
| 25241 ], | |
| 25242 "variant": "ref-R447G?var_name=CGC761145GGT&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447G" | |
| 25243 }, | |
| 25244 "gyrA_H85S-CAC7554AGT": { | |
| 25245 "info": { | |
| 25246 "contamination_depths": [], | |
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| 25248 "alternate": { | |
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| 25251 "percent_coverage": 0.0, | |
| 25252 "kmer_count": 0 | |
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| 25254 "reference": { | |
| 25255 "median_depth": 15, | |
| 25256 "min_non_zero_depth": 13, | |
| 25257 "percent_coverage": 100.0, | |
| 25258 "kmer_count": 343 | |
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| 25260 }, | |
| 25261 "expected_depths": [ | |
| 25262 17.0 | |
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| 25265 "conf": 99999996 | |
| 25266 }, | |
| 25267 "genotype_likelihoods": [ | |
| 25268 -2.6844045563309873, | |
| 25269 -99999999, | |
| 25270 -99999999 | |
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| 25272 "_cls": "Call.VariantCall", | |
| 25273 "genotype": [ | |
| 25274 0, | |
| 25275 0 | |
| 25276 ], | |
| 25277 "variant": "ref-H85S?var_name=CAC7554AGT&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85S" | |
| 25278 }, | |
| 25279 "rpoB_A451N-GCG761157AAC": { | |
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| 25281 "contamination_depths": [], | |
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| 25283 "alternate": { | |
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| 25287 "kmer_count": 0 | |
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| 25289 "reference": { | |
| 25290 "median_depth": 14, | |
| 25291 "min_non_zero_depth": 14, | |
| 25292 "percent_coverage": 100.0, | |
| 25293 "kmer_count": 319 | |
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| 25296 "expected_depths": [ | |
| 25297 17.0 | |
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| 25300 "conf": 99999996 | |
| 25301 }, | |
| 25302 "genotype_likelihoods": [ | |
| 25303 -2.8095676992849885, | |
| 25304 -99999999, | |
| 25305 -99999999 | |
| 25306 ], | |
| 25307 "_cls": "Call.VariantCall", | |
| 25308 "genotype": [ | |
| 25309 0, | |
| 25310 0 | |
| 25311 ], | |
| 25312 "variant": "ref-A451N?var_name=GCG761157AAC&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451N" | |
| 25313 }, | |
| 25314 "pncA_T47A-GGT2289101CGC": { | |
| 25315 "info": { | |
| 25316 "contamination_depths": [], | |
| 25317 "coverage": { | |
| 25318 "alternate": { | |
| 25319 "median_depth": 0, | |
| 25320 "min_non_zero_depth": 15, | |
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| 25322 "kmer_count": 94 | |
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| 25324 "reference": { | |
| 25325 "median_depth": 16, | |
| 25326 "min_non_zero_depth": 14, | |
| 25327 "percent_coverage": 100.0, | |
| 25328 "kmer_count": 340 | |
| 25329 } | |
| 25330 }, | |
| 25331 "expected_depths": [ | |
| 25332 17.0 | |
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| 25335 "conf": 99999996 | |
| 25336 }, | |
| 25337 "genotype_likelihoods": [ | |
| 25338 -2.62377993451455, | |
| 25339 -99999999, | |
| 25340 -99999999 | |
| 25341 ], | |
| 25342 "_cls": "Call.VariantCall", | |
| 25343 "genotype": [ | |
| 25344 0, | |
| 25345 0 | |
| 25346 ], | |
| 25347 "variant": "ref-T47A?var_name=GGT2289101CGC&num_alts=18&ref=NC_000962.3&enum=0&gene=pncA&mut=T47A" | |
| 25348 }, | |
| 25349 "rpoB_N437S-AAC761115TCA": { | |
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| 25351 "contamination_depths": [], | |
| 25352 "coverage": { | |
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| 25355 "min_non_zero_depth": 17, | |
| 25356 "percent_coverage": 22.73, | |
| 25357 "kmer_count": 85 | |
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| 25359 "reference": { | |
| 25360 "median_depth": 18, | |
| 25361 "min_non_zero_depth": 17, | |
| 25362 "percent_coverage": 100.0, | |
| 25363 "kmer_count": 408 | |
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| 25366 "expected_depths": [ | |
| 25367 17.0 | |
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| 25370 "conf": 99999996 | |
| 25371 }, | |
| 25372 "genotype_likelihoods": [ | |
| 25373 -2.6809383483544966, | |
| 25374 -99999999, | |
| 25375 -99999999 | |
| 25376 ], | |
| 25377 "_cls": "Call.VariantCall", | |
| 25378 "genotype": [ | |
| 25379 0, | |
| 25380 0 | |
| 25381 ], | |
| 25382 "variant": "ref-N437S?var_name=AAC761115TCA&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437S" | |
| 25383 }, | |
| 25384 "rpoB_Q436V-CAG761112GTG": { | |
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| 25386 "contamination_depths": [], | |
| 25387 "coverage": { | |
| 25388 "alternate": { | |
| 25389 "median_depth": 0, | |
| 25390 "min_non_zero_depth": 17, | |
| 25391 "percent_coverage": 27.27, | |
| 25392 "kmer_count": 104 | |
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| 25394 "reference": { | |
| 25395 "median_depth": 19, | |
| 25396 "min_non_zero_depth": 17, | |
| 25397 "percent_coverage": 100.0, | |
| 25398 "kmer_count": 413 | |
| 25399 } | |
| 25400 }, | |
| 25401 "expected_depths": [ | |
| 25402 17.0 | |
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| 25404 "filter": "PASS", | |
| 25405 "conf": 99999996 | |
| 25406 }, | |
| 25407 "genotype_likelihoods": [ | |
| 25408 -2.79216398346472, | |
| 25409 -99999999, | |
| 25410 -99999999 | |
| 25411 ], | |
| 25412 "_cls": "Call.VariantCall", | |
| 25413 "genotype": [ | |
| 25414 0, | |
| 25415 0 | |
| 25416 ], | |
| 25417 "variant": "ref-Q436V?var_name=CAG761112GTG&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436V" | |
| 25418 }, | |
| 25419 "pncA_W68R-CCA2289038TCT": { | |
| 25420 "info": { | |
| 25421 "contamination_depths": [], | |
| 25422 "coverage": { | |
| 25423 "alternate": { | |
| 25424 "median_depth": 0, | |
| 25425 "min_non_zero_depth": 11, | |
| 25426 "percent_coverage": 22.73, | |
| 25427 "kmer_count": 55 | |
| 25428 }, | |
| 25429 "reference": { | |
| 25430 "median_depth": 11, | |
| 25431 "min_non_zero_depth": 10, | |
| 25432 "percent_coverage": 100.0, | |
| 25433 "kmer_count": 238 | |
| 25434 } | |
| 25435 }, | |
| 25436 "expected_depths": [ | |
| 25437 17.0 | |
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| 25439 "filter": "PASS", | |
| 25440 "conf": 99999995 | |
| 25441 }, | |
| 25442 "genotype_likelihoods": [ | |
| 25443 -3.620294394588841, | |
| 25444 -99999999, | |
| 25445 -99999999 | |
| 25446 ], | |
| 25447 "_cls": "Call.VariantCall", | |
| 25448 "genotype": [ | |
| 25449 0, | |
| 25450 0 | |
| 25451 ], | |
| 25452 "variant": "ref-W68R?var_name=CCA2289038TCT&num_alts=39&ref=NC_000962.3&enum=0&gene=pncA&mut=W68R" | |
| 25453 }, | |
| 25454 "gid_Q125K-CTG4407828CTT": { | |
| 25455 "info": { | |
| 25456 "contamination_depths": [], | |
| 25457 "coverage": { | |
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| 25460 "min_non_zero_depth": 17, | |
| 25461 "percent_coverage": 4.55, | |
| 25462 "kmer_count": 17 | |
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| 25464 "reference": { | |
| 25465 "median_depth": 13, | |
| 25466 "min_non_zero_depth": 13, | |
| 25467 "percent_coverage": 100.0, | |
| 25468 "kmer_count": 313 | |
| 25469 } | |
| 25470 }, | |
| 25471 "expected_depths": [ | |
| 25472 17.0 | |
| 25473 ], | |
| 25474 "filter": "PASS", | |
| 25475 "conf": 99999996 | |
| 25476 }, | |
| 25477 "genotype_likelihoods": [ | |
| 25478 -3.0037237137259485, | |
| 25479 -99999999, | |
| 25480 -99999999 | |
| 25481 ], | |
| 25482 "_cls": "Call.VariantCall", | |
| 25483 "genotype": [ | |
| 25484 0, | |
| 25485 0 | |
| 25486 ], | |
| 25487 "variant": "ref-Q125K?var_name=CTG4407828CTT&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125K" | |
| 25488 }, | |
| 25489 "rpoB_S428D-AGC761088GAT": { | |
| 25490 "info": { | |
| 25491 "contamination_depths": [], | |
| 25492 "coverage": { | |
| 25493 "alternate": { | |
| 25494 "median_depth": 0, | |
| 25495 "min_non_zero_depth": 0, | |
| 25496 "percent_coverage": 0.0, | |
| 25497 "kmer_count": 0 | |
| 25498 }, | |
| 25499 "reference": { | |
| 25500 "median_depth": 18, | |
| 25501 "min_non_zero_depth": 14, | |
| 25502 "percent_coverage": 100.0, | |
| 25503 "kmer_count": 382 | |
| 25504 } | |
| 25505 }, | |
| 25506 "expected_depths": [ | |
| 25507 17.0 | |
| 25508 ], | |
| 25509 "filter": "PASS", | |
| 25510 "conf": 99999996 | |
| 25511 }, | |
| 25512 "genotype_likelihoods": [ | |
| 25513 -2.6809383483544966, | |
| 25514 -99999999, | |
| 25515 -99999999 | |
| 25516 ], | |
| 25517 "_cls": "Call.VariantCall", | |
| 25518 "genotype": [ | |
| 25519 0, | |
| 25520 0 | |
| 25521 ], | |
| 25522 "variant": "ref-S428D?var_name=AGC761088GAT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428D" | |
| 25523 }, | |
| 25524 "rpoB_L452R-CTG761160CGA": { | |
| 25525 "info": { | |
| 25526 "contamination_depths": [], | |
| 25527 "coverage": { | |
| 25528 "alternate": { | |
| 25529 "median_depth": 0, | |
| 25530 "min_non_zero_depth": 0, | |
| 25531 "percent_coverage": 0.0, | |
| 25532 "kmer_count": 0 | |
| 25533 }, | |
| 25534 "reference": { | |
| 25535 "median_depth": 14, | |
| 25536 "min_non_zero_depth": 14, | |
| 25537 "percent_coverage": 100.0, | |
| 25538 "kmer_count": 315 | |
| 25539 } | |
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| 25541 "expected_depths": [ | |
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| 25660 0 | |
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| 25727 "_cls": "Call.VariantCall", | |
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| 25730 0 | |
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| 25832 "_cls": "Call.VariantCall", | |
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| 25838 }, | |
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| 25908 }, | |
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| 25937 "_cls": "Call.VariantCall", | |
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| 25943 }, | |
| 25944 "gyrA_S91L-TCG7572CTC": { | |
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| 25975 0 | |
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| 25978 }, | |
| 25979 "rpoB_K446L-AAG761142CTC": { | |
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| 26002 "genotype_likelihoods": [ | |
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| 26004 -99999999, | |
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| 26007 "_cls": "Call.VariantCall", | |
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| 26010 0 | |
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| 26012 "variant": "ref-K446L?var_name=AAG761142CTC&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446L" | |
| 26013 }, | |
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| 26037 "genotype_likelihoods": [ | |
| 26038 -2.6237799345145465, | |
| 26039 -99999999, | |
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| 26042 "_cls": "Call.VariantCall", | |
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| 26044 0, | |
| 26045 0 | |
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| 26047 "variant": "ref-G69D?var_name=ACC4407996ATC&num_alts=55&ref=NC_000962.3&enum=0&gene=gid&mut=G69D" | |
| 26048 }, | |
| 26049 "rpoB_S431V-AGC761097GTA": { | |
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| 26072 "genotype_likelihoods": [ | |
| 26073 -2.79216398346472, | |
| 26074 -99999999, | |
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| 26077 "_cls": "Call.VariantCall", | |
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| 26080 0 | |
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| 26082 "variant": "ref-S431V?var_name=AGC761097GTA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431V" | |
| 26083 }, | |
| 26084 "gyrA_D94G-GAC7581GGT": { | |
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| 26106 }, | |
| 26107 "genotype_likelihoods": [ | |
| 26108 -2.79216398346472, | |
| 26109 -99999999, | |
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| 26112 "_cls": "Call.VariantCall", | |
| 26113 "genotype": [ | |
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| 26115 0 | |
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| 26117 "variant": "ref-D94G?var_name=GAC7581GGT&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94G" | |
| 26118 }, | |
| 26119 "gid_A80P-CGC4407963TGG": { | |
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| 28452 "genotype_likelihoods": [ | |
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| 28487 "genotype_likelihoods": [ | |
| 28488 -2.6809383483544966, | |
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| 28492 "_cls": "Call.VariantCall", | |
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| 28497 "variant": "ref-N438R?var_name=AAC761118CGC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438R" | |
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| 29102 "kmer_count": 0 | |
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| 29105 "median_depth": 15, | |
| 29106 "min_non_zero_depth": 14, | |
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| 29108 "kmer_count": 327 | |
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| 29110 }, | |
| 29111 "expected_depths": [ | |
| 29112 17.0 | |
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| 29116 }, | |
| 29117 "genotype_likelihoods": [ | |
| 29118 -2.6844045563309873, | |
| 29119 -99999999, | |
| 29120 -99999999 | |
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| 29122 "_cls": "Call.VariantCall", | |
| 29123 "genotype": [ | |
| 29124 0, | |
| 29125 0 | |
| 29126 ], | |
| 29127 "variant": "ref-S136P?var_name=TGA4407795GGG&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136P" | |
| 29128 }, | |
| 29129 "gyrA_D89E-GAC7566GAA": { | |
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| 29135 "min_non_zero_depth": 16, | |
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| 29137 "kmer_count": 16 | |
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| 29141 "min_non_zero_depth": 16, | |
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| 29143 "kmer_count": 400 | |
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| 29145 }, | |
| 29146 "expected_depths": [ | |
| 29147 17.0 | |
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| 29151 }, | |
| 29152 "genotype_likelihoods": [ | |
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| 29154 -99999999, | |
| 29155 -99999999 | |
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| 29157 "_cls": "Call.VariantCall", | |
| 29158 "genotype": [ | |
| 29159 0, | |
| 29160 0 | |
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| 29162 "variant": "ref-D89E?var_name=GAC7566GAA&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89E" | |
| 29163 }, | |
| 29164 "rpoB_G426K-GGC761082AAG": { | |
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| 29172 "kmer_count": 18 | |
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| 29176 "min_non_zero_depth": 14, | |
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| 29178 "kmer_count": 373 | |
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| 29180 }, | |
| 29181 "expected_depths": [ | |
| 29182 17.0 | |
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| 29185 "conf": 0 | |
| 29186 }, | |
| 29187 "genotype_likelihoods": [ | |
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| 29189 -99999999, | |
| 29190 -99999999 | |
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| 29192 "_cls": "Call.VariantCall", | |
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| 29194 0, | |
| 29195 0 | |
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| 29197 "variant": "ref-G426K?var_name=GGC761082AAG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426K" | |
| 29198 }, | |
| 29199 "pncA_Q10R-CTG2289212CCT": { | |
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| 29211 "min_non_zero_depth": 14, | |
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| 29213 "kmer_count": 333 | |
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| 29215 }, | |
| 29216 "expected_depths": [ | |
| 29217 17.0 | |
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| 29221 }, | |
| 29222 "genotype_likelihoods": [ | |
| 29223 -2.6844045563309873, | |
| 29224 -99999999, | |
| 29225 -99999999 | |
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| 29227 "_cls": "Call.VariantCall", | |
| 29228 "genotype": [ | |
| 29229 0, | |
| 29230 0 | |
| 29231 ], | |
| 29232 "variant": "ref-Q10R?var_name=CTG2289212CCT&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10R" | |
| 29233 }, | |
| 29234 "gyrA_H85F-CAC7554TTT": { | |
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| 29246 "min_non_zero_depth": 13, | |
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| 29251 "expected_depths": [ | |
| 29252 17.0 | |
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| 29256 }, | |
| 29257 "genotype_likelihoods": [ | |
| 29258 -2.6844045563309873, | |
| 29259 -99999999, | |
| 29260 -99999999 | |
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| 29262 "_cls": "Call.VariantCall", | |
| 29263 "genotype": [ | |
| 29264 0, | |
| 29265 0 | |
| 29266 ], | |
| 29267 "variant": "ref-H85F?var_name=CAC7554TTT&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85F" | |
| 29268 }, | |
| 29269 "rpoB_T444C-ACC761136TGC": { | |
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| 29275 "min_non_zero_depth": 16, | |
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| 29281 "min_non_zero_depth": 16, | |
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| 29283 "kmer_count": 380 | |
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| 29286 "expected_depths": [ | |
| 29287 17.0 | |
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| 29291 }, | |
| 29292 "genotype_likelihoods": [ | |
| 29293 -2.6237799345145465, | |
| 29294 -99999999, | |
| 29295 -99999999 | |
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| 29297 "_cls": "Call.VariantCall", | |
| 29298 "genotype": [ | |
| 29299 0, | |
| 29300 0 | |
| 29301 ], | |
| 29302 "variant": "ref-T444C?var_name=ACC761136TGC&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444C" | |
| 29303 }, | |
| 29304 "rpoB_F425D-TTC761079GAT": { | |
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| 29309 "median_depth": 0, | |
| 29310 "min_non_zero_depth": 16, | |
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| 29312 "kmer_count": 48 | |
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| 29316 "min_non_zero_depth": 14, | |
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| 29318 "kmer_count": 344 | |
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| 29321 "expected_depths": [ | |
| 29322 17.0 | |
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| 29327 "genotype_likelihoods": [ | |
| 29328 -2.6844045563309873, | |
| 29329 -99999999, | |
| 29330 -99999999 | |
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| 29332 "_cls": "Call.VariantCall", | |
| 29333 "genotype": [ | |
| 29334 0, | |
| 29335 0 | |
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| 29337 "variant": "ref-F425D?var_name=TTC761079GAT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425D" | |
| 29338 }, | |
| 29339 "rpoB_L440R-CTG761124AGA": { | |
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| 29345 "min_non_zero_depth": 18, | |
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| 29347 "kmer_count": 54 | |
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| 29351 "min_non_zero_depth": 17, | |
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| 29353 "kmer_count": 385 | |
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| 29356 "expected_depths": [ | |
| 29357 17.0 | |
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| 29362 "genotype_likelihoods": [ | |
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| 29368 "genotype": [ | |
| 29369 0, | |
| 29370 0 | |
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| 29372 "variant": "ref-L440R?var_name=CTG761124AGA&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440R" | |
| 29373 }, | |
| 29374 "pncA_G162D-ACC2288756ATC": { | |
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| 29380 "min_non_zero_depth": 17, | |
| 29381 "percent_coverage": 4.55, | |
| 29382 "kmer_count": 17 | |
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| 29384 "reference": { | |
| 29385 "median_depth": 18, | |
| 29386 "min_non_zero_depth": 16, | |
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| 29388 "kmer_count": 388 | |
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| 29391 "expected_depths": [ | |
| 29392 17.0 | |
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| 29397 "genotype_likelihoods": [ | |
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| 29402 "_cls": "Call.VariantCall", | |
| 29403 "genotype": [ | |
| 29404 0, | |
| 29405 0 | |
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| 29407 "variant": "ref-G162D?var_name=ACC2288756ATC&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=G162D" | |
| 29408 }, | |
| 29409 "rpoB_A451W-GCG761157TGG": { | |
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| 29415 "min_non_zero_depth": 15, | |
| 29416 "percent_coverage": 4.55, | |
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| 29419 "reference": { | |
| 29420 "median_depth": 14, | |
| 29421 "min_non_zero_depth": 14, | |
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| 29427 17.0 | |
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| 29432 "genotype_likelihoods": [ | |
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| 29437 "_cls": "Call.VariantCall", | |
| 29438 "genotype": [ | |
| 29439 0, | |
| 29440 0 | |
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| 29442 "variant": "ref-A451W?var_name=GCG761157TGG&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451W" | |
| 29443 }, | |
| 29444 "gyrA_Y93S-TAC7578AGT": { | |
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| 29455 "median_depth": 19, | |
| 29456 "min_non_zero_depth": 17, | |
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| 29458 "kmer_count": 412 | |
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| 29461 "expected_depths": [ | |
| 29462 17.0 | |
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| 29467 "genotype_likelihoods": [ | |
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| 29472 "_cls": "Call.VariantCall", | |
| 29473 "genotype": [ | |
| 29474 0, | |
| 29475 0 | |
| 29476 ], | |
| 29477 "variant": "ref-Y93S?var_name=TAC7578AGT&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93S" | |
| 29478 }, | |
| 29479 "rpoB_T444K-ACC761136AAA": { | |
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| 29491 "min_non_zero_depth": 16, | |
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| 29496 "expected_depths": [ | |
| 29497 17.0 | |
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| 29502 "genotype_likelihoods": [ | |
| 29503 -2.6237799345145465, | |
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| 29507 "_cls": "Call.VariantCall", | |
| 29508 "genotype": [ | |
| 29509 0, | |
| 29510 0 | |
| 29511 ], | |
| 29512 "variant": "ref-T444K?var_name=ACC761136AAA&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444K" | |
| 29513 }, | |
| 29514 "gyrA_P86A-CCG7557GCT": { | |
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| 29528 "kmer_count": 359 | |
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| 29532 17.0 | |
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| 29537 "genotype_likelihoods": [ | |
| 29538 -2.62377993451455, | |
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| 29542 "_cls": "Call.VariantCall", | |
| 29543 "genotype": [ | |
| 29544 0, | |
| 29545 0 | |
| 29546 ], | |
| 29547 "variant": "ref-P86A?var_name=CCG7557GCT&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86A" | |
| 29548 }, | |
| 29549 "rpoB_H445E-CAC761139GAG": { | |
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| 29572 "genotype_likelihoods": [ | |
| 29573 -2.6237799345145465, | |
| 29574 -99999999, | |
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| 29577 "_cls": "Call.VariantCall", | |
| 29578 "genotype": [ | |
| 29579 0, | |
| 29580 0 | |
| 29581 ], | |
| 29582 "variant": "ref-H445E?var_name=CAC761139GAG&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445E" | |
| 29583 }, | |
| 29584 "gyrA_I92F-ATC7575TTC": { | |
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| 29590 "min_non_zero_depth": 18, | |
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| 29601 "expected_depths": [ | |
| 29602 17.0 | |
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| 29607 "genotype_likelihoods": [ | |
| 29608 -2.79216398346472, | |
| 29609 -99999999, | |
| 29610 -99999999 | |
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| 29612 "_cls": "Call.VariantCall", | |
| 29613 "genotype": [ | |
| 29614 0, | |
| 29615 0 | |
| 29616 ], | |
| 29617 "variant": "ref-I92F?var_name=ATC7575TTC&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92F" | |
| 29618 }, | |
| 29619 "rpoB_L430N-CTG761094AAT": { | |
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| 29623 "alternate": { | |
| 29624 "median_depth": 0, | |
| 29625 "min_non_zero_depth": 20, | |
| 29626 "percent_coverage": 22.73, | |
| 29627 "kmer_count": 100 | |
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| 29629 "reference": { | |
| 29630 "median_depth": 18, | |
| 29631 "min_non_zero_depth": 17, | |
| 29632 "percent_coverage": 100.0, | |
| 29633 "kmer_count": 404 | |
| 29634 } | |
| 29635 }, | |
| 29636 "expected_depths": [ | |
| 29637 17.0 | |
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| 29641 }, | |
| 29642 "genotype_likelihoods": [ | |
| 29643 -2.6809383483544966, | |
| 29644 -99999999, | |
| 29645 -99999999 | |
| 29646 ], | |
| 29647 "_cls": "Call.VariantCall", | |
| 29648 "genotype": [ | |
| 29649 0, | |
| 29650 0 | |
| 29651 ], | |
| 29652 "variant": "ref-L430N?var_name=CTG761094AAT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430N" | |
| 29653 }, | |
| 29654 "gyrA_D89I-GAC7566ATA": { | |
| 29655 "info": { | |
| 29656 "contamination_depths": [], | |
| 29657 "coverage": { | |
| 29658 "alternate": { | |
| 29659 "median_depth": 0, | |
| 29660 "min_non_zero_depth": 0, | |
| 29661 "percent_coverage": 0.0, | |
| 29662 "kmer_count": 0 | |
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| 29664 "reference": { | |
| 29665 "median_depth": 18, | |
| 29666 "min_non_zero_depth": 16, | |
| 29667 "percent_coverage": 100.0, | |
| 29668 "kmer_count": 400 | |
| 29669 } | |
| 29670 }, | |
| 29671 "expected_depths": [ | |
| 29672 17.0 | |
| 29673 ], | |
| 29674 "filter": "PASS", | |
| 29675 "conf": 99999996 | |
| 29676 }, | |
| 29677 "genotype_likelihoods": [ | |
| 29678 -2.6809383483544966, | |
| 29679 -99999999, | |
| 29680 -99999999 | |
| 29681 ], | |
| 29682 "_cls": "Call.VariantCall", | |
| 29683 "genotype": [ | |
| 29684 0, | |
| 29685 0 | |
| 29686 ], | |
| 29687 "variant": "ref-D89I?var_name=GAC7566ATA&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89I" | |
| 29688 }, | |
| 29689 "gyrA_P86L-CCG7557CTC": { | |
| 29690 "info": { | |
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| 29702 "percent_coverage": 100.0, | |
| 29703 "kmer_count": 359 | |
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| 29705 }, | |
| 29706 "expected_depths": [ | |
| 29707 17.0 | |
| 29708 ], | |
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| 29710 "conf": 99999996 | |
| 29711 }, | |
| 29712 "genotype_likelihoods": [ | |
| 29713 -2.62377993451455, | |
| 29714 -99999999, | |
| 29715 -99999999 | |
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| 29717 "_cls": "Call.VariantCall", | |
| 29718 "genotype": [ | |
| 29719 0, | |
| 29720 0 | |
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| 29722 "variant": "ref-P86L?var_name=CCG7557CTC&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86L" | |
| 29723 }, | |
| 29724 "rpoB_H445R-CAC761139CGC": { | |
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| 29727 "coverage": { | |
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| 29730 "min_non_zero_depth": 15, | |
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| 29736 "min_non_zero_depth": 15, | |
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| 29738 "kmer_count": 377 | |
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| 29740 }, | |
| 29741 "expected_depths": [ | |
| 29742 17.0 | |
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| 29746 }, | |
| 29747 "genotype_likelihoods": [ | |
| 29748 -2.6237799345145465, | |
| 29749 -99999999, | |
| 29750 -99999999 | |
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| 29752 "_cls": "Call.VariantCall", | |
| 29753 "genotype": [ | |
| 29754 0, | |
| 29755 0 | |
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| 29757 "variant": "ref-H445R?var_name=CAC761139CGC&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445R" | |
| 29758 }, | |
| 29759 "rpoB_A451I-GCG761157ATT": { | |
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| 29771 "min_non_zero_depth": 14, | |
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| 29773 "kmer_count": 319 | |
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| 29775 }, | |
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| 29777 17.0 | |
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| 29781 }, | |
| 29782 "genotype_likelihoods": [ | |
| 29783 -2.8095676992849885, | |
| 29784 -99999999, | |
| 29785 -99999999 | |
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| 29787 "_cls": "Call.VariantCall", | |
| 29788 "genotype": [ | |
| 29789 0, | |
| 29790 0 | |
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| 29792 "variant": "ref-A451I?var_name=GCG761157ATT&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451I" | |
| 29793 }, | |
| 29794 "rpoB_N438P-AAC761118CCC": { | |
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| 29800 "min_non_zero_depth": 17, | |
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| 29802 "kmer_count": 103 | |
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| 29806 "min_non_zero_depth": 17, | |
| 29807 "percent_coverage": 100.0, | |
| 29808 "kmer_count": 399 | |
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| 29810 }, | |
| 29811 "expected_depths": [ | |
| 29812 17.0 | |
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| 29816 }, | |
| 29817 "genotype_likelihoods": [ | |
| 29818 -2.6809383483544966, | |
| 29819 -99999999, | |
| 29820 -99999999 | |
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| 29822 "_cls": "Call.VariantCall", | |
| 29823 "genotype": [ | |
| 29824 0, | |
| 29825 0 | |
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| 29827 "variant": "ref-N438P?var_name=AAC761118CCC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438P" | |
| 29828 }, | |
| 29829 "gid_P75L-CGG4407978CAA": { | |
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| 29841 "min_non_zero_depth": 18, | |
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| 29843 "kmer_count": 437 | |
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| 29845 }, | |
| 29846 "expected_depths": [ | |
| 29847 17.0 | |
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| 29851 }, | |
| 29852 "genotype_likelihoods": [ | |
| 29853 -2.9546829129624985, | |
| 29854 -99999999, | |
| 29855 -99999999 | |
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| 29857 "_cls": "Call.VariantCall", | |
| 29858 "genotype": [ | |
| 29859 0, | |
| 29860 0 | |
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| 29862 "variant": "ref-P75L?var_name=CGG4407978CAA&num_alts=29&ref=NC_000962.3&enum=0&gene=gid&mut=P75L" | |
| 29863 }, | |
| 29864 "gid_V65G-GAC4408008CCC": { | |
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| 29872 "kmer_count": 20 | |
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| 29881 "expected_depths": [ | |
| 29882 17.0 | |
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| 29885 "conf": 99999996 | |
| 29886 }, | |
| 29887 "genotype_likelihoods": [ | |
| 29888 -2.6809383483544966, | |
| 29889 -99999999, | |
| 29890 -99999999 | |
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| 29892 "_cls": "Call.VariantCall", | |
| 29893 "genotype": [ | |
| 29894 0, | |
| 29895 0 | |
| 29896 ], | |
| 29897 "variant": "ref-V65G?var_name=GAC4408008CCC&num_alts=26&ref=NC_000962.3&enum=0&gene=gid&mut=V65G" | |
| 29898 }, | |
| 29899 "rpoB_M434H-ATG761106CAC": { | |
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| 29913 "kmer_count": 420 | |
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| 29915 }, | |
| 29916 "expected_depths": [ | |
| 29917 17.0 | |
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| 29921 }, | |
| 29922 "genotype_likelihoods": [ | |
| 29923 -2.79216398346472, | |
| 29924 -99999999, | |
| 29925 -99999999 | |
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| 29927 "_cls": "Call.VariantCall", | |
| 29928 "genotype": [ | |
| 29929 0, | |
| 29930 0 | |
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| 29932 "variant": "ref-M434H?var_name=ATG761106CAC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434H" | |
| 29933 }, | |
| 29934 "rpoB_L440E-CTG761124GAG": { | |
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| 29952 17.0 | |
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| 29956 }, | |
| 29957 "genotype_likelihoods": [ | |
| 29958 -2.6237799345145465, | |
| 29959 -99999999, | |
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| 29962 "_cls": "Call.VariantCall", | |
| 29963 "genotype": [ | |
| 29964 0, | |
| 29965 0 | |
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| 29967 "variant": "ref-L440E?var_name=CTG761124GAG&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440E" | |
| 29968 }, | |
| 29969 "gyrA_S91Y-TCG7572TAC": { | |
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| 29997 "_cls": "Call.VariantCall", | |
| 29998 "genotype": [ | |
| 29999 0, | |
| 30000 0 | |
| 30001 ], | |
| 30002 "variant": "ref-S91Y?var_name=TCG7572TAC&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91Y" | |
| 30003 }, | |
| 30004 "pncA_Y99P-GTA2288945CGG": { | |
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| 30010 "min_non_zero_depth": 16, | |
| 30011 "percent_coverage": 9.09, | |
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| 30027 "genotype_likelihoods": [ | |
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| 30032 "_cls": "Call.VariantCall", | |
| 30033 "genotype": [ | |
| 30034 0, | |
| 30035 0 | |
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| 30037 "variant": "ref-Y99P?var_name=GTA2288945CGG&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99P" | |
| 30038 }, | |
| 30039 "gid_Q125Y-CTG4407828GTA": { | |
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| 30049 "reference": { | |
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| 30057 17.0 | |
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| 30062 "genotype_likelihoods": [ | |
| 30063 -3.0037237137259485, | |
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| 30067 "_cls": "Call.VariantCall", | |
| 30068 "genotype": [ | |
| 30069 0, | |
| 30070 0 | |
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| 30072 "variant": "ref-Q125Y?var_name=CTG4407828GTA&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125Y" | |
| 30073 }, | |
| 30074 "gyrA_D94P-GAC7581CCT": { | |
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| 30086 "min_non_zero_depth": 17, | |
| 30087 "percent_coverage": 100.0, | |
| 30088 "kmer_count": 406 | |
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| 30091 "expected_depths": [ | |
| 30092 17.0 | |
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| 30096 }, | |
| 30097 "genotype_likelihoods": [ | |
| 30098 -2.79216398346472, | |
| 30099 -99999999, | |
| 30100 -99999999 | |
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| 30102 "_cls": "Call.VariantCall", | |
| 30103 "genotype": [ | |
| 30104 0, | |
| 30105 0 | |
| 30106 ], | |
| 30107 "variant": "ref-D94P?var_name=GAC7581CCT&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94P" | |
| 30108 }, | |
| 30109 "rpoB_Q429V-CAG761091GTT": { | |
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| 30115 "min_non_zero_depth": 14, | |
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| 30117 "kmer_count": 43 | |
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| 30121 "min_non_zero_depth": 15, | |
| 30122 "percent_coverage": 100.0, | |
| 30123 "kmer_count": 395 | |
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| 30126 "expected_depths": [ | |
| 30127 17.0 | |
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| 30131 }, | |
| 30132 "genotype_likelihoods": [ | |
| 30133 -2.6809383483544966, | |
| 30134 -99999999, | |
| 30135 -99999999 | |
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| 30137 "_cls": "Call.VariantCall", | |
| 30138 "genotype": [ | |
| 30139 0, | |
| 30140 0 | |
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| 30142 "variant": "ref-Q429V?var_name=CAG761091GTT&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429V" | |
| 30143 }, | |
| 30144 "rpoB_L452Y-CTG761160TAC": { | |
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| 30154 "reference": { | |
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| 30157 "percent_coverage": 100.0, | |
| 30158 "kmer_count": 315 | |
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| 30161 "expected_depths": [ | |
| 30162 17.0 | |
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| 30166 }, | |
| 30167 "genotype_likelihoods": [ | |
| 30168 -2.8095676992849885, | |
| 30169 -99999999, | |
| 30170 -99999999 | |
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| 30172 "_cls": "Call.VariantCall", | |
| 30173 "genotype": [ | |
| 30174 0, | |
| 30175 0 | |
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| 30177 "variant": "ref-L452Y?var_name=CTG761160TAC&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452Y" | |
| 30178 }, | |
| 30179 "rpoB_L440S-CTG761124TCG": { | |
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| 30185 "min_non_zero_depth": 18, | |
| 30186 "percent_coverage": 18.18, | |
| 30187 "kmer_count": 72 | |
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| 30189 "reference": { | |
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| 30191 "min_non_zero_depth": 17, | |
| 30192 "percent_coverage": 100.0, | |
| 30193 "kmer_count": 385 | |
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| 30196 "expected_depths": [ | |
| 30197 17.0 | |
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| 30200 "conf": 99999996 | |
| 30201 }, | |
| 30202 "genotype_likelihoods": [ | |
| 30203 -2.6237799345145465, | |
| 30204 -99999999, | |
| 30205 -99999999 | |
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| 30207 "_cls": "Call.VariantCall", | |
| 30208 "genotype": [ | |
| 30209 0, | |
| 30210 0 | |
| 30211 ], | |
| 30212 "variant": "ref-L440S?var_name=CTG761124TCG&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440S" | |
| 30213 }, | |
| 30214 "rpoB_L440P-CTG761124CCA": { | |
| 30215 "info": { | |
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| 30220 "min_non_zero_depth": 18, | |
| 30221 "percent_coverage": 13.64, | |
| 30222 "kmer_count": 54 | |
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| 30224 "reference": { | |
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| 30226 "min_non_zero_depth": 17, | |
| 30227 "percent_coverage": 100.0, | |
| 30228 "kmer_count": 385 | |
| 30229 } | |
| 30230 }, | |
| 30231 "expected_depths": [ | |
| 30232 17.0 | |
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| 30236 }, | |
| 30237 "genotype_likelihoods": [ | |
| 30238 -2.6237799345145465, | |
| 30239 -99999999, | |
| 30240 -99999999 | |
| 30241 ], | |
| 30242 "_cls": "Call.VariantCall", | |
| 30243 "genotype": [ | |
| 30244 0, | |
| 30245 0 | |
| 30246 ], | |
| 30247 "variant": "ref-L440P?var_name=CTG761124CCA&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440P" | |
| 30248 }, | |
| 30249 "rpoB_Q429D-CAG761091GAT": { | |
| 30250 "info": { | |
| 30251 "contamination_depths": [], | |
| 30252 "coverage": { | |
| 30253 "alternate": { | |
| 30254 "median_depth": 0, | |
| 30255 "min_non_zero_depth": 14, | |
| 30256 "percent_coverage": 13.64, | |
| 30257 "kmer_count": 43 | |
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| 30259 "reference": { | |
| 30260 "median_depth": 18, | |
| 30261 "min_non_zero_depth": 15, | |
| 30262 "percent_coverage": 100.0, | |
| 30263 "kmer_count": 395 | |
| 30264 } | |
| 30265 }, | |
| 30266 "expected_depths": [ | |
| 30267 17.0 | |
| 30268 ], | |
| 30269 "filter": "PASS", | |
| 30270 "conf": 99999996 | |
| 30271 }, | |
| 30272 "genotype_likelihoods": [ | |
| 30273 -2.6809383483544966, | |
| 30274 -99999999, | |
| 30275 -99999999 | |
| 30276 ], | |
| 30277 "_cls": "Call.VariantCall", | |
| 30278 "genotype": [ | |
| 30279 0, | |
| 30280 0 | |
| 30281 ], | |
| 30282 "variant": "ref-Q429D?var_name=CAG761091GAT&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429D" | |
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| 30877 "variant": "ref-M306P?var_name=ATG4247429CCC&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306P" | |
| 30878 }, | |
| 30879 "gid_R64W-CCG4408011CCA": { | |
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| 30887 "kmer_count": 18 | |
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| 30891 "min_non_zero_depth": 17, | |
| 30892 "percent_coverage": 100.0, | |
| 30893 "kmer_count": 414 | |
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| 30895 }, | |
| 30896 "expected_depths": [ | |
| 30897 17.0 | |
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| 30900 "conf": 99999996 | |
| 30901 }, | |
| 30902 "genotype_likelihoods": [ | |
| 30903 -2.79216398346472, | |
| 30904 -99999999, | |
| 30905 -99999999 | |
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| 30907 "_cls": "Call.VariantCall", | |
| 30908 "genotype": [ | |
| 30909 0, | |
| 30910 0 | |
| 30911 ], | |
| 30912 "variant": "ref-R64W?var_name=CCG4408011CCA&num_alts=36&ref=NC_000962.3&enum=0&gene=gid&mut=R64W" | |
| 30913 }, | |
| 30914 "rpoB_S431L-AGC761097TTA": { | |
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| 30930 }, | |
| 30931 "expected_depths": [ | |
| 30932 17.0 | |
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| 30936 }, | |
| 30937 "genotype_likelihoods": [ | |
| 30938 -2.79216398346472, | |
| 30939 -99999999, | |
| 30940 -99999999 | |
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| 30942 "_cls": "Call.VariantCall", | |
| 30943 "genotype": [ | |
| 30944 0, | |
| 30945 0 | |
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| 30947 "variant": "ref-S431L?var_name=AGC761097TTA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431L" | |
| 30948 }, | |
| 30949 "gyrA_H87M-CAC7560ATG": { | |
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| 30961 "min_non_zero_depth": 15, | |
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| 30963 "kmer_count": 377 | |
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| 30966 "expected_depths": [ | |
| 30967 17.0 | |
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| 30971 }, | |
| 30972 "genotype_likelihoods": [ | |
| 30973 -2.6809383483544966, | |
| 30974 -99999999, | |
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| 30977 "_cls": "Call.VariantCall", | |
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| 30979 0, | |
| 30980 0 | |
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| 30982 "variant": "ref-H87M?var_name=CAC7560ATG&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87M" | |
| 30983 }, | |
| 30984 "gyrA_G88P-GGC7563CCG": { | |
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| 30996 "min_non_zero_depth": 15, | |
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| 30998 "kmer_count": 370 | |
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| 31000 }, | |
| 31001 "expected_depths": [ | |
| 31002 17.0 | |
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| 31004 "filter": "LOW_GT_CONF", | |
| 31005 "conf": 0 | |
| 31006 }, | |
| 31007 "genotype_likelihoods": [ | |
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| 31009 -99999999, | |
| 31010 -99999999 | |
| 31011 ], | |
| 31012 "_cls": "Call.VariantCall", | |
| 31013 "genotype": [ | |
| 31014 0, | |
| 31015 0 | |
| 31016 ], | |
| 31017 "variant": "ref-G88P?var_name=GGC7563CCG&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88P" | |
| 31018 }, | |
| 31019 "gyrA_P86E-CCG7557GAA": { | |
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| 31036 "expected_depths": [ | |
| 31037 17.0 | |
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| 31041 }, | |
| 31042 "genotype_likelihoods": [ | |
| 31043 -2.62377993451455, | |
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| 31045 -99999999 | |
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| 31047 "_cls": "Call.VariantCall", | |
| 31048 "genotype": [ | |
| 31049 0, | |
| 31050 0 | |
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| 31052 "variant": "ref-P86E?var_name=CCG7557GAA&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86E" | |
| 31053 }, | |
| 31054 "gyrA_Y93L-TAC7578CTA": { | |
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| 31071 "expected_depths": [ | |
| 31072 17.0 | |
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| 31077 "genotype_likelihoods": [ | |
| 31078 -2.79216398346472, | |
| 31079 -99999999, | |
| 31080 -99999999 | |
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| 31082 "_cls": "Call.VariantCall", | |
| 31083 "genotype": [ | |
| 31084 0, | |
| 31085 0 | |
| 31086 ], | |
| 31087 "variant": "ref-Y93L?var_name=TAC7578CTA&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93L" | |
| 31088 }, | |
| 31089 "pncA_V7L-GAC2289221CAG": { | |
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| 31101 "min_non_zero_depth": 14, | |
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| 31111 }, | |
| 31112 "genotype_likelihoods": [ | |
| 31113 -2.6844045563309873, | |
| 31114 -99999999, | |
| 31115 -99999999 | |
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| 31117 "_cls": "Call.VariantCall", | |
| 31118 "genotype": [ | |
| 31119 0, | |
| 31120 0 | |
| 31121 ], | |
| 31122 "variant": "ref-V7L?var_name=GAC2289221CAG&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=V7L" | |
| 31123 }, | |
| 31124 "rpoB_G442S-GGG761130TCT": { | |
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| 31138 "kmer_count": 387 | |
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| 31142 17.0 | |
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| 31147 "genotype_likelihoods": [ | |
| 31148 -2.6809383483544966, | |
| 31149 -99999999, | |
| 31150 -99999999 | |
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| 31152 "_cls": "Call.VariantCall", | |
| 31153 "genotype": [ | |
| 31154 0, | |
| 31155 0 | |
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| 31157 "variant": "ref-G442S?var_name=GGG761130TCT&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442S" | |
| 31158 }, | |
| 31159 "pncA_V139L-CAC2288825TAA": { | |
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| 31182 "genotype_likelihoods": [ | |
| 31183 -2.8095676992849885, | |
| 31184 -99999999, | |
| 31185 -99999999 | |
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| 31188 "genotype": [ | |
| 31189 0, | |
| 31190 0 | |
| 31191 ], | |
| 31192 "variant": "ref-V139L?var_name=CAC2288825TAA&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=V139L" | |
| 31193 }, | |
| 31194 "pncA_H137R-ATG2288831TCG": { | |
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| 31200 "min_non_zero_depth": 16, | |
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| 31206 "min_non_zero_depth": 14, | |
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| 31217 "genotype_likelihoods": [ | |
| 31218 -2.6844045563309873, | |
| 31219 -99999999, | |
| 31220 -99999999 | |
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| 31222 "_cls": "Call.VariantCall", | |
| 31223 "genotype": [ | |
| 31224 0, | |
| 31225 0 | |
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| 31227 "variant": "ref-H137R?var_name=ATG2288831TCG&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=H137R" | |
| 31228 }, | |
| 31229 "rpoB_L452Q-CTG761160CAG": { | |
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| 31234 "median_depth": 0, | |
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| 31241 "min_non_zero_depth": 14, | |
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| 31246 "expected_depths": [ | |
| 31247 17.0 | |
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| 31252 "genotype_likelihoods": [ | |
| 31253 -2.8095676992849885, | |
| 31254 -99999999, | |
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| 31257 "_cls": "Call.VariantCall", | |
| 31258 "genotype": [ | |
| 31259 0, | |
| 31260 0 | |
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| 31262 "variant": "ref-L452Q?var_name=CTG761160CAG&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452Q" | |
| 31263 }, | |
| 31264 "gid_E173V-CTC4407684AAC": { | |
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| 31275 "median_depth": 22, | |
| 31276 "min_non_zero_depth": 21, | |
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| 31282 17.0 | |
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| 31287 "genotype_likelihoods": [ | |
| 31288 -3.423821115931803, | |
| 31289 -99999999, | |
| 31290 -99999999 | |
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| 31292 "_cls": "Call.VariantCall", | |
| 31293 "genotype": [ | |
| 31294 0, | |
| 31295 0 | |
| 31296 ], | |
| 31297 "variant": "ref-E173V?var_name=CTC4407684AAC&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173V" | |
| 31298 }, | |
| 31299 "rpoB_S441G-TCG761127GGT": { | |
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| 31311 "min_non_zero_depth": 17, | |
| 31312 "percent_coverage": 100.0, | |
| 31313 "kmer_count": 384 | |
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| 31317 17.0 | |
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| 31322 "genotype_likelihoods": [ | |
| 31323 -2.6237799345145465, | |
| 31324 -99999999, | |
| 31325 -99999999 | |
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| 31327 "_cls": "Call.VariantCall", | |
| 31328 "genotype": [ | |
| 31329 0, | |
| 31330 0 | |
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| 31332 "variant": "ref-S441G?var_name=TCG761127GGT&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441G" | |
| 31333 }, | |
| 31334 "gyrA_S91P-TCG7572CCT": { | |
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| 31351 "expected_depths": [ | |
| 31352 17.0 | |
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| 31356 }, | |
| 31357 "genotype_likelihoods": [ | |
| 31358 -2.79216398346472, | |
| 31359 -99999999, | |
| 31360 -99999999 | |
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| 31362 "_cls": "Call.VariantCall", | |
| 31363 "genotype": [ | |
| 31364 0, | |
| 31365 0 | |
| 31366 ], | |
| 31367 "variant": "ref-S91P?var_name=TCG7572CCT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91P" | |
| 31368 }, | |
| 31369 "pncA_V180G-GAC2288702GCC": { | |
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| 31377 "kmer_count": 19 | |
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| 31379 "reference": { | |
| 31380 "median_depth": 20, | |
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| 31383 "kmer_count": 444 | |
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| 31386 "expected_depths": [ | |
| 31387 17.0 | |
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| 31391 }, | |
| 31392 "genotype_likelihoods": [ | |
| 31393 -2.9546829129624985, | |
| 31394 -99999999, | |
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| 31397 "_cls": "Call.VariantCall", | |
| 31398 "genotype": [ | |
| 31399 0, | |
| 31400 0 | |
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| 31402 "variant": "ref-V180G?var_name=GAC2288702GCC&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=V180G" | |
| 31403 }, | |
| 31404 "rpoB_Q432A-CAA761100GCT": { | |
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| 31410 "min_non_zero_depth": 17, | |
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| 31412 "kmer_count": 93 | |
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| 31416 "min_non_zero_depth": 17, | |
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| 31418 "kmer_count": 417 | |
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| 31421 "expected_depths": [ | |
| 31422 17.0 | |
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| 31426 }, | |
| 31427 "genotype_likelihoods": [ | |
| 31428 -2.79216398346472, | |
| 31429 -99999999, | |
| 31430 -99999999 | |
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| 31432 "_cls": "Call.VariantCall", | |
| 31433 "genotype": [ | |
| 31434 0, | |
| 31435 0 | |
| 31436 ], | |
| 31437 "variant": "ref-Q432A?var_name=CAA761100GCT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432A" | |
| 31438 }, | |
| 31439 "rpoB_N438I-AAC761118ATT": { | |
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| 31444 "median_depth": 0, | |
| 31445 "min_non_zero_depth": 17, | |
| 31446 "percent_coverage": 22.73, | |
| 31447 "kmer_count": 86 | |
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| 31449 "reference": { | |
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| 31451 "min_non_zero_depth": 17, | |
| 31452 "percent_coverage": 100.0, | |
| 31453 "kmer_count": 399 | |
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| 31455 }, | |
| 31456 "expected_depths": [ | |
| 31457 17.0 | |
| 31458 ], | |
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| 31461 }, | |
| 31462 "genotype_likelihoods": [ | |
| 31463 -2.6809383483544966, | |
| 31464 -99999999, | |
| 31465 -99999999 | |
| 31466 ], | |
| 31467 "_cls": "Call.VariantCall", | |
| 31468 "genotype": [ | |
| 31469 0, | |
| 31470 0 | |
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| 31718 }, | |
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| 31789 "gyrA_D94V-GAC7581GTC": { | |
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| 31822 "variant": "ref-D94V?var_name=GAC7581GTC&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94V" | |
| 31823 }, | |
| 31824 "pncA_L4S-CAA2289230CGA": { | |
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| 31857 "variant": "ref-L4S?var_name=CAA2289230CGA&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=L4S" | |
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| 31859 "gid_G30D-ACC4408113GTC": { | |
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| 31882 "genotype_likelihoods": [ | |
| 31883 -7.545943220905956, | |
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| 31892 "variant": "ref-G30D?var_name=ACC4408113GTC&num_alts=57&ref=NC_000962.3&enum=0&gene=gid&mut=G30D" | |
| 31893 }, | |
| 31894 "rpoB_F433P-TTC761103CCC": { | |
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| 31917 "genotype_likelihoods": [ | |
| 31918 -2.79216398346472, | |
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| 31922 "_cls": "Call.VariantCall", | |
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| 31925 0 | |
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| 31927 "variant": "ref-F433P?var_name=TTC761103CCC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=F433P" | |
| 31928 }, | |
| 31929 "rpoB_K446S-AAG761142TCT": { | |
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| 31947 17.0 | |
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| 31952 "genotype_likelihoods": [ | |
| 31953 -2.6237799345145465, | |
| 31954 -99999999, | |
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| 31962 "variant": "ref-K446S?var_name=AAG761142TCT&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446S" | |
| 31963 }, | |
| 31964 "rpoB_G426S-GGC761082TCG": { | |
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| 31976 "min_non_zero_depth": 14, | |
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| 31985 "conf": 0 | |
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| 31987 "genotype_likelihoods": [ | |
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| 31989 -99999999, | |
| 31990 -99999999 | |
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| 31992 "_cls": "Call.VariantCall", | |
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| 31995 0 | |
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| 31997 "variant": "ref-G426S?var_name=GGC761082TCG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426S" | |
| 31998 }, | |
| 31999 "gyrA_P86T-CCG7557ACC": { | |
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| 32016 "expected_depths": [ | |
| 32017 17.0 | |
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| 32020 "conf": 99999996 | |
| 32021 }, | |
| 32022 "genotype_likelihoods": [ | |
| 32023 -2.62377993451455, | |
| 32024 -99999999, | |
| 32025 -99999999 | |
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| 32027 "_cls": "Call.VariantCall", | |
| 32028 "genotype": [ | |
| 32029 0, | |
| 32030 0 | |
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| 32032 "variant": "ref-P86T?var_name=CCG7557ACC&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86T" | |
| 32033 }, | |
| 32034 "rpoB_R448G-CGA761148GGG": { | |
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| 32051 "expected_depths": [ | |
| 32052 17.0 | |
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| 32056 }, | |
| 32057 "genotype_likelihoods": [ | |
| 32058 -2.62377993451455, | |
| 32059 -99999999, | |
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| 32062 "_cls": "Call.VariantCall", | |
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| 32064 0, | |
| 32065 0 | |
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| 32068 }, | |
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| 32086 "expected_depths": [ | |
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| 32099 0, | |
| 32100 0 | |
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| 32103 }, | |
| 32104 "rpoB_N437S-AAC761115TCT": { | |
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| 32134 0, | |
| 32135 0 | |
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| 32137 "variant": "ref-N437S?var_name=AAC761115TCT&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437S" | |
| 32138 }, | |
| 32139 "rpoB_H445P-CAC761139CCG": { | |
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| 32162 "genotype_likelihoods": [ | |
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| 32169 0, | |
| 32170 0 | |
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| 32173 }, | |
| 32174 "rpoB_Q436R-CAG761112CGT": { | |
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| 32191 "expected_depths": [ | |
| 32192 17.0 | |
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| 32197 "genotype_likelihoods": [ | |
| 32198 -2.79216398346472, | |
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| 32202 "_cls": "Call.VariantCall", | |
| 32203 "genotype": [ | |
| 32204 0, | |
| 32205 0 | |
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| 32207 "variant": "ref-Q436R?var_name=CAG761112CGT&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436R" | |
| 32208 }, | |
| 32209 "rpoB_G442I-GGG761130ATC": { | |
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| 32227 17.0 | |
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| 32232 "genotype_likelihoods": [ | |
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| 32239 0, | |
| 32240 0 | |
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| 32242 "variant": "ref-G442I?var_name=GGG761130ATC&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442I" | |
| 32243 }, | |
| 32244 "gid_A138T-CGC4407789GGT": { | |
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| 32267 "genotype_likelihoods": [ | |
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| 32272 "_cls": "Call.VariantCall", | |
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| 32274 0, | |
| 32275 0 | |
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| 32277 "variant": "ref-A138T?var_name=CGC4407789GGT&num_alts=73&ref=NC_000962.3&enum=0&gene=gid&mut=A138T" | |
| 32278 }, | |
| 32279 "gid_Q125D-CTG4407828GTC": { | |
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| 32302 "genotype_likelihoods": [ | |
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| 32307 "_cls": "Call.VariantCall", | |
| 32308 "genotype": [ | |
| 32309 0, | |
| 32310 0 | |
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| 32312 "variant": "ref-Q125D?var_name=CTG4407828GTC&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125D" | |
| 32313 }, | |
| 32314 "gyrA_A90F-GCG7569TTC": { | |
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| 32337 "genotype_likelihoods": [ | |
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| 32344 0, | |
| 32345 0 | |
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| 32347 "variant": "ref-A90F?var_name=GCG7569TTC&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90F" | |
| 32348 }, | |
| 32349 "pncA_I133T-AAT2288843GGT": { | |
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| 32372 "genotype_likelihoods": [ | |
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| 32380 0 | |
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| 32382 "variant": "ref-I133T?var_name=AAT2288843GGT&num_alts=15&ref=NC_000962.3&enum=0&gene=pncA&mut=I133T" | |
| 32383 }, | |
| 32384 "rpoB_S441I-TCG761127ATA": { | |
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| 32407 "genotype_likelihoods": [ | |
| 32408 -2.6237799345145465, | |
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| 32412 "_cls": "Call.VariantCall", | |
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| 32414 0, | |
| 32415 0 | |
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| 32417 "variant": "ref-S441I?var_name=TCG761127ATA&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441I" | |
| 32418 }, | |
| 32419 "rpoB_M434R-ATG761106CGC": { | |
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| 32442 "genotype_likelihoods": [ | |
| 32443 -2.79216398346472, | |
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| 32447 "_cls": "Call.VariantCall", | |
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| 32450 0 | |
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| 32452 "variant": "ref-M434R?var_name=ATG761106CGC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434R" | |
| 32453 }, | |
| 32454 "katG_G182R-CCC2155566TCT": { | |
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| 32477 "genotype_likelihoods": [ | |
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| 32482 "_cls": "Call.VariantCall", | |
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| 32487 "variant": "ref-G182R?var_name=CCC2155566TCT&num_alts=3&ref=NC_000962.3&enum=0&gene=katG&mut=G182R" | |
| 32488 }, | |
| 32489 "rpoB_P439W-CCG761121TGG": { | |
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| 32507 17.0 | |
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| 32512 "genotype_likelihoods": [ | |
| 32513 -2.6237799345145465, | |
| 32514 -99999999, | |
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| 32517 "_cls": "Call.VariantCall", | |
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| 32520 0 | |
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| 32522 "variant": "ref-P439W?var_name=CCG761121TGG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439W" | |
| 32523 }, | |
| 32524 "rpoB_M434L-ATG761106CTG": { | |
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| 32542 17.0 | |
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| 32547 "genotype_likelihoods": [ | |
| 32548 -2.79216398346472, | |
| 32549 -99999999, | |
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| 32552 "_cls": "Call.VariantCall", | |
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| 32557 "variant": "ref-M434L?var_name=ATG761106CTG&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434L" | |
| 32558 }, | |
| 32559 "rpoB_S441R-TCG761127CGA": { | |
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| 32582 "genotype_likelihoods": [ | |
| 32583 -2.6237799345145465, | |
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| 32587 "_cls": "Call.VariantCall", | |
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| 32590 0 | |
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| 32592 "variant": "ref-S441R?var_name=TCG761127CGA&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441R" | |
| 32593 }, | |
| 32594 "rpoB_N437S-AAC761115TCG": { | |
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| 32610 }, | |
| 32611 "expected_depths": [ | |
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| 32617 "genotype_likelihoods": [ | |
| 32618 -2.6809383483544966, | |
| 32619 -99999999, | |
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| 32622 "_cls": "Call.VariantCall", | |
| 32623 "genotype": [ | |
| 32624 0, | |
| 32625 0 | |
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| 32627 "variant": "ref-N437S?var_name=AAC761115TCG&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437S" | |
| 32628 }, | |
| 32629 "katG_W505A-CCA2154597GGC": { | |
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| 32641 "min_non_zero_depth": 16, | |
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| 32644 } | |
| 32645 }, | |
| 32646 "expected_depths": [ | |
| 32647 17.0 | |
| 32648 ], | |
| 32649 "filter": "PASS", | |
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| 33013 }, | |
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| 33048 }, | |
| 33049 "rpoB_H445L-CAC761139TTA": { | |
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| 33077 "_cls": "Call.VariantCall", | |
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| 33083 }, | |
| 33084 "gyrA_S91G-TCG7572GGT": { | |
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| 33115 0 | |
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| 33117 "variant": "ref-S91G?var_name=TCG7572GGT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91G" | |
| 33118 }, | |
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| 33147 "_cls": "Call.VariantCall", | |
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| 33153 }, | |
| 33154 "rpoB_N438V-AAC761118GTT": { | |
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| 33182 "_cls": "Call.VariantCall", | |
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| 33187 "variant": "ref-N438V?var_name=AAC761118GTT&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438V" | |
| 33188 }, | |
| 33189 "rpoB_N438R-AAC761118AGG": { | |
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| 33211 }, | |
| 33212 "genotype_likelihoods": [ | |
| 33213 -2.6809383483544966, | |
| 33214 -99999999, | |
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| 33217 "_cls": "Call.VariantCall", | |
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| 33220 0 | |
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| 33223 }, | |
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| 33246 }, | |
| 33247 "genotype_likelihoods": [ | |
| 33248 -99999999, | |
| 33249 -99999999, | |
| 33250 -99999999 | |
| 33251 ], | |
| 33252 "_cls": "Call.VariantCall", | |
| 33253 "genotype": [ | |
| 33254 0, | |
| 33255 0 | |
| 33256 ], | |
| 33257 "variant": "ref-S450I?var_name=TCG761154ATC&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450I" | |
| 33258 }, | |
| 33259 "rpoB_L443T-TTG761133ACG": { | |
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| 33271 "min_non_zero_depth": 17, | |
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| 33275 }, | |
| 33276 "expected_depths": [ | |
| 33277 17.0 | |
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| 33279 "filter": "LOW_GT_CONF", | |
| 33280 "conf": 0 | |
| 33281 }, | |
| 33282 "genotype_likelihoods": [ | |
| 33283 -99999999, | |
| 33284 -99999999, | |
| 33285 -99999999 | |
| 33286 ], | |
| 33287 "_cls": "Call.VariantCall", | |
| 33288 "genotype": [ | |
| 33289 0, | |
| 33290 0 | |
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| 33292 "variant": "ref-L443T?var_name=TTG761133ACG&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443T" | |
| 33293 }, | |
| 33294 "gyrA_P86I-CCG7557ATT": { | |
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| 33306 "min_non_zero_depth": 13, | |
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| 33308 "kmer_count": 359 | |
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| 33310 }, | |
| 33311 "expected_depths": [ | |
| 33312 17.0 | |
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| 33315 "conf": 99999996 | |
| 33316 }, | |
| 33317 "genotype_likelihoods": [ | |
| 33318 -2.62377993451455, | |
| 33319 -99999999, | |
| 33320 -99999999 | |
| 33321 ], | |
| 33322 "_cls": "Call.VariantCall", | |
| 33323 "genotype": [ | |
| 33324 0, | |
| 33325 0 | |
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| 33327 "variant": "ref-P86I?var_name=CCG7557ATT&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86I" | |
| 33328 }, | |
| 33329 "rpoB_Q432K-CAA761100AAA": { | |
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| 33341 "min_non_zero_depth": 17, | |
| 33342 "percent_coverage": 100.0, | |
| 33343 "kmer_count": 417 | |
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| 33345 }, | |
| 33346 "expected_depths": [ | |
| 33347 17.0 | |
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| 33351 }, | |
| 33352 "genotype_likelihoods": [ | |
| 33353 -2.79216398346472, | |
| 33354 -99999999, | |
| 33355 -99999999 | |
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| 33357 "_cls": "Call.VariantCall", | |
| 33358 "genotype": [ | |
| 33359 0, | |
| 33360 0 | |
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| 33362 "variant": "ref-Q432K?var_name=CAA761100AAA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432K" | |
| 33363 }, | |
| 33364 "rpoB_D435G-GAC761109GGG": { | |
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| 33376 "min_non_zero_depth": 17, | |
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| 33378 "kmer_count": 416 | |
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| 33380 }, | |
| 33381 "expected_depths": [ | |
| 33382 17.0 | |
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| 33386 }, | |
| 33387 "genotype_likelihoods": [ | |
| 33388 -2.79216398346472, | |
| 33389 -99999999, | |
| 33390 -99999999 | |
| 33391 ], | |
| 33392 "_cls": "Call.VariantCall", | |
| 33393 "genotype": [ | |
| 33394 0, | |
| 33395 0 | |
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| 33397 "variant": "ref-D435G?var_name=GAC761109GGG&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435G" | |
| 33398 }, | |
| 33399 "rpoB_G426S-GGC761082TCA": { | |
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| 33405 "min_non_zero_depth": 18, | |
| 33406 "percent_coverage": 4.0, | |
| 33407 "kmer_count": 18 | |
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| 33409 "reference": { | |
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| 33411 "min_non_zero_depth": 14, | |
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| 33413 "kmer_count": 373 | |
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| 33415 }, | |
| 33416 "expected_depths": [ | |
| 33417 17.0 | |
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| 33419 "filter": "LOW_GT_CONF", | |
| 33420 "conf": 0 | |
| 33421 }, | |
| 33422 "genotype_likelihoods": [ | |
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| 33424 -99999999, | |
| 33425 -99999999 | |
| 33426 ], | |
| 33427 "_cls": "Call.VariantCall", | |
| 33428 "genotype": [ | |
| 33429 0, | |
| 33430 0 | |
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| 33432 "variant": "ref-G426S?var_name=GGC761082TCA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426S" | |
| 33433 }, | |
| 33434 "gyrA_D94P-GAC7581CCG": { | |
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| 33448 "kmer_count": 406 | |
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| 33450 }, | |
| 33451 "expected_depths": [ | |
| 33452 17.0 | |
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| 33455 "conf": 99999996 | |
| 33456 }, | |
| 33457 "genotype_likelihoods": [ | |
| 33458 -2.79216398346472, | |
| 33459 -99999999, | |
| 33460 -99999999 | |
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| 33462 "_cls": "Call.VariantCall", | |
| 33463 "genotype": [ | |
| 33464 0, | |
| 33465 0 | |
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| 33467 "variant": "ref-D94P?var_name=GAC7581CCG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94P" | |
| 33468 }, | |
| 33469 "rpoB_R448K-CGA761148AAA": { | |
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| 33481 "min_non_zero_depth": 14, | |
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| 33483 "kmer_count": 346 | |
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| 33485 }, | |
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| 33487 17.0 | |
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| 33491 }, | |
| 33492 "genotype_likelihoods": [ | |
| 33493 -2.62377993451455, | |
| 33494 -99999999, | |
| 33495 -99999999 | |
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| 33497 "_cls": "Call.VariantCall", | |
| 33498 "genotype": [ | |
| 33499 0, | |
| 33500 0 | |
| 33501 ], | |
| 33502 "variant": "ref-R448K?var_name=CGA761148AAA&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448K" | |
| 33503 }, | |
| 33504 "rpoB_T427D-ACC761085GAC": { | |
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| 33507 "coverage": { | |
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| 33510 "min_non_zero_depth": 18, | |
| 33511 "percent_coverage": 4.55, | |
| 33512 "kmer_count": 18 | |
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| 33514 "reference": { | |
| 33515 "median_depth": 17, | |
| 33516 "min_non_zero_depth": 14, | |
| 33517 "percent_coverage": 100.0, | |
| 33518 "kmer_count": 367 | |
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| 33520 }, | |
| 33521 "expected_depths": [ | |
| 33522 17.0 | |
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| 33525 "conf": 99999996 | |
| 33526 }, | |
| 33527 "genotype_likelihoods": [ | |
| 33528 -2.6237799345145465, | |
| 33529 -99999999, | |
| 33530 -99999999 | |
| 33531 ], | |
| 33532 "_cls": "Call.VariantCall", | |
| 33533 "genotype": [ | |
| 33534 0, | |
| 33535 0 | |
| 33536 ], | |
| 33537 "variant": "ref-T427D?var_name=ACC761085GAC&num_alts=32&ref=NC_000962.3&enum=0&gene=rpoB&mut=T427D" | |
| 33538 }, | |
| 33539 "gyrA_D94L-GAC7581TTA": { | |
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| 33547 "kmer_count": 0 | |
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| 33551 "min_non_zero_depth": 17, | |
| 33552 "percent_coverage": 100.0, | |
| 33553 "kmer_count": 406 | |
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| 33555 }, | |
| 33556 "expected_depths": [ | |
| 33557 17.0 | |
| 33558 ], | |
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| 33560 "conf": 99999996 | |
| 33561 }, | |
| 33562 "genotype_likelihoods": [ | |
| 33563 -2.79216398346472, | |
| 33564 -99999999, | |
| 33565 -99999999 | |
| 33566 ], | |
| 33567 "_cls": "Call.VariantCall", | |
| 33568 "genotype": [ | |
| 33569 0, | |
| 33570 0 | |
| 33571 ], | |
| 33572 "variant": "ref-D94L?var_name=GAC7581TTA&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94L" | |
| 33573 }, | |
| 33574 "gyrA_D94A-GAC7581GCG": { | |
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| 33586 "min_non_zero_depth": 17, | |
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| 33588 "kmer_count": 406 | |
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| 33590 }, | |
| 33591 "expected_depths": [ | |
| 33592 17.0 | |
| 33593 ], | |
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| 33595 "conf": 99999996 | |
| 33596 }, | |
| 33597 "genotype_likelihoods": [ | |
| 33598 -2.79216398346472, | |
| 33599 -99999999, | |
| 33600 -99999999 | |
| 33601 ], | |
| 33602 "_cls": "Call.VariantCall", | |
| 33603 "genotype": [ | |
| 33604 0, | |
| 33605 0 | |
| 33606 ], | |
| 33607 "variant": "ref-D94A?var_name=GAC7581GCG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94A" | |
| 33608 }, | |
| 33609 "gyrA_I92V-ATC7575GTT": { | |
| 33610 "info": { | |
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| 33612 "coverage": { | |
| 33613 "alternate": { | |
| 33614 "median_depth": 0, | |
| 33615 "min_non_zero_depth": 0, | |
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| 33617 "kmer_count": 0 | |
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| 33620 "median_depth": 19, | |
| 33621 "min_non_zero_depth": 18, | |
| 33622 "percent_coverage": 100.0, | |
| 33623 "kmer_count": 414 | |
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| 33625 }, | |
| 33626 "expected_depths": [ | |
| 33627 17.0 | |
| 33628 ], | |
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| 33630 "conf": 99999996 | |
| 33631 }, | |
| 33632 "genotype_likelihoods": [ | |
| 33633 -2.79216398346472, | |
| 33634 -99999999, | |
| 33635 -99999999 | |
| 33636 ], | |
| 33637 "_cls": "Call.VariantCall", | |
| 33638 "genotype": [ | |
| 33639 0, | |
| 33640 0 | |
| 33641 ], | |
| 33642 "variant": "ref-I92V?var_name=ATC7575GTT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92V" | |
| 33643 }, | |
| 33644 "rpoB_G426E-GGC761082GAA": { | |
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| 33647 "coverage": { | |
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| 33650 "min_non_zero_depth": 18, | |
| 33651 "percent_coverage": 4.0, | |
| 33652 "kmer_count": 18 | |
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| 33654 "reference": { | |
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| 33656 "min_non_zero_depth": 14, | |
| 33657 "percent_coverage": 92.0, | |
| 33658 "kmer_count": 373 | |
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| 33660 }, | |
| 33661 "expected_depths": [ | |
| 33662 17.0 | |
| 33663 ], | |
| 33664 "filter": "LOW_GT_CONF", | |
| 33665 "conf": 0 | |
| 33666 }, | |
| 33667 "genotype_likelihoods": [ | |
| 33668 -99999999, | |
| 33669 -99999999, | |
| 33670 -99999999 | |
| 33671 ], | |
| 33672 "_cls": "Call.VariantCall", | |
| 33673 "genotype": [ | |
| 33674 0, | |
| 33675 0 | |
| 33676 ], | |
| 33677 "variant": "ref-G426E?var_name=GGC761082GAA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426E" | |
| 33678 }, | |
| 33679 "rpoB_H445S-CAC761139AGC": { | |
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| 33681 "contamination_depths": [], | |
| 33682 "coverage": { | |
| 33683 "alternate": { | |
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| 33685 "min_non_zero_depth": 15, | |
| 33686 "percent_coverage": 4.55, | |
| 33687 "kmer_count": 15 | |
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| 33689 "reference": { | |
| 33690 "median_depth": 17, | |
| 33691 "min_non_zero_depth": 15, | |
| 33692 "percent_coverage": 100.0, | |
| 33693 "kmer_count": 377 | |
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| 33695 }, | |
| 33696 "expected_depths": [ | |
| 33697 17.0 | |
| 33698 ], | |
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| 33700 "conf": 99999996 | |
| 33701 }, | |
| 33702 "genotype_likelihoods": [ | |
| 33703 -2.6237799345145465, | |
| 33704 -99999999, | |
| 33705 -99999999 | |
| 33706 ], | |
| 33707 "_cls": "Call.VariantCall", | |
| 33708 "genotype": [ | |
| 33709 0, | |
| 33710 0 | |
| 33711 ], | |
| 33712 "variant": "ref-H445S?var_name=CAC761139AGC&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445S" | |
| 33713 }, | |
| 33714 "pncA_K96T-CTT2288954GGT": { | |
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| 33717 "coverage": { | |
| 33718 "alternate": { | |
| 33719 "median_depth": 0, | |
| 33720 "min_non_zero_depth": 15, | |
| 33721 "percent_coverage": 9.09, | |
| 33722 "kmer_count": 31 | |
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| 33724 "reference": { | |
| 33725 "median_depth": 16, | |
| 33726 "min_non_zero_depth": 16, | |
| 33727 "percent_coverage": 100.0, | |
| 33728 "kmer_count": 355 | |
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| 33730 }, | |
| 33731 "expected_depths": [ | |
| 33732 17.0 | |
| 33733 ], | |
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| 33735 "conf": 99999996 | |
| 33736 }, | |
| 33737 "genotype_likelihoods": [ | |
| 33738 -2.62377993451455, | |
| 33739 -99999999, | |
| 33740 -99999999 | |
| 33741 ], | |
| 33742 "_cls": "Call.VariantCall", | |
| 33743 "genotype": [ | |
| 33744 0, | |
| 33745 0 | |
| 33746 ], | |
| 33747 "variant": "ref-K96T?var_name=CTT2288954GGT&num_alts=8&ref=NC_000962.3&enum=0&gene=pncA&mut=K96T" | |
| 33748 }, | |
| 33749 "rpoB_G442M-GGG761130ATG": { | |
| 33750 "info": { | |
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| 33752 "coverage": { | |
| 33753 "alternate": { | |
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| 33755 "min_non_zero_depth": 18, | |
| 33756 "percent_coverage": 4.55, | |
| 33757 "kmer_count": 18 | |
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| 33759 "reference": { | |
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| 33761 "min_non_zero_depth": 17, | |
| 33762 "percent_coverage": 100.0, | |
| 33763 "kmer_count": 387 | |
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| 33765 }, | |
| 33766 "expected_depths": [ | |
| 33767 17.0 | |
| 33768 ], | |
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| 33770 "conf": 99999996 | |
| 33771 }, | |
| 33772 "genotype_likelihoods": [ | |
| 33773 -2.6809383483544966, | |
| 33774 -99999999, | |
| 33775 -99999999 | |
| 33776 ], | |
| 33777 "_cls": "Call.VariantCall", | |
| 33778 "genotype": [ | |
| 33779 0, | |
| 33780 0 | |
| 33781 ], | |
| 33782 "variant": "ref-G442M?var_name=GGG761130ATG&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442M" | |
| 33783 }, | |
| 33784 "rpoB_H445R-CAC761139AGG": { | |
| 33785 "info": { | |
| 33786 "contamination_depths": [], | |
| 33787 "coverage": { | |
| 33788 "alternate": { | |
| 33789 "median_depth": 0, | |
| 33790 "min_non_zero_depth": 0, | |
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| 33792 "kmer_count": 0 | |
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| 33794 "reference": { | |
| 33795 "median_depth": 17, | |
| 33796 "min_non_zero_depth": 15, | |
| 33797 "percent_coverage": 100.0, | |
| 33798 "kmer_count": 377 | |
| 33799 } | |
| 33800 }, | |
| 33801 "expected_depths": [ | |
| 33802 17.0 | |
| 33803 ], | |
| 33804 "filter": "PASS", | |
| 33805 "conf": 99999996 | |
| 33806 }, | |
| 33807 "genotype_likelihoods": [ | |
| 33808 -2.6237799345145465, | |
| 33809 -99999999, | |
| 33810 -99999999 | |
| 33811 ], | |
| 33812 "_cls": "Call.VariantCall", | |
| 33813 "genotype": [ | |
| 33814 0, | |
| 33815 0 | |
| 33816 ], | |
| 33817 "variant": "ref-H445R?var_name=CAC761139AGG&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445R" | |
| 33818 }, | |
| 33819 "rpoB_S450E-TCG761154GAG": { | |
| 33820 "info": { | |
| 33821 "contamination_depths": [], | |
| 33822 "coverage": { | |
| 33823 "alternate": { | |
| 33824 "median_depth": 0, | |
| 33825 "min_non_zero_depth": 14, | |
| 33826 "percent_coverage": 4.55, | |
| 33827 "kmer_count": 14 | |
| 33828 }, | |
| 33829 "reference": { | |
| 33830 "median_depth": 0, | |
| 33831 "min_non_zero_depth": 14, | |
| 33832 "percent_coverage": 4.55, | |
| 33833 "kmer_count": 14 | |
| 33834 } | |
| 33835 }, | |
| 33836 "expected_depths": [ | |
| 33837 17.0 | |
| 33838 ], | |
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| 34168 }, | |
| 34169 "embB_M306W-ATG4247429TGG": { | |
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| 34203 }, | |
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| 34227 "genotype_likelihoods": [ | |
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| 34238 }, | |
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| 34274 "rpoB_T427C-ACC761085TGC": { | |
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| 34308 }, | |
| 34309 "rpoB_D435C-GAC761109TGC": { | |
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| 34342 "variant": "ref-D435C?var_name=GAC761109TGC&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435C" | |
| 34343 }, | |
| 34344 "rpoB_Q429R-CAG761091CGC": { | |
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| 34367 "genotype_likelihoods": [ | |
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| 34402 "genotype_likelihoods": [ | |
| 34403 -2.8095676992849885, | |
| 34404 -99999999, | |
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| 34407 "_cls": "Call.VariantCall", | |
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| 34410 0 | |
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| 35026 "expected_depths": [ | |
| 35027 17.0 | |
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| 35032 "genotype_likelihoods": [ | |
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| 35034 -99999999, | |
| 35035 -99999999 | |
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| 35039 0, | |
| 35040 0 | |
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| 35043 }, | |
| 35044 "rpoB_T444H-ACC761136CAT": { | |
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| 35056 "min_non_zero_depth": 16, | |
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| 35061 "expected_depths": [ | |
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| 35067 "genotype_likelihoods": [ | |
| 35068 -2.6237799345145465, | |
| 35069 -99999999, | |
| 35070 -99999999 | |
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| 35072 "_cls": "Call.VariantCall", | |
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| 35074 0, | |
| 35075 0 | |
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| 35077 "variant": "ref-T444H?var_name=ACC761136CAT&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444H" | |
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| 35079 "embB_G406S-GGC4247729TCC": { | |
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| 35096 "expected_depths": [ | |
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| 35102 "genotype_likelihoods": [ | |
| 35103 -2.79216398346472, | |
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| 35107 "_cls": "Call.VariantCall", | |
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| 35109 0, | |
| 35110 0 | |
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| 35112 "variant": "ref-G406S?var_name=GGC4247729TCC&num_alts=2&ref=NC_000962.3&enum=0&gene=embB&mut=G406S" | |
| 35113 }, | |
| 35114 "pncA_L159V-CAG2288765GAC": { | |
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| 35148 }, | |
| 35149 "rpoB_D435G-GAC761109GGT": { | |
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| 35167 17.0 | |
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| 35177 "_cls": "Call.VariantCall", | |
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| 35179 0, | |
| 35180 0 | |
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| 35183 }, | |
| 35184 "rrs_C517G-C1472362G": { | |
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| 35207 "genotype_likelihoods": [ | |
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| 35214 0, | |
| 35215 0 | |
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| 35217 "variant": "ref-C517G?var_name=C1472362G&num_alts=12&ref=NC_000962.3&enum=0&gene=rrs&mut=C517G" | |
| 35218 }, | |
| 35219 "gyrA_D94Y-GAC7581TAT": { | |
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| 35242 "genotype_likelihoods": [ | |
| 35243 -2.79216398346472, | |
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| 35249 0, | |
| 35250 0 | |
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| 35252 "variant": "ref-D94Y?var_name=GAC7581TAT&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94Y" | |
| 35253 }, | |
| 35254 "rpoB_F425G-TTC761079GGT": { | |
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| 35277 "genotype_likelihoods": [ | |
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| 35280 -99999999 | |
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| 35282 "_cls": "Call.VariantCall", | |
| 35283 "genotype": [ | |
| 35284 0, | |
| 35285 0 | |
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| 35287 "variant": "ref-F425G?var_name=TTC761079GGT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425G" | |
| 35288 }, | |
| 35289 "rpoB_M434T-ATG761106ACA": { | |
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| 35307 17.0 | |
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| 35317 "_cls": "Call.VariantCall", | |
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| 35319 0, | |
| 35320 0 | |
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| 35322 "variant": "ref-M434T?var_name=ATG761106ACA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434T" | |
| 35323 }, | |
| 35324 "pncA_V7L-GAC2289221CAA": { | |
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| 35342 17.0 | |
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| 35347 "genotype_likelihoods": [ | |
| 35348 -2.6844045563309873, | |
| 35349 -99999999, | |
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| 35352 "_cls": "Call.VariantCall", | |
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| 35354 0, | |
| 35355 0 | |
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| 35357 "variant": "ref-V7L?var_name=GAC2289221CAA&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=V7L" | |
| 35358 }, | |
| 35359 "gid_S136K-TGA4407795TTT": { | |
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| 35377 17.0 | |
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| 35382 "genotype_likelihoods": [ | |
| 35383 -2.6844045563309873, | |
| 35384 -99999999, | |
| 35385 -99999999 | |
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| 35387 "_cls": "Call.VariantCall", | |
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| 35389 0, | |
| 35390 0 | |
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| 35392 "variant": "ref-S136K?var_name=TGA4407795TTT&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136K" | |
| 35393 }, | |
| 35394 "pncA_Q141L-CTG2288819AAG": { | |
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| 35406 "min_non_zero_depth": 14, | |
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| 35411 "expected_depths": [ | |
| 35412 17.0 | |
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| 35414 "filter": "LOW_GT_CONF", | |
| 35415 "conf": 0 | |
| 35416 }, | |
| 35417 "genotype_likelihoods": [ | |
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| 35419 -99999999, | |
| 35420 -99999999 | |
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| 35422 "_cls": "Call.VariantCall", | |
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| 35424 0, | |
| 35425 0 | |
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| 35427 "variant": "ref-Q141L?var_name=CTG2288819AAG&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141L" | |
| 35428 }, | |
| 35429 "gyrA_I92K-ATC7575AAA": { | |
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| 35447 17.0 | |
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| 35452 "genotype_likelihoods": [ | |
| 35453 -2.79216398346472, | |
| 35454 -99999999, | |
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| 35457 "_cls": "Call.VariantCall", | |
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| 35460 0 | |
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| 35462 "variant": "ref-I92K?var_name=ATC7575AAA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92K" | |
| 35463 }, | |
| 35464 "katG_S315R-GCT2155167GCG": { | |
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| 35482 17.0 | |
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| 35487 "genotype_likelihoods": [ | |
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| 35489 -99999999, | |
| 35490 -99999999 | |
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| 35492 "_cls": "Call.VariantCall", | |
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| 35494 0, | |
| 35495 0 | |
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| 35497 "variant": "ref-S315R?var_name=GCT2155167GCG&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315R" | |
| 35498 }, | |
| 35499 "gyrA_D89L-GAC7566CTC": { | |
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| 35517 17.0 | |
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| 35522 "genotype_likelihoods": [ | |
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| 35524 -99999999, | |
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| 35527 "_cls": "Call.VariantCall", | |
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| 35530 0 | |
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| 35532 "variant": "ref-D89L?var_name=GAC7566CTC&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89L" | |
| 35533 }, | |
| 35534 "gid_E173T-CTC4407684AGT": { | |
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| 35557 "genotype_likelihoods": [ | |
| 35558 -3.423821115931803, | |
| 35559 -99999999, | |
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| 35562 "_cls": "Call.VariantCall", | |
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| 35565 0 | |
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| 35567 "variant": "ref-E173T?var_name=CTC4407684AGT&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173T" | |
| 35568 }, | |
| 35569 "rpoB_S428Y-AGC761088TAC": { | |
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| 35581 "min_non_zero_depth": 14, | |
| 35582 "percent_coverage": 100.0, | |
| 35583 "kmer_count": 382 | |
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| 35586 "expected_depths": [ | |
| 35587 17.0 | |
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| 35591 }, | |
| 35592 "genotype_likelihoods": [ | |
| 35593 -2.6809383483544966, | |
| 35594 -99999999, | |
| 35595 -99999999 | |
| 35596 ], | |
| 35597 "_cls": "Call.VariantCall", | |
| 35598 "genotype": [ | |
| 35599 0, | |
| 35600 0 | |
| 35601 ], | |
| 35602 "variant": "ref-S428Y?var_name=AGC761088TAC&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428Y" | |
| 35603 }, | |
| 35604 "pncA_Q141D-CTG2288819GTC": { | |
| 35605 "info": { | |
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| 35608 "alternate": { | |
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| 38009 -99999999, | |
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| 38019 "embB_M306L-ATG4247429TTG": { | |
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| 38089 "gyrA_H85G-CAC7554GGT": { | |
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| 38120 0 | |
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| 38123 }, | |
| 38124 "rpoB_L443G-TTG761133GGA": { | |
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| 38190 0 | |
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| 38194 "rpoB_I491F-ATC761277TTT": { | |
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| 38228 }, | |
| 38229 "katG_S315L-GCT2155167GAG": { | |
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| 38263 }, | |
| 38264 "katG_P232R-CGG2155416CCT": { | |
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| 38295 0 | |
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| 38297 "variant": "ref-P232R?var_name=CGG2155416CCT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=P232R" | |
| 38298 }, | |
| 38299 "rpoB_S441Q-TCG761127CAG": { | |
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| 38322 "genotype_likelihoods": [ | |
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| 38330 0 | |
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| 38332 "variant": "ref-S441Q?var_name=TCG761127CAG&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441Q" | |
| 38333 }, | |
| 38334 "gid_E173I-CTC4407684TAT": { | |
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| 38357 "genotype_likelihoods": [ | |
| 38358 -3.423821115931803, | |
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| 38365 0 | |
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| 38367 "variant": "ref-E173I?var_name=CTC4407684TAT&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173I" | |
| 38368 }, | |
| 38369 "gyrA_G88S-GGC7563TCC": { | |
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| 38392 "genotype_likelihoods": [ | |
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| 38400 0 | |
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| 38402 "variant": "ref-G88S?var_name=GGC7563TCC&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88S" | |
| 38403 }, | |
| 38404 "rpoB_L452V-CTG761160GTA": { | |
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| 38437 "variant": "ref-L452V?var_name=CTG761160GTA&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452V" | |
| 38438 }, | |
| 38439 "rpoB_A451L-GCG761157CTC": { | |
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| 38463 -2.8095676992849885, | |
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| 38470 0 | |
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| 38472 "variant": "ref-A451L?var_name=GCG761157CTC&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451L" | |
| 38473 }, | |
| 38474 "rpoB_P439G-CCG761121GGG": { | |
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| 38502 "_cls": "Call.VariantCall", | |
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| 38505 0 | |
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| 38507 "variant": "ref-P439G?var_name=CCG761121GGG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439G" | |
| 38508 }, | |
| 38509 "gyrA_D94R-GAC7581CGG": { | |
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| 38526 "expected_depths": [ | |
| 38527 17.0 | |
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| 38531 }, | |
| 38532 "genotype_likelihoods": [ | |
| 38533 -2.79216398346472, | |
| 38534 -99999999, | |
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| 38537 "_cls": "Call.VariantCall", | |
| 38538 "genotype": [ | |
| 38539 0, | |
| 38540 0 | |
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| 38542 "variant": "ref-D94R?var_name=GAC7581CGG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94R" | |
| 38543 }, | |
| 38544 "gid_E173R-CTC4407684CCT": { | |
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| 38552 "kmer_count": 22 | |
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| 38556 "min_non_zero_depth": 21, | |
| 38557 "percent_coverage": 100.0, | |
| 38558 "kmer_count": 484 | |
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| 38561 "expected_depths": [ | |
| 38562 17.0 | |
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| 38566 }, | |
| 38567 "genotype_likelihoods": [ | |
| 38568 -3.423821115931803, | |
| 38569 -99999999, | |
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| 38571 ], | |
| 38572 "_cls": "Call.VariantCall", | |
| 38573 "genotype": [ | |
| 38574 0, | |
| 38575 0 | |
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| 38578 }, | |
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| 38999 "gyrA_G88D-GGC7563GAC": { | |
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| 39034 "gyrA_S91R-TCG7572AGA": { | |
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| 39102 "variant": "ref-S136G?var_name=TGA4407795ACC&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136G" | |
| 39103 }, | |
| 39104 "gyrA_P86L-CCG7557CTA": { | |
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| 39132 "_cls": "Call.VariantCall", | |
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| 39137 "variant": "ref-P86L?var_name=CCG7557CTA&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86L" | |
| 39138 }, | |
| 39139 "rpoB_P439G-CCG761121GGC": { | |
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| 41541 }, | |
| 41542 "genotype_likelihoods": [ | |
| 41543 -2.62377993451455, | |
| 41544 -99999999, | |
| 41545 -99999999 | |
| 41546 ], | |
| 41547 "_cls": "Call.VariantCall", | |
| 41548 "genotype": [ | |
| 41549 0, | |
| 41550 0 | |
| 41551 ], | |
| 41552 "variant": "ref-R448S?var_name=CGA761148AGT&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448S" | |
| 41553 }, | |
| 41554 "rpoB_S441N-TCG761127AAC": { | |
| 41555 "info": { | |
| 41556 "contamination_depths": [], | |
| 41557 "coverage": { | |
| 41558 "alternate": { | |
| 41559 "median_depth": 0, | |
| 41560 "min_non_zero_depth": 0, | |
| 41561 "percent_coverage": 0.0, | |
| 41562 "kmer_count": 0 | |
| 41563 }, | |
| 41564 "reference": { | |
| 41565 "median_depth": 17, | |
| 41566 "min_non_zero_depth": 17, | |
| 41567 "percent_coverage": 100.0, | |
| 41568 "kmer_count": 384 | |
| 41569 } | |
| 41570 }, | |
| 41571 "expected_depths": [ | |
| 41572 17.0 | |
| 41573 ], | |
| 41574 "filter": "PASS", | |
| 41575 "conf": 99999996 | |
| 41576 }, | |
| 41577 "genotype_likelihoods": [ | |
| 41578 -2.6237799345145465, | |
| 41579 -99999999, | |
| 41580 -99999999 | |
| 41581 ], | |
| 41582 "_cls": "Call.VariantCall", | |
| 41583 "genotype": [ | |
| 41584 0, | |
| 41585 0 | |
| 41586 ], | |
| 41587 "variant": "ref-S441N?var_name=TCG761127AAC&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441N" | |
| 41588 }, | |
| 41589 "rpoB_K446L-AAG761142TTG": { | |
| 41590 "info": { | |
| 41591 "contamination_depths": [], | |
| 41592 "coverage": { | |
| 41593 "alternate": { | |
| 41594 "median_depth": 0, | |
| 41595 "min_non_zero_depth": 14, | |
| 41596 "percent_coverage": 4.55, | |
| 41597 "kmer_count": 14 | |
| 41598 }, | |
| 41599 "reference": { | |
| 41600 "median_depth": 17, | |
| 41601 "min_non_zero_depth": 14, | |
| 41602 "percent_coverage": 100.0, | |
| 41603 "kmer_count": 368 | |
| 41604 } | |
| 41605 }, | |
| 41606 "expected_depths": [ | |
| 41607 17.0 | |
| 41608 ], | |
| 41609 "filter": "PASS", | |
| 41610 "conf": 99999996 | |
| 41611 }, | |
| 41612 "genotype_likelihoods": [ | |
| 41613 -2.6237799345145465, | |
| 41614 -99999999, | |
| 41615 -99999999 | |
| 41616 ], | |
| 41617 "_cls": "Call.VariantCall", | |
| 41618 "genotype": [ | |
| 41619 0, | |
| 41620 0 | |
| 41621 ], | |
| 41622 "variant": "ref-K446L?var_name=AAG761142TTG&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446L" | |
| 41623 }, | |
| 41624 "rpoB_Q432D-CAA761100GAT": { | |
| 41625 "info": { | |
| 41626 "contamination_depths": [], | |
| 41627 "coverage": { | |
| 41628 "alternate": { | |
| 41629 "median_depth": 0, | |
| 41630 "min_non_zero_depth": 17, | |
| 41631 "percent_coverage": 22.73, | |
| 41632 "kmer_count": 93 | |
| 41633 }, | |
| 41634 "reference": { | |
| 41635 "median_depth": 19, | |
| 41636 "min_non_zero_depth": 17, | |
| 41637 "percent_coverage": 100.0, | |
| 41638 "kmer_count": 417 | |
| 41639 } | |
| 41640 }, | |
| 41641 "expected_depths": [ | |
| 41642 17.0 | |
| 41643 ], | |
| 41644 "filter": "PASS", | |
| 41645 "conf": 99999996 | |
| 41646 }, | |
| 41647 "genotype_likelihoods": [ | |
| 41648 -2.79216398346472, | |
| 41649 -99999999, | |
| 41650 -99999999 | |
| 41651 ], | |
| 41652 "_cls": "Call.VariantCall", | |
| 41653 "genotype": [ | |
| 41654 0, | |
| 41655 0 | |
| 41656 ], | |
| 41657 "variant": "ref-Q432D?var_name=CAA761100GAT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432D" | |
| 41658 }, | |
| 41659 "rpoB_T444I-ACC761136ATT": { | |
| 41660 "info": { | |
| 41661 "contamination_depths": [], | |
| 41662 "coverage": { | |
| 41663 "alternate": { | |
| 41664 "median_depth": 0, | |
| 41665 "min_non_zero_depth": 0, | |
| 41666 "percent_coverage": 0.0, | |
| 41667 "kmer_count": 0 | |
| 41668 }, | |
| 41669 "reference": { | |
| 41670 "median_depth": 17, | |
| 41671 "min_non_zero_depth": 16, | |
| 41672 "percent_coverage": 100.0, | |
| 41673 "kmer_count": 380 | |
| 41674 } | |
| 41675 }, | |
| 41676 "expected_depths": [ | |
| 41677 17.0 | |
| 41678 ], | |
| 41679 "filter": "PASS", | |
| 41680 "conf": 99999996 | |
| 41681 }, | |
| 41682 "genotype_likelihoods": [ | |
| 41683 -2.6237799345145465, | |
| 41684 -99999999, | |
| 41685 -99999999 | |
| 41686 ], | |
| 41687 "_cls": "Call.VariantCall", | |
| 41688 "genotype": [ | |
| 41689 0, | |
| 41690 0 | |
| 41691 ], | |
| 41692 "variant": "ref-T444I?var_name=ACC761136ATT&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444I" | |
| 41693 }, | |
| 41694 "pncA_Q141R-CTG2288819CCG": { | |
| 41695 "info": { | |
| 41696 "contamination_depths": [], | |
| 41697 "coverage": { | |
| 41698 "alternate": { | |
| 41699 "median_depth": 0, | |
| 41700 "min_non_zero_depth": 14, | |
| 41701 "percent_coverage": 4.55, | |
| 41702 "kmer_count": 14 | |
| 41703 }, | |
| 41704 "reference": { | |
| 41705 "median_depth": 0, | |
| 41706 "min_non_zero_depth": 14, | |
| 41707 "percent_coverage": 4.55, | |
| 41708 "kmer_count": 14 | |
| 41709 } | |
| 41710 }, | |
| 41711 "expected_depths": [ | |
| 41712 17.0 | |
| 41713 ], | |
| 41714 "filter": "LOW_GT_CONF", | |
| 41715 "conf": 0 | |
| 41716 }, | |
| 41717 "genotype_likelihoods": [ | |
| 41718 -99999999, | |
| 41719 -99999999, | |
| 41720 -99999999 | |
| 41721 ], | |
| 41722 "_cls": "Call.VariantCall", | |
| 41723 "genotype": [ | |
| 41724 0, | |
| 41725 0 | |
| 41726 ], | |
| 41727 "variant": "ref-Q141R?var_name=CTG2288819CCG&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141R" | |
| 41728 }, | |
| 41729 "rpoB_D435G-GAC761109GGC": { | |
| 41730 "info": { | |
| 41731 "contamination_depths": [], | |
| 41732 "coverage": { | |
| 41733 "alternate": { | |
| 41734 "median_depth": 0, | |
| 41735 "min_non_zero_depth": 1, | |
| 41736 "percent_coverage": 13.64, | |
| 41737 "kmer_count": 20 | |
| 41738 }, | |
| 41739 "reference": { | |
| 41740 "median_depth": 19, | |
| 41741 "min_non_zero_depth": 17, | |
| 41742 "percent_coverage": 100.0, | |
| 41743 "kmer_count": 416 | |
| 41744 } | |
| 41745 }, | |
| 41746 "expected_depths": [ | |
| 41747 17.0 | |
| 41748 ], | |
| 41749 "filter": "PASS", | |
| 41750 "conf": 99999996 | |
| 41751 }, | |
| 41752 "genotype_likelihoods": [ | |
| 41753 -2.79216398346472, | |
| 41754 -99999999, | |
| 41755 -99999999 | |
| 41756 ], | |
| 41757 "_cls": "Call.VariantCall", | |
| 41758 "genotype": [ | |
| 41759 0, | |
| 41760 0 | |
| 41761 ], | |
| 41762 "variant": "ref-D435G?var_name=GAC761109GGC&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435G" | |
| 41763 }, | |
| 41764 "katG_W505G-CCA2154597TCC": { | |
| 41765 "info": { | |
| 41766 "contamination_depths": [], | |
| 41767 "coverage": { | |
| 41768 "alternate": { | |
| 41769 "median_depth": 0, | |
| 41770 "min_non_zero_depth": 0, | |
| 41771 "percent_coverage": 0.0, | |
| 41772 "kmer_count": 0 | |
| 41773 }, | |
| 41774 "reference": { | |
| 41775 "median_depth": 18, | |
| 41776 "min_non_zero_depth": 16, | |
| 41777 "percent_coverage": 100.0, | |
| 41778 "kmer_count": 385 | |
| 41779 } | |
| 41780 }, | |
| 41781 "expected_depths": [ | |
| 41782 17.0 | |
| 41783 ], | |
| 41784 "filter": "PASS", | |
| 41785 "conf": 99999996 | |
| 41786 }, | |
| 41787 "genotype_likelihoods": [ | |
| 41788 -2.6809383483544966, | |
| 41789 -99999999, | |
| 41790 -99999999 | |
| 41791 ], | |
| 41792 "_cls": "Call.VariantCall", | |
| 41793 "genotype": [ | |
| 41794 0, | |
| 41795 0 | |
| 41796 ], | |
| 41797 "variant": "ref-W505G?var_name=CCA2154597TCC&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505G" | |
| 41798 }, | |
| 41799 "rpoB_K446G-AAG761142GGC": { | |
| 41800 "info": { | |
| 41801 "contamination_depths": [], | |
| 41802 "coverage": { | |
| 41803 "alternate": { | |
| 41804 "median_depth": 0, | |
| 41805 "min_non_zero_depth": 0, | |
| 41806 "percent_coverage": 0.0, | |
| 41807 "kmer_count": 0 | |
| 41808 }, | |
| 41809 "reference": { | |
| 41810 "median_depth": 17, | |
| 41811 "min_non_zero_depth": 14, | |
| 41812 "percent_coverage": 100.0, | |
| 41813 "kmer_count": 368 | |
| 41814 } | |
| 41815 }, | |
| 41816 "expected_depths": [ | |
| 41817 17.0 | |
| 41818 ], | |
| 41819 "filter": "PASS", | |
| 41820 "conf": 99999996 | |
| 41821 }, | |
| 41822 "genotype_likelihoods": [ | |
| 41823 -2.6237799345145465, | |
| 41824 -99999999, | |
| 41825 -99999999 | |
| 41826 ], | |
| 41827 "_cls": "Call.VariantCall", | |
| 41828 "genotype": [ | |
| 41829 0, | |
| 41830 0 | |
| 41831 ], | |
| 41832 "variant": "ref-K446G?var_name=AAG761142GGC&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446G" | |
| 41833 }, | |
| 41834 "gid_S136N-TGA4407795ATT": { | |
| 41835 "info": { | |
| 41836 "contamination_depths": [], | |
| 41837 "coverage": { | |
| 41838 "alternate": { | |
| 41839 "median_depth": 0, | |
| 41840 "min_non_zero_depth": 0, | |
| 41841 "percent_coverage": 0.0, | |
| 41842 "kmer_count": 0 | |
| 41843 }, | |
| 41844 "reference": { | |
| 41845 "median_depth": 15, | |
| 41846 "min_non_zero_depth": 14, | |
| 41847 "percent_coverage": 100.0, | |
| 41848 "kmer_count": 327 | |
| 41849 } | |
| 41850 }, | |
| 41851 "expected_depths": [ | |
| 41852 17.0 | |
| 41853 ], | |
| 41854 "filter": "PASS", | |
| 41855 "conf": 99999996 | |
| 41856 }, | |
| 41857 "genotype_likelihoods": [ | |
| 41858 -2.6844045563309873, | |
| 41859 -99999999, | |
| 41860 -99999999 | |
| 41861 ], | |
| 41862 "_cls": "Call.VariantCall", | |
| 41863 "genotype": [ | |
| 41864 0, | |
| 41865 0 | |
| 41866 ], | |
| 41867 "variant": "ref-S136N?var_name=TGA4407795ATT&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136N" | |
| 41868 }, | |
| 41869 "gyrA_Y93S-TAC7578TCC": { | |
| 41870 "info": { | |
| 41871 "contamination_depths": [], | |
| 41872 "coverage": { | |
| 41873 "alternate": { | |
| 41874 "median_depth": 0, | |
| 41875 "min_non_zero_depth": 17, | |
| 41876 "percent_coverage": 4.55, | |
| 41877 "kmer_count": 17 | |
| 41878 }, | |
| 41879 "reference": { | |
| 41880 "median_depth": 19, | |
| 41881 "min_non_zero_depth": 17, | |
| 41882 "percent_coverage": 100.0, | |
| 41883 "kmer_count": 412 | |
| 41884 } | |
| 41885 }, | |
| 41886 "expected_depths": [ | |
| 41887 17.0 | |
| 41888 ], | |
| 41889 "filter": "PASS", | |
| 41890 "conf": 99999996 | |
| 41891 }, | |
| 41892 "genotype_likelihoods": [ | |
| 41893 -2.79216398346472, | |
| 41894 -99999999, | |
| 41895 -99999999 | |
| 41896 ], | |
| 41897 "_cls": "Call.VariantCall", | |
| 41898 "genotype": [ | |
| 41899 0, | |
| 41900 0 | |
| 41901 ], | |
| 41902 "variant": "ref-Y93S?var_name=TAC7578TCC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93S" | |
| 41903 }, | |
| 41904 "embB_M306S-ATG4247429AGT": { | |
| 41905 "info": { | |
| 41906 "contamination_depths": [], | |
| 41907 "coverage": { | |
| 41908 "alternate": { | |
| 41909 "median_depth": 0, | |
| 41910 "min_non_zero_depth": 0, | |
| 41911 "percent_coverage": 0.0, | |
| 41912 "kmer_count": 0 | |
| 41913 }, | |
| 41914 "reference": { | |
| 41915 "median_depth": 14, | |
| 41916 "min_non_zero_depth": 8, | |
| 41917 "percent_coverage": 100.0, | |
| 41918 "kmer_count": 293 | |
| 41919 } | |
| 41920 }, | |
| 41921 "expected_depths": [ | |
| 41922 17.0 | |
| 41923 ], | |
| 41924 "filter": "PASS", | |
| 41925 "conf": 99999996 | |
| 41926 }, | |
| 41927 "genotype_likelihoods": [ | |
| 41928 -2.8095676992849885, | |
| 41929 -99999999, | |
| 41930 -99999999 | |
| 41931 ], | |
| 41932 "_cls": "Call.VariantCall", | |
| 41933 "genotype": [ | |
| 41934 0, | |
| 41935 0 | |
| 41936 ], | |
| 41937 "variant": "ref-M306S?var_name=ATG4247429AGT&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306S" | |
| 41938 }, | |
| 41939 "rpoB_G442A-GGG761130GCC": { | |
| 41940 "info": { | |
| 41941 "contamination_depths": [], | |
| 41942 "coverage": { | |
| 41943 "alternate": { | |
| 41944 "median_depth": 0, | |
| 41945 "min_non_zero_depth": 17, | |
| 41946 "percent_coverage": 4.55, | |
| 41947 "kmer_count": 17 | |
| 41948 }, | |
| 41949 "reference": { | |
| 41950 "median_depth": 18, | |
| 41951 "min_non_zero_depth": 17, | |
| 41952 "percent_coverage": 100.0, | |
| 41953 "kmer_count": 387 | |
| 41954 } | |
| 41955 }, | |
| 41956 "expected_depths": [ | |
| 41957 17.0 | |
| 41958 ], | |
| 41959 "filter": "PASS", | |
| 41960 "conf": 99999996 | |
| 41961 }, | |
| 41962 "genotype_likelihoods": [ | |
| 41963 -2.6809383483544966, | |
| 41964 -99999999, | |
| 41965 -99999999 | |
| 41966 ], | |
| 41967 "_cls": "Call.VariantCall", | |
| 41968 "genotype": [ | |
| 41969 0, | |
| 41970 0 | |
| 41971 ], | |
| 41972 "variant": "ref-G442A?var_name=GGG761130GCC&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442A" | |
| 41973 }, | |
| 41974 "rrs_C516T-C1472361T": { | |
| 41975 "info": { | |
| 41976 "contamination_depths": [], | |
| 41977 "coverage": { | |
| 41978 "alternate": { | |
| 41979 "median_depth": 0, | |
| 41980 "min_non_zero_depth": 18, | |
| 41981 "percent_coverage": 9.09, | |
| 41982 "kmer_count": 36 | |
| 41983 }, | |
| 41984 "reference": { | |
| 41985 "median_depth": 18, | |
| 41986 "min_non_zero_depth": 17, | |
| 41987 "percent_coverage": 100.0, | |
| 41988 "kmer_count": 425 | |
| 41989 } | |
| 41990 }, | |
| 41991 "expected_depths": [ | |
| 41992 17.0 | |
| 41993 ], | |
| 41994 "filter": "PASS", | |
| 41995 "conf": 99999996 | |
| 41996 }, | |
| 41997 "genotype_likelihoods": [ | |
| 41998 -2.6809383483544966, | |
| 41999 -99999999, | |
| 42000 -99999999 | |
| 42001 ], | |
| 42002 "_cls": "Call.VariantCall", | |
| 42003 "genotype": [ | |
| 42004 0, | |
| 42005 0 | |
| 42006 ], | |
| 42007 "variant": "ref-C516T?var_name=C1472361T&num_alts=12&ref=NC_000962.3&enum=0&gene=rrs&mut=C516T" | |
| 42008 }, | |
| 42009 "rpoB_T444M-ACC761136ATG": { | |
| 42010 "info": { | |
| 42011 "contamination_depths": [], | |
| 42012 "coverage": { | |
| 42013 "alternate": { | |
| 42014 "median_depth": 0, | |
| 42015 "min_non_zero_depth": 0, | |
| 42016 "percent_coverage": 0.0, | |
| 42017 "kmer_count": 0 | |
| 42018 }, | |
| 42019 "reference": { | |
| 42020 "median_depth": 17, | |
| 42021 "min_non_zero_depth": 16, | |
| 42022 "percent_coverage": 100.0, | |
| 42023 "kmer_count": 380 | |
| 42024 } | |
| 42025 }, | |
| 42026 "expected_depths": [ | |
| 42027 17.0 | |
| 42028 ], | |
| 42029 "filter": "PASS", | |
| 42030 "conf": 99999996 | |
| 42031 }, | |
| 42032 "genotype_likelihoods": [ | |
| 42033 -2.6237799345145465, | |
| 42034 -99999999, | |
| 42035 -99999999 | |
| 42036 ], | |
| 42037 "_cls": "Call.VariantCall", | |
| 42038 "genotype": [ | |
| 42039 0, | |
| 42040 0 | |
| 42041 ], | |
| 42042 "variant": "ref-T444M?var_name=ACC761136ATG&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444M" | |
| 42043 }, | |
| 42044 "katG_S315I-GCT2155167GAT": { | |
| 42045 "info": { | |
| 42046 "contamination_depths": [], | |
| 42047 "coverage": { | |
| 42048 "alternate": { | |
| 42049 "median_depth": 0, | |
| 42050 "min_non_zero_depth": 17, | |
| 42051 "percent_coverage": 4.55, | |
| 42052 "kmer_count": 17 | |
| 42053 }, | |
| 42054 "reference": { | |
| 42055 "median_depth": 0, | |
| 42056 "min_non_zero_depth": 17, | |
| 42057 "percent_coverage": 4.55, | |
| 42058 "kmer_count": 17 | |
| 42059 } | |
| 42060 }, | |
| 42061 "expected_depths": [ | |
| 42062 17.0 | |
| 42063 ], | |
| 42064 "filter": "LOW_GT_CONF", | |
| 42065 "conf": 0 | |
| 42066 }, | |
| 42067 "genotype_likelihoods": [ | |
| 42068 -99999999, | |
| 42069 -99999999, | |
| 42070 -99999999 | |
| 42071 ], | |
| 42072 "_cls": "Call.VariantCall", | |
| 42073 "genotype": [ | |
| 42074 0, | |
| 42075 0 | |
| 42076 ], | |
| 42077 "variant": "ref-S315I?var_name=GCT2155167GAT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315I" | |
| 42078 }, | |
| 42079 "pncA_Q10E-CTG2289212TTC": { | |
| 42080 "info": { | |
| 42081 "contamination_depths": [], | |
| 42082 "coverage": { | |
| 42083 "alternate": { | |
| 42084 "median_depth": 0, | |
| 42085 "min_non_zero_depth": 0, | |
| 42086 "percent_coverage": 0.0, | |
| 42087 "kmer_count": 0 | |
| 42088 }, | |
| 42089 "reference": { | |
| 42090 "median_depth": 15, | |
| 42091 "min_non_zero_depth": 14, | |
| 42092 "percent_coverage": 100.0, | |
| 42093 "kmer_count": 333 | |
| 42094 } | |
| 42095 }, | |
| 42096 "expected_depths": [ | |
| 42097 17.0 | |
| 42098 ], | |
| 42099 "filter": "PASS", | |
| 42100 "conf": 99999996 | |
| 42101 }, | |
| 42102 "genotype_likelihoods": [ | |
| 42103 -2.6844045563309873, | |
| 42104 -99999999, | |
| 42105 -99999999 | |
| 42106 ], | |
| 42107 "_cls": "Call.VariantCall", | |
| 42108 "genotype": [ | |
| 42109 0, | |
| 42110 0 | |
| 42111 ], | |
| 42112 "variant": "ref-Q10E?var_name=CTG2289212TTC&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10E" | |
| 42113 }, | |
| 42114 "katG_G125D-GCC2155737GTC": { | |
| 42115 "info": { | |
| 42116 "contamination_depths": [], | |
| 42117 "coverage": { | |
| 42118 "alternate": { | |
| 42119 "median_depth": 0, | |
| 42120 "min_non_zero_depth": 17, | |
| 42121 "percent_coverage": 4.55, | |
| 42122 "kmer_count": 17 | |
| 42123 }, | |
| 42124 "reference": { | |
| 42125 "median_depth": 17, | |
| 42126 "min_non_zero_depth": 14, | |
| 42127 "percent_coverage": 100.0, | |
| 42128 "kmer_count": 346 | |
| 42129 } | |
| 42130 }, | |
| 42131 "expected_depths": [ | |
| 42132 17.0 | |
| 42133 ], | |
| 42134 "filter": "PASS", | |
| 42135 "conf": 99999996 | |
| 42136 }, | |
| 42137 "genotype_likelihoods": [ | |
| 42138 -2.6237799345145465, | |
| 42139 -99999999, | |
| 42140 -99999999 | |
| 42141 ], | |
| 42142 "_cls": "Call.VariantCall", | |
| 42143 "genotype": [ | |
| 42144 0, | |
| 42145 0 | |
| 42146 ], | |
| 42147 "variant": "ref-G125D?var_name=GCC2155737GTC&num_alts=7&ref=NC_000962.3&enum=0&gene=katG&mut=G125D" | |
| 42148 }, | |
| 42149 "pncA_H57D-GTG2289071GTC": { | |
| 42150 "info": { | |
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| 42154 "median_depth": 0, | |
| 42155 "min_non_zero_depth": 14, | |
| 42156 "percent_coverage": 4.55, | |
| 42157 "kmer_count": 14 | |
| 42158 }, | |
| 42159 "reference": { | |
| 42160 "median_depth": 15, | |
| 42161 "min_non_zero_depth": 14, | |
| 42162 "percent_coverage": 100.0, | |
| 42163 "kmer_count": 323 | |
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| 42165 }, | |
| 42166 "expected_depths": [ | |
| 42167 17.0 | |
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| 42169 "filter": "PASS", | |
| 42170 "conf": 99999996 | |
| 42171 }, | |
| 42172 "genotype_likelihoods": [ | |
| 42173 -2.6844045563309873, | |
| 42174 -99999999, | |
| 42175 -99999999 | |
| 42176 ], | |
| 42177 "_cls": "Call.VariantCall", | |
| 42178 "genotype": [ | |
| 42179 0, | |
| 42180 0 | |
| 42181 ], | |
| 42182 "variant": "ref-H57D?var_name=GTG2289071GTC&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=H57D" | |
| 42183 }, | |
| 42184 "rpoB_R448S-CGA761148TCC": { | |
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| 42192 "kmer_count": 0 | |
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| 42194 "reference": { | |
| 42195 "median_depth": 16, | |
| 42196 "min_non_zero_depth": 14, | |
| 42197 "percent_coverage": 100.0, | |
| 42198 "kmer_count": 346 | |
| 42199 } | |
| 42200 }, | |
| 42201 "expected_depths": [ | |
| 42202 17.0 | |
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| 42205 "conf": 99999996 | |
| 42206 }, | |
| 42207 "genotype_likelihoods": [ | |
| 42208 -2.62377993451455, | |
| 42209 -99999999, | |
| 42210 -99999999 | |
| 42211 ], | |
| 42212 "_cls": "Call.VariantCall", | |
| 42213 "genotype": [ | |
| 42214 0, | |
| 42215 0 | |
| 42216 ], | |
| 42217 "variant": "ref-R448S?var_name=CGA761148TCC&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448S" | |
| 42218 }, | |
| 42219 "rpoB_M434S-ATG761106TCG": { | |
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| 42225 "min_non_zero_depth": 17, | |
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| 42227 "kmer_count": 17 | |
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| 42229 "reference": { | |
| 42230 "median_depth": 19, | |
| 42231 "min_non_zero_depth": 17, | |
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| 42233 "kmer_count": 420 | |
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| 42235 }, | |
| 42236 "expected_depths": [ | |
| 42237 17.0 | |
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| 42240 "conf": 99999996 | |
| 42241 }, | |
| 42242 "genotype_likelihoods": [ | |
| 42243 -2.79216398346472, | |
| 42244 -99999999, | |
| 42245 -99999999 | |
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| 42247 "_cls": "Call.VariantCall", | |
| 42248 "genotype": [ | |
| 42249 0, | |
| 42250 0 | |
| 42251 ], | |
| 42252 "variant": "ref-M434S?var_name=ATG761106TCG&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434S" | |
| 42253 }, | |
| 42254 "rpoB_T676P-ACT761832CCG": { | |
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| 42260 "min_non_zero_depth": 0, | |
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| 42262 "kmer_count": 0 | |
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| 42264 "reference": { | |
| 42265 "median_depth": 16, | |
| 42266 "min_non_zero_depth": 14, | |
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| 42268 "kmer_count": 348 | |
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| 42270 }, | |
| 42271 "expected_depths": [ | |
| 42272 17.0 | |
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| 42275 "conf": 99999996 | |
| 42276 }, | |
| 42277 "genotype_likelihoods": [ | |
| 42278 -2.62377993451455, | |
| 42279 -99999999, | |
| 42280 -99999999 | |
| 42281 ], | |
| 42282 "_cls": "Call.VariantCall", | |
| 42283 "genotype": [ | |
| 42284 0, | |
| 42285 0 | |
| 42286 ], | |
| 42287 "variant": "ref-T676P?var_name=ACT761832CCG&num_alts=3&ref=NC_000962.3&enum=0&gene=rpoB&mut=T676P" | |
| 42288 }, | |
| 42289 "rpoB_S431E-AGC761097GAA": { | |
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| 42295 "min_non_zero_depth": 19, | |
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| 42297 "kmer_count": 98 | |
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| 42301 "min_non_zero_depth": 17, | |
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| 42303 "kmer_count": 411 | |
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| 42305 }, | |
| 42306 "expected_depths": [ | |
| 42307 17.0 | |
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| 42310 "conf": 99999996 | |
| 42311 }, | |
| 42312 "genotype_likelihoods": [ | |
| 42313 -2.79216398346472, | |
| 42314 -99999999, | |
| 42315 -99999999 | |
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| 42317 "_cls": "Call.VariantCall", | |
| 42318 "genotype": [ | |
| 42319 0, | |
| 42320 0 | |
| 42321 ], | |
| 42322 "variant": "ref-S431E?var_name=AGC761097GAA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431E" | |
| 42323 }, | |
| 42324 "rpoB_T676P-ACT761832CCC": { | |
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| 42329 "median_depth": 0, | |
| 42330 "min_non_zero_depth": 0, | |
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| 42332 "kmer_count": 0 | |
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| 42334 "reference": { | |
| 42335 "median_depth": 16, | |
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| 42338 "kmer_count": 348 | |
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| 42340 }, | |
| 42341 "expected_depths": [ | |
| 42342 17.0 | |
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| 42345 "conf": 99999996 | |
| 42346 }, | |
| 42347 "genotype_likelihoods": [ | |
| 42348 -2.62377993451455, | |
| 42349 -99999999, | |
| 42350 -99999999 | |
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| 42352 "_cls": "Call.VariantCall", | |
| 42353 "genotype": [ | |
| 42354 0, | |
| 42355 0 | |
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| 42357 "variant": "ref-T676P?var_name=ACT761832CCC&num_alts=3&ref=NC_000962.3&enum=0&gene=rpoB&mut=T676P" | |
| 42358 }, | |
| 42359 "rpoB_R448T-CGA761148ACA": { | |
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| 42367 "kmer_count": 14 | |
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| 42370 "median_depth": 16, | |
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| 42377 17.0 | |
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| 42381 }, | |
| 42382 "genotype_likelihoods": [ | |
| 42383 -2.62377993451455, | |
| 42384 -99999999, | |
| 42385 -99999999 | |
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| 42387 "_cls": "Call.VariantCall", | |
| 42388 "genotype": [ | |
| 42389 0, | |
| 42390 0 | |
| 42391 ], | |
| 42392 "variant": "ref-R448T?var_name=CGA761148ACA&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448T" | |
| 42393 }, | |
| 42394 "gid_L79S-CAA4407966CGA": { | |
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| 42399 "median_depth": 0, | |
| 42400 "min_non_zero_depth": 20, | |
| 42401 "percent_coverage": 4.55, | |
| 42402 "kmer_count": 20 | |
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| 42404 "reference": { | |
| 42405 "median_depth": 23, | |
| 42406 "min_non_zero_depth": 20, | |
| 42407 "percent_coverage": 100.0, | |
| 42408 "kmer_count": 498 | |
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| 42411 "expected_depths": [ | |
| 42412 17.0 | |
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| 42415 "conf": 99999995 | |
| 42416 }, | |
| 42417 "genotype_likelihoods": [ | |
| 42418 -3.726101987804734, | |
| 42419 -99999999, | |
| 42420 -99999999 | |
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| 42422 "_cls": "Call.VariantCall", | |
| 42423 "genotype": [ | |
| 42424 0, | |
| 42425 0 | |
| 42426 ], | |
| 42427 "variant": "ref-L79S?var_name=CAA4407966CGA&num_alts=34&ref=NC_000962.3&enum=0&gene=gid&mut=L79S" | |
| 42428 }, | |
| 42429 "rpoB_T444Q-ACC761136CAG": { | |
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| 42437 "kmer_count": 0 | |
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| 42439 "reference": { | |
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| 42441 "min_non_zero_depth": 16, | |
| 42442 "percent_coverage": 100.0, | |
| 42443 "kmer_count": 380 | |
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| 42446 "expected_depths": [ | |
| 42447 17.0 | |
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| 42450 "conf": 99999996 | |
| 42451 }, | |
| 42452 "genotype_likelihoods": [ | |
| 42453 -2.6237799345145465, | |
| 42454 -99999999, | |
| 42455 -99999999 | |
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| 42457 "_cls": "Call.VariantCall", | |
| 42458 "genotype": [ | |
| 42459 0, | |
| 42460 0 | |
| 42461 ], | |
| 42462 "variant": "ref-T444Q?var_name=ACC761136CAG&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444Q" | |
| 42463 }, | |
| 42464 "rpoB_S428A-AGC761088GCT": { | |
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| 42474 "reference": { | |
| 42475 "median_depth": 18, | |
| 42476 "min_non_zero_depth": 14, | |
| 42477 "percent_coverage": 100.0, | |
| 42478 "kmer_count": 382 | |
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| 42481 "expected_depths": [ | |
| 42482 17.0 | |
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| 42485 "conf": 99999996 | |
| 42486 }, | |
| 42487 "genotype_likelihoods": [ | |
| 42488 -2.6809383483544966, | |
| 42489 -99999999, | |
| 42490 -99999999 | |
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| 42492 "_cls": "Call.VariantCall", | |
| 42493 "genotype": [ | |
| 42494 0, | |
| 42495 0 | |
| 42496 ], | |
| 42497 "variant": "ref-S428A?var_name=AGC761088GCT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428A" | |
| 42498 }, | |
| 42499 "rpoB_N438T-AAC761118ACC": { | |
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| 42505 "min_non_zero_depth": 17, | |
| 42506 "percent_coverage": 27.27, | |
| 42507 "kmer_count": 103 | |
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| 42509 "reference": { | |
| 42510 "median_depth": 18, | |
| 42511 "min_non_zero_depth": 17, | |
| 42512 "percent_coverage": 100.0, | |
| 42513 "kmer_count": 399 | |
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| 42516 "expected_depths": [ | |
| 42517 17.0 | |
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| 42521 }, | |
| 42522 "genotype_likelihoods": [ | |
| 42523 -2.6809383483544966, | |
| 42524 -99999999, | |
| 42525 -99999999 | |
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| 42527 "_cls": "Call.VariantCall", | |
| 42528 "genotype": [ | |
| 42529 0, | |
| 42530 0 | |
| 42531 ], | |
| 42532 "variant": "ref-N438T?var_name=AAC761118ACC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438T" | |
| 42533 }, | |
| 42534 "rpoB_Q432I-CAA761100ATA": { | |
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| 42540 "min_non_zero_depth": 17, | |
| 42541 "percent_coverage": 27.27, | |
| 42542 "kmer_count": 113 | |
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| 42545 "median_depth": 19, | |
| 42546 "min_non_zero_depth": 17, | |
| 42547 "percent_coverage": 100.0, | |
| 42548 "kmer_count": 417 | |
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| 42551 "expected_depths": [ | |
| 42552 17.0 | |
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| 42555 "conf": 99999996 | |
| 42556 }, | |
| 42557 "genotype_likelihoods": [ | |
| 42558 -2.79216398346472, | |
| 42559 -99999999, | |
| 42560 -99999999 | |
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| 42562 "_cls": "Call.VariantCall", | |
| 42563 "genotype": [ | |
| 42564 0, | |
| 42565 0 | |
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| 42567 "variant": "ref-Q432I?var_name=CAA761100ATA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432I" | |
| 42568 }, | |
| 42569 "gyrA_I92D-ATC7575GAT": { | |
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| 42573 "alternate": { | |
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| 42581 "min_non_zero_depth": 18, | |
| 42582 "percent_coverage": 100.0, | |
| 42583 "kmer_count": 414 | |
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| 42586 "expected_depths": [ | |
| 42587 17.0 | |
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| 42591 }, | |
| 42592 "genotype_likelihoods": [ | |
| 42593 -2.79216398346472, | |
| 42594 -99999999, | |
| 42595 -99999999 | |
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| 42597 "_cls": "Call.VariantCall", | |
| 42598 "genotype": [ | |
| 42599 0, | |
| 42600 0 | |
| 42601 ], | |
| 42602 "variant": "ref-I92D?var_name=ATC7575GAT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92D" | |
| 42603 }, | |
| 42604 "pncA_P54L-CGG2289080AAG": { | |
| 42605 "info": { | |
| 42606 "contamination_depths": [], | |
| 42607 "coverage": { | |
| 42608 "alternate": { | |
| 42609 "median_depth": 0, | |
| 42610 "min_non_zero_depth": 15, | |
| 42611 "percent_coverage": 18.18, | |
| 42612 "kmer_count": 60 | |
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| 42614 "reference": { | |
| 42615 "median_depth": 14, | |
| 42616 "min_non_zero_depth": 13, | |
| 42617 "percent_coverage": 100.0, | |
| 42618 "kmer_count": 315 | |
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| 42621 "expected_depths": [ | |
| 42622 17.0 | |
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| 42627 "genotype_likelihoods": [ | |
| 42628 -2.8095676992849885, | |
| 42629 -99999999, | |
| 42630 -99999999 | |
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| 42632 "_cls": "Call.VariantCall", | |
| 42633 "genotype": [ | |
| 42634 0, | |
| 42635 0 | |
| 42636 ], | |
| 42637 "variant": "ref-P54L?var_name=CGG2289080AAG&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=P54L" | |
| 42638 }, | |
| 42639 "rpoB_N437L-AAC761115TTA": { | |
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| 42641 "contamination_depths": [], | |
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| 42645 "min_non_zero_depth": 17, | |
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| 42647 "kmer_count": 85 | |
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| 42649 "reference": { | |
| 42650 "median_depth": 18, | |
| 42651 "min_non_zero_depth": 17, | |
| 42652 "percent_coverage": 100.0, | |
| 42653 "kmer_count": 408 | |
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| 42656 "expected_depths": [ | |
| 42657 17.0 | |
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| 42660 "conf": 99999996 | |
| 42661 }, | |
| 42662 "genotype_likelihoods": [ | |
| 42663 -2.6809383483544966, | |
| 42664 -99999999, | |
| 42665 -99999999 | |
| 42666 ], | |
| 42667 "_cls": "Call.VariantCall", | |
| 42668 "genotype": [ | |
| 42669 0, | |
| 42670 0 | |
| 42671 ], | |
| 42672 "variant": "ref-N437L?var_name=AAC761115TTA&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437L" | |
| 42673 }, | |
| 42674 "rpoB_M434N-ATG761106AAC": { | |
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| 42682 "kmer_count": 0 | |
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| 42684 "reference": { | |
| 42685 "median_depth": 19, | |
| 42686 "min_non_zero_depth": 17, | |
| 42687 "percent_coverage": 100.0, | |
| 42688 "kmer_count": 420 | |
| 42689 } | |
| 42690 }, | |
| 42691 "expected_depths": [ | |
| 42692 17.0 | |
| 42693 ], | |
| 42694 "filter": "PASS", | |
| 42695 "conf": 99999996 | |
| 42696 }, | |
| 42697 "genotype_likelihoods": [ | |
| 42698 -2.79216398346472, | |
| 42699 -99999999, | |
| 42700 -99999999 | |
| 42701 ], | |
| 42702 "_cls": "Call.VariantCall", | |
| 42703 "genotype": [ | |
| 42704 0, | |
| 42705 0 | |
| 42706 ], | |
| 42707 "variant": "ref-M434N?var_name=ATG761106AAC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434N" | |
| 42708 }, | |
| 42709 "rrs_C1402G-C1473247G": { | |
| 42710 "info": { | |
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| 42713 "alternate": { | |
| 42714 "median_depth": 0, | |
| 42715 "min_non_zero_depth": 17, | |
| 42716 "percent_coverage": 9.09, | |
| 42717 "kmer_count": 34 | |
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| 42719 "reference": { | |
| 42720 "median_depth": 17, | |
| 42721 "min_non_zero_depth": 11, | |
| 42722 "percent_coverage": 100.0, | |
| 42723 "kmer_count": 347 | |
| 42724 } | |
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| 43297 "_cls": "Call.VariantCall", | |
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| 43302 "variant": "ref-D94K?var_name=GAC7581AAA&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94K" | |
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| 43304 "pncA_Y99A-GTA2288945AGC": { | |
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| 43320 }, | |
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| 43475 0 | |
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| 43502 "genotype_likelihoods": [ | |
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| 43537 "genotype_likelihoods": [ | |
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| 43712 "genotype_likelihoods": [ | |
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| 43759 "embB_M306R-ATG4247429AGG": { | |
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| 43929 0, | |
| 43930 0 | |
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| 43933 }, | |
| 43934 "gyrA_Y93L-TAC7578CTT": { | |
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| 44032 "_cls": "Call.VariantCall", | |
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| 44034 0, | |
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| 44037 "variant": "ref-P75R?var_name=CGG4407978ACG&num_alts=29&ref=NC_000962.3&enum=0&gene=gid&mut=P75R" | |
| 44038 }, | |
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| 44070 0 | |
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| 44072 "variant": "ref-D435I?var_name=GAC761109ATT&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435I" | |
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| 44074 "rpoB_S450R-TCG761154AGA": { | |
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| 44100 -99999999 | |
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| 44105 0 | |
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| 44107 "variant": "ref-S450R?var_name=TCG761154AGA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450R" | |
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| 44109 "katG_S315V-GCT2155167AAC": { | |
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| 44135 -99999999 | |
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| 44139 0, | |
| 44140 0 | |
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| 44142 "variant": "ref-S315V?var_name=GCT2155167AAC&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315V" | |
| 44143 }, | |
| 44144 "rpoB_N437I-AAC761115ATC": { | |
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| 44175 0 | |
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| 44177 "variant": "ref-N437I?var_name=AAC761115ATC&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437I" | |
| 44178 }, | |
| 44179 "rpoB_Q432S-CAA761100TCC": { | |
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| 44210 0 | |
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| 44212 "variant": "ref-Q432S?var_name=CAA761100TCC&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432S" | |
| 44213 }, | |
| 44214 "rpoB_R447S-CGC761145AGC": { | |
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| 44245 0 | |
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| 44247 "variant": "ref-R447S?var_name=CGC761145AGC&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447S" | |
| 44248 }, | |
| 44249 "pncA_Y99L-GTA2288945CAG": { | |
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| 44280 0 | |
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| 44282 "variant": "ref-Y99L?var_name=GTA2288945CAG&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99L" | |
| 44283 }, | |
| 44284 "rpoB_T427H-ACC761085CAC": { | |
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| 44307 "genotype_likelihoods": [ | |
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| 44315 0 | |
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| 44317 "variant": "ref-T427H?var_name=ACC761085CAC&num_alts=32&ref=NC_000962.3&enum=0&gene=rpoB&mut=T427H" | |
| 44318 }, | |
| 44319 "embB_M306G-ATG4247429GGC": { | |
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| 44342 "genotype_likelihoods": [ | |
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| 44347 "_cls": "Call.VariantCall", | |
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| 44350 0 | |
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| 44352 "variant": "ref-M306G?var_name=ATG4247429GGC&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306G" | |
| 44353 }, | |
| 44354 "pncA_Y99G-GTA2288945CCC": { | |
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| 44377 "genotype_likelihoods": [ | |
| 44378 -2.62377993451455, | |
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| 44382 "_cls": "Call.VariantCall", | |
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| 44384 0, | |
| 44385 0 | |
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| 44387 "variant": "ref-Y99G?var_name=GTA2288945CCC&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99G" | |
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| 44389 "pncA_Q10A-CTG2289212AGC": { | |
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| 44412 "genotype_likelihoods": [ | |
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| 44418 "genotype": [ | |
| 44419 0, | |
| 44420 0 | |
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| 44422 "variant": "ref-Q10A?var_name=CTG2289212AGC&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10A" | |
| 44423 }, | |
| 44424 "rpoB_L443E-TTG761133GAA": { | |
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| 44447 "genotype_likelihoods": [ | |
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| 44449 -99999999, | |
| 44450 -99999999 | |
| 44451 ], | |
| 44452 "_cls": "Call.VariantCall", | |
| 44453 "genotype": [ | |
| 44454 0, | |
| 44455 0 | |
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| 44457 "variant": "ref-L443E?var_name=TTG761133GAA&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443E" | |
| 44458 }, | |
| 44459 "gyrA_D94S-GAC7581AGT": { | |
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| 44477 17.0 | |
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| 44482 "genotype_likelihoods": [ | |
| 44483 -2.79216398346472, | |
| 44484 -99999999, | |
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| 44487 "_cls": "Call.VariantCall", | |
| 44488 "genotype": [ | |
| 44489 0, | |
| 44490 0 | |
| 44491 ], | |
| 44492 "variant": "ref-D94S?var_name=GAC7581AGT&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94S" | |
| 44493 }, | |
| 44494 "rpoB_D435F-GAC761109TTT": { | |
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| 45700 }, | |
| 45701 "expected_depths": [ | |
| 45702 17.0 | |
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| 45706 }, | |
| 45707 "genotype_likelihoods": [ | |
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| 45709 -99999999, | |
| 45710 -99999999 | |
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| 45712 "_cls": "Call.VariantCall", | |
| 45713 "genotype": [ | |
| 45714 0, | |
| 45715 0 | |
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| 45718 }, | |
| 45719 "rpoB_L452V-CTG761160GTT": { | |
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| 45735 }, | |
| 45736 "expected_depths": [ | |
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| 45742 "genotype_likelihoods": [ | |
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| 45744 -99999999, | |
| 45745 -99999999 | |
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| 45749 0, | |
| 45750 0 | |
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| 45752 "variant": "ref-L452V?var_name=CTG761160GTT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452V" | |
| 45753 }, | |
| 45754 "gyrA_A90V-GCG7569GTC": { | |
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| 45779 -99999999, | |
| 45780 -99999999 | |
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| 45782 "_cls": "Call.VariantCall", | |
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| 45784 0, | |
| 45785 0 | |
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| 45787 "variant": "ref-A90V?var_name=GCG7569GTC&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90V" | |
| 45788 }, | |
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| 45805 }, | |
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| 45814 -99999999, | |
| 45815 -99999999 | |
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| 45819 0, | |
| 45820 0 | |
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| 45822 "variant": "ref-G88F?var_name=GGC7563TTT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88F" | |
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| 45824 "rpoB_A451R-GCG761157AGA": { | |
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| 45854 0, | |
| 45855 0 | |
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| 45857 "variant": "ref-A451R?var_name=GCG761157AGA&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451R" | |
| 45858 }, | |
| 45859 "rpoB_L430T-CTG761094ACT": { | |
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| 45883 -2.6809383483544966, | |
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| 45889 0, | |
| 45890 0 | |
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| 45893 }, | |
| 45894 "rpoB_H445K-CAC761139AAA": { | |
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| 45917 "genotype_likelihoods": [ | |
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| 45924 0, | |
| 45925 0 | |
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| 45927 "variant": "ref-H445K?var_name=CAC761139AAA&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445K" | |
| 45928 }, | |
| 45929 "pncA_V7L-GAC2289221AAG": { | |
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| 45952 "genotype_likelihoods": [ | |
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| 45958 "genotype": [ | |
| 45959 0, | |
| 45960 0 | |
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| 45962 "variant": "ref-V7L?var_name=GAC2289221AAG&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=V7L" | |
| 45963 }, | |
| 45964 "pncA_V139L-CAC2288825AAG": { | |
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| 45992 "_cls": "Call.VariantCall", | |
| 45993 "genotype": [ | |
| 45994 0, | |
| 45995 0 | |
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| 45997 "variant": "ref-V139L?var_name=CAC2288825AAG&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=V139L" | |
| 45998 }, | |
| 45999 "rpoB_Q432T-CAA761100ACT": { | |
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| 46022 "genotype_likelihoods": [ | |
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| 46027 "_cls": "Call.VariantCall", | |
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| 46029 0, | |
| 46030 0 | |
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| 46032 "variant": "ref-Q432T?var_name=CAA761100ACT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432T" | |
| 46033 }, | |
| 46034 "gyrA_S91K-TCG7572AAA": { | |
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| 46052 17.0 | |
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| 46057 "genotype_likelihoods": [ | |
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| 46059 -99999999, | |
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| 46062 "_cls": "Call.VariantCall", | |
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| 46064 0, | |
| 46065 0 | |
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| 46067 "variant": "ref-S91K?var_name=TCG7572AAA&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91K" | |
| 46068 }, | |
| 46069 "gyrA_H87R-CAC7560CGA": { | |
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| 46086 "expected_depths": [ | |
| 46087 17.0 | |
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| 46092 "genotype_likelihoods": [ | |
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| 46094 -99999999, | |
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| 46097 "_cls": "Call.VariantCall", | |
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| 46099 0, | |
| 46100 0 | |
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| 46102 "variant": "ref-H87R?var_name=CAC7560CGA&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87R" | |
| 46103 }, | |
| 46104 "gyrA_A90D-GCG7569GAT": { | |
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| 46116 "min_non_zero_depth": 18, | |
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| 46121 "expected_depths": [ | |
| 46122 17.0 | |
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| 46127 "genotype_likelihoods": [ | |
| 46128 -2.79216398346472, | |
| 46129 -99999999, | |
| 46130 -99999999 | |
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| 46132 "_cls": "Call.VariantCall", | |
| 46133 "genotype": [ | |
| 46134 0, | |
| 46135 0 | |
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| 46137 "variant": "ref-A90D?var_name=GCG7569GAT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90D" | |
| 46138 }, | |
| 46139 "rpoB_P439R-CCG761121CGG": { | |
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| 46151 "min_non_zero_depth": 17, | |
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| 46156 "expected_depths": [ | |
| 46157 17.0 | |
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| 46162 "genotype_likelihoods": [ | |
| 46163 -2.6237799345145465, | |
| 46164 -99999999, | |
| 46165 -99999999 | |
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| 46167 "_cls": "Call.VariantCall", | |
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| 46169 0, | |
| 46170 0 | |
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| 46172 "variant": "ref-P439R?var_name=CCG761121CGG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439R" | |
| 46173 }, | |
| 46174 "rpoB_Q436N-CAG761112AAT": { | |
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| 46191 "expected_depths": [ | |
| 46192 17.0 | |
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| 46196 }, | |
| 46197 "genotype_likelihoods": [ | |
| 46198 -2.79216398346472, | |
| 46199 -99999999, | |
| 46200 -99999999 | |
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| 46202 "_cls": "Call.VariantCall", | |
| 46203 "genotype": [ | |
| 46204 0, | |
| 46205 0 | |
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| 46207 "variant": "ref-Q436N?var_name=CAG761112AAT&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436N" | |
| 46208 }, | |
| 46209 "gyrA_D94R-GAC7581AGG": { | |
| 46210 "info": { | |
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| 46221 "min_non_zero_depth": 17, | |
| 46222 "percent_coverage": 100.0, | |
| 46223 "kmer_count": 406 | |
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| 46226 "expected_depths": [ | |
| 46227 17.0 | |
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| 46231 }, | |
| 46232 "genotype_likelihoods": [ | |
| 46233 -2.79216398346472, | |
| 46234 -99999999, | |
| 46235 -99999999 | |
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| 46237 "_cls": "Call.VariantCall", | |
| 46238 "genotype": [ | |
| 46239 0, | |
| 46240 0 | |
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| 46242 "variant": "ref-D94R?var_name=GAC7581AGG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94R" | |
| 46243 }, | |
| 46244 "rpoB_S441L-TCG761127CTG": { | |
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| 46252 "kmer_count": 18 | |
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| 46256 "min_non_zero_depth": 17, | |
| 46257 "percent_coverage": 100.0, | |
| 46258 "kmer_count": 384 | |
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| 46260 }, | |
| 46261 "expected_depths": [ | |
| 46262 17.0 | |
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| 46266 }, | |
| 46267 "genotype_likelihoods": [ | |
| 46268 -2.6237799345145465, | |
| 46269 -99999999, | |
| 46270 -99999999 | |
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| 46272 "_cls": "Call.VariantCall", | |
| 46273 "genotype": [ | |
| 46274 0, | |
| 46275 0 | |
| 46276 ], | |
| 46277 "variant": "ref-S441L?var_name=TCG761127CTG&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441L" | |
| 46278 }, | |
| 46279 "gyrA_A90H-GCG7569CAT": { | |
| 46280 "info": { | |
| 46281 "contamination_depths": [], | |
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| 47292 "variant": "ref-S149R?var_name=GCT4407756CCT&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=S149R" | |
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| 47397 "variant": "ref-I92P?var_name=ATC7575CCT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92P" | |
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| 48029 "gyrA_D89G-GAC7566GGT": { | |
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| 48690 0 | |
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| 48693 }, | |
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| 48757 "_cls": "Call.VariantCall", | |
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| 48760 0 | |
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| 48763 }, | |
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| 48822 "genotype_likelihoods": [ | |
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| 48830 0 | |
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| 48833 }, | |
| 48834 "pncA_Q141I-CTG2288819GAT": { | |
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| 48864 0, | |
| 48865 0 | |
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| 48899 0, | |
| 48900 0 | |
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| 48903 }, | |
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| 48938 }, | |
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| 49002 "_cls": "Call.VariantCall", | |
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| 49005 0 | |
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| 49007 "variant": "ref-T444P?var_name=ACC761136CCA&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444P" | |
| 49008 }, | |
| 49009 "embB_M306T-ATG4247429ACA": { | |
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| 49032 "genotype_likelihoods": [ | |
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| 49037 "_cls": "Call.VariantCall", | |
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| 49040 0 | |
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| 49042 "variant": "ref-M306T?var_name=ATG4247429ACA&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306T" | |
| 49043 }, | |
| 49044 "rpoB_S428L-AGC761088TTG": { | |
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| 49067 "genotype_likelihoods": [ | |
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| 49072 "_cls": "Call.VariantCall", | |
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| 49074 0, | |
| 49075 0 | |
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| 49077 "variant": "ref-S428L?var_name=AGC761088TTG&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428L" | |
| 49078 }, | |
| 49079 "rpoB_N438K-AAC761118AAG": { | |
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| 49102 "genotype_likelihoods": [ | |
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| 49107 "_cls": "Call.VariantCall", | |
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| 49110 0 | |
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| 49112 "variant": "ref-N438K?var_name=AAC761118AAG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438K" | |
| 49113 }, | |
| 49114 "gid_Q125S-CTG4407828AGA": { | |
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| 49137 "genotype_likelihoods": [ | |
| 49138 -3.0037237137259485, | |
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| 49142 "_cls": "Call.VariantCall", | |
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| 49147 "variant": "ref-Q125S?var_name=CTG4407828AGA&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125S" | |
| 49148 }, | |
| 49149 "rpoB_F433L-TTC761103CTC": { | |
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| 49172 "genotype_likelihoods": [ | |
| 49173 -2.79216398346472, | |
| 49174 -99999999, | |
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| 49177 "_cls": "Call.VariantCall", | |
| 49178 "genotype": [ | |
| 49179 0, | |
| 49180 0 | |
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| 49182 "variant": "ref-F433L?var_name=TTC761103CTC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=F433L" | |
| 49183 }, | |
| 49184 "gid_Q125V-CTG4407828CAC": { | |
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| 49207 "genotype_likelihoods": [ | |
| 49208 -3.0037237137259485, | |
| 49209 -99999999, | |
| 49210 -99999999 | |
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| 49212 "_cls": "Call.VariantCall", | |
| 49213 "genotype": [ | |
| 49214 0, | |
| 49215 0 | |
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| 49217 "variant": "ref-Q125V?var_name=CTG4407828CAC&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125V" | |
| 49218 }, | |
| 49219 "rpoB_M434L-ATG761106CTA": { | |
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| 49231 "min_non_zero_depth": 17, | |
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| 49236 "expected_depths": [ | |
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| 49241 }, | |
| 49242 "genotype_likelihoods": [ | |
| 49243 -2.79216398346472, | |
| 49244 -99999999, | |
| 49245 -99999999 | |
| 49246 ], | |
| 49247 "_cls": "Call.VariantCall", | |
| 49248 "genotype": [ | |
| 49249 0, | |
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| 50163 }, | |
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| 50222 "genotype_likelihoods": [ | |
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| 50233 }, | |
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| 50262 "_cls": "Call.VariantCall", | |
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| 50297 "_cls": "Call.VariantCall", | |
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| 50304 "rpoB_R448E-CGA761148GAG": { | |
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| 50327 "genotype_likelihoods": [ | |
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| 50332 "_cls": "Call.VariantCall", | |
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| 50367 "_cls": "Call.VariantCall", | |
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| 50397 "genotype_likelihoods": [ | |
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| 50399 -99999999, | |
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| 50402 "_cls": "Call.VariantCall", | |
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| 50405 0 | |
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| 50408 }, | |
| 50409 "rpoB_L430A-CTG761094GCT": { | |
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| 51025 "conf": 99999996 | |
| 51026 }, | |
| 51027 "genotype_likelihoods": [ | |
| 51028 -2.79216398346472, | |
| 51029 -99999999, | |
| 51030 -99999999 | |
| 51031 ], | |
| 51032 "_cls": "Call.VariantCall", | |
| 51033 "genotype": [ | |
| 51034 0, | |
| 51035 0 | |
| 51036 ], | |
| 51037 "variant": "ref-D435V?var_name=GAC761109GTT&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435V" | |
| 51038 }, | |
| 51039 "rpoB_S428R-AGC761088AGA": { | |
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| 51047 "kmer_count": 14 | |
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| 51049 "reference": { | |
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| 51051 "min_non_zero_depth": 14, | |
| 51052 "percent_coverage": 100.0, | |
| 51053 "kmer_count": 382 | |
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| 51055 }, | |
| 51056 "expected_depths": [ | |
| 51057 17.0 | |
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| 51060 "conf": 99999996 | |
| 51061 }, | |
| 51062 "genotype_likelihoods": [ | |
| 51063 -2.6809383483544966, | |
| 51064 -99999999, | |
| 51065 -99999999 | |
| 51066 ], | |
| 51067 "_cls": "Call.VariantCall", | |
| 51068 "genotype": [ | |
| 51069 0, | |
| 51070 0 | |
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| 51072 "variant": "ref-S428R?var_name=AGC761088AGA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428R" | |
| 51073 }, | |
| 51074 "rpoB_Q429Y-CAG761091TAT": { | |
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| 51082 "kmer_count": 43 | |
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| 51085 "median_depth": 18, | |
| 51086 "min_non_zero_depth": 15, | |
| 51087 "percent_coverage": 100.0, | |
| 51088 "kmer_count": 395 | |
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| 51090 }, | |
| 51091 "expected_depths": [ | |
| 51092 17.0 | |
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| 51095 "conf": 99999996 | |
| 51096 }, | |
| 51097 "genotype_likelihoods": [ | |
| 51098 -2.6809383483544966, | |
| 51099 -99999999, | |
| 51100 -99999999 | |
| 51101 ], | |
| 51102 "_cls": "Call.VariantCall", | |
| 51103 "genotype": [ | |
| 51104 0, | |
| 51105 0 | |
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| 51107 "variant": "ref-Q429Y?var_name=CAG761091TAT&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429Y" | |
| 51108 }, | |
| 51109 "rpoB_N437R-AAC761115CGC": { | |
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| 51116 "percent_coverage": 27.27, | |
| 51117 "kmer_count": 102 | |
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| 51119 "reference": { | |
| 51120 "median_depth": 18, | |
| 51121 "min_non_zero_depth": 17, | |
| 51122 "percent_coverage": 100.0, | |
| 51123 "kmer_count": 408 | |
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| 51125 }, | |
| 51126 "expected_depths": [ | |
| 51127 17.0 | |
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| 51130 "conf": 99999996 | |
| 51131 }, | |
| 51132 "genotype_likelihoods": [ | |
| 51133 -2.6809383483544966, | |
| 51134 -99999999, | |
| 51135 -99999999 | |
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| 51137 "_cls": "Call.VariantCall", | |
| 51138 "genotype": [ | |
| 51139 0, | |
| 51140 0 | |
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| 51142 "variant": "ref-N437R?var_name=AAC761115CGC&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437R" | |
| 51143 }, | |
| 51144 "rpoB_S441L-TCG761127CTA": { | |
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| 51154 "reference": { | |
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| 51156 "min_non_zero_depth": 17, | |
| 51157 "percent_coverage": 100.0, | |
| 51158 "kmer_count": 384 | |
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| 51160 }, | |
| 51161 "expected_depths": [ | |
| 51162 17.0 | |
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| 51165 "conf": 99999996 | |
| 51166 }, | |
| 51167 "genotype_likelihoods": [ | |
| 51168 -2.6237799345145465, | |
| 51169 -99999999, | |
| 51170 -99999999 | |
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| 51172 "_cls": "Call.VariantCall", | |
| 51173 "genotype": [ | |
| 51174 0, | |
| 51175 0 | |
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| 51177 "variant": "ref-S441L?var_name=TCG761127CTA&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441L" | |
| 51178 }, | |
| 51179 "gid_S136R-TGA4407795GCG": { | |
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| 51189 "reference": { | |
| 51190 "median_depth": 15, | |
| 51191 "min_non_zero_depth": 14, | |
| 51192 "percent_coverage": 100.0, | |
| 51193 "kmer_count": 327 | |
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| 51195 }, | |
| 51196 "expected_depths": [ | |
| 51197 17.0 | |
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| 51200 "conf": 99999996 | |
| 51201 }, | |
| 51202 "genotype_likelihoods": [ | |
| 51203 -2.6844045563309873, | |
| 51204 -99999999, | |
| 51205 -99999999 | |
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| 51207 "_cls": "Call.VariantCall", | |
| 51208 "genotype": [ | |
| 51209 0, | |
| 51210 0 | |
| 51211 ], | |
| 51212 "variant": "ref-S136R?var_name=TGA4407795GCG&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136R" | |
| 51213 }, | |
| 51214 "gid_I162S-GAT4407717GCT": { | |
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| 51219 "median_depth": 0, | |
| 51220 "min_non_zero_depth": 14, | |
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| 51222 "kmer_count": 14 | |
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| 51224 "reference": { | |
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| 51226 "min_non_zero_depth": 14, | |
| 51227 "percent_coverage": 100.0, | |
| 51228 "kmer_count": 368 | |
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| 51230 }, | |
| 51231 "expected_depths": [ | |
| 51232 17.0 | |
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| 51235 "conf": 99999996 | |
| 51236 }, | |
| 51237 "genotype_likelihoods": [ | |
| 51238 -2.6237799345145465, | |
| 51239 -99999999, | |
| 51240 -99999999 | |
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| 51242 "_cls": "Call.VariantCall", | |
| 51243 "genotype": [ | |
| 51244 0, | |
| 51245 0 | |
| 51246 ], | |
| 51247 "variant": "ref-I162S?var_name=GAT4407717GCT&num_alts=15&ref=NC_000962.3&enum=0&gene=gid&mut=I162S" | |
| 51248 }, | |
| 51249 "rpoB_N438W-AAC761118TGG": { | |
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| 51257 "kmer_count": 86 | |
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| 51261 "min_non_zero_depth": 17, | |
| 51262 "percent_coverage": 100.0, | |
| 51263 "kmer_count": 399 | |
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| 51265 }, | |
| 51266 "expected_depths": [ | |
| 51267 17.0 | |
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| 51271 }, | |
| 51272 "genotype_likelihoods": [ | |
| 51273 -2.6809383483544966, | |
| 51274 -99999999, | |
| 51275 -99999999 | |
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| 51277 "_cls": "Call.VariantCall", | |
| 51278 "genotype": [ | |
| 51279 0, | |
| 51280 0 | |
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| 51282 "variant": "ref-N438W?var_name=AAC761118TGG&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438W" | |
| 51283 }, | |
| 51284 "rpoB_Q432H-CAA761100CAC": { | |
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| 51289 "median_depth": 0, | |
| 51290 "min_non_zero_depth": 17, | |
| 51291 "percent_coverage": 22.73, | |
| 51292 "kmer_count": 93 | |
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| 51294 "reference": { | |
| 51295 "median_depth": 19, | |
| 51296 "min_non_zero_depth": 17, | |
| 51297 "percent_coverage": 100.0, | |
| 51298 "kmer_count": 417 | |
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| 51300 }, | |
| 51301 "expected_depths": [ | |
| 51302 17.0 | |
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| 51305 "conf": 99999996 | |
| 51306 }, | |
| 51307 "genotype_likelihoods": [ | |
| 51308 -2.79216398346472, | |
| 51309 -99999999, | |
| 51310 -99999999 | |
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| 51312 "_cls": "Call.VariantCall", | |
| 51313 "genotype": [ | |
| 51314 0, | |
| 51315 0 | |
| 51316 ], | |
| 51317 "variant": "ref-Q432H?var_name=CAA761100CAC&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432H" | |
| 51318 }, | |
| 51319 "rpoB_S431P-AGC761097CCC": { | |
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| 51322 "coverage": { | |
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| 51324 "median_depth": 0, | |
| 51325 "min_non_zero_depth": 19, | |
| 51326 "percent_coverage": 27.27, | |
| 51327 "kmer_count": 118 | |
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| 51331 "min_non_zero_depth": 17, | |
| 51332 "percent_coverage": 100.0, | |
| 51333 "kmer_count": 411 | |
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| 51335 }, | |
| 51336 "expected_depths": [ | |
| 51337 17.0 | |
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| 51340 "conf": 99999996 | |
| 51341 }, | |
| 51342 "genotype_likelihoods": [ | |
| 51343 -2.79216398346472, | |
| 51344 -99999999, | |
| 51345 -99999999 | |
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| 51347 "_cls": "Call.VariantCall", | |
| 51348 "genotype": [ | |
| 51349 0, | |
| 51350 0 | |
| 51351 ], | |
| 51352 "variant": "ref-S431P?var_name=AGC761097CCC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431P" | |
| 51353 }, | |
| 51354 "katG_W505T-CCA2154597GGT": { | |
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| 51364 "reference": { | |
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| 51366 "min_non_zero_depth": 16, | |
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| 51368 "kmer_count": 385 | |
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| 51370 }, | |
| 51371 "expected_depths": [ | |
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| 51375 "conf": 99999996 | |
| 51376 }, | |
| 51377 "genotype_likelihoods": [ | |
| 51378 -2.6809383483544966, | |
| 51379 -99999999, | |
| 51380 -99999999 | |
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| 51382 "_cls": "Call.VariantCall", | |
| 51383 "genotype": [ | |
| 51384 0, | |
| 51385 0 | |
| 51386 ], | |
| 51387 "variant": "ref-W505T?var_name=CCA2154597GGT&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505T" | |
| 51388 }, | |
| 51389 "rpoB_L440Y-CTG761124TAT": { | |
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| 51391 "contamination_depths": [], | |
| 51392 "coverage": { | |
| 51393 "alternate": { | |
| 51394 "median_depth": 0, | |
| 51395 "min_non_zero_depth": 18, | |
| 51396 "percent_coverage": 13.64, | |
| 51397 "kmer_count": 54 | |
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| 51399 "reference": { | |
| 51400 "median_depth": 17, | |
| 51401 "min_non_zero_depth": 17, | |
| 51402 "percent_coverage": 100.0, | |
| 51403 "kmer_count": 385 | |
| 51404 } | |
| 51405 }, | |
| 51406 "expected_depths": [ | |
| 51407 17.0 | |
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| 51409 "filter": "PASS", | |
| 51410 "conf": 99999996 | |
| 51411 }, | |
| 51412 "genotype_likelihoods": [ | |
| 51413 -2.6237799345145465, | |
| 51414 -99999999, | |
| 51415 -99999999 | |
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| 51417 "_cls": "Call.VariantCall", | |
| 51418 "genotype": [ | |
| 51419 0, | |
| 51420 0 | |
| 51421 ], | |
| 51422 "variant": "ref-L440Y?var_name=CTG761124TAT&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440Y" | |
| 51423 }, | |
| 51424 "gyrA_H85G-CAC7554GGC": { | |
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| 51427 "coverage": { | |
| 51428 "alternate": { | |
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| 51430 "min_non_zero_depth": 18, | |
| 51431 "percent_coverage": 4.55, | |
| 51432 "kmer_count": 18 | |
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| 51434 "reference": { | |
| 51435 "median_depth": 15, | |
| 51436 "min_non_zero_depth": 13, | |
| 51437 "percent_coverage": 100.0, | |
| 51438 "kmer_count": 343 | |
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| 51440 }, | |
| 51441 "expected_depths": [ | |
| 51442 17.0 | |
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| 51444 "filter": "PASS", | |
| 51445 "conf": 99999996 | |
| 51446 }, | |
| 51447 "genotype_likelihoods": [ | |
| 51448 -2.6844045563309873, | |
| 51449 -99999999, | |
| 51450 -99999999 | |
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| 51452 "_cls": "Call.VariantCall", | |
| 51453 "genotype": [ | |
| 51454 0, | |
| 51455 0 | |
| 51456 ], | |
| 51457 "variant": "ref-H85G?var_name=CAC7554GGC&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85G" | |
| 51458 }, | |
| 51459 "katG_S315N-GCT2155167GTT": { | |
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| 51463 "alternate": { | |
| 51464 "median_depth": 15, | |
| 51465 "min_non_zero_depth": 14, | |
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| 51467 "kmer_count": 328 | |
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| 51469 "reference": { | |
| 51470 "median_depth": 0, | |
| 51471 "min_non_zero_depth": 17, | |
| 51472 "percent_coverage": 4.55, | |
| 51473 "kmer_count": 17 | |
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| 51476 "expected_depths": [ | |
| 51477 17.0 | |
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| 51479 "filter": "PASS", | |
| 51480 "conf": 99999996 | |
| 51481 }, | |
| 51482 "genotype_likelihoods": [ | |
| 51483 -99999999, | |
| 51484 -99999999, | |
| 51485 -2.6844045563309873 | |
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| 51487 "_cls": "Call.VariantCall", | |
| 51488 "genotype": [ | |
| 51489 1, | |
| 51490 1 | |
| 51491 ], | |
| 51492 "variant": null | |
| 51493 }, | |
| 51494 "rpoB_G442E-GGG761130GAA": { | |
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| 51496 "contamination_depths": [], | |
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| 51498 "alternate": { | |
| 51499 "median_depth": 0, | |
| 51500 "min_non_zero_depth": 17, | |
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| 51502 "kmer_count": 17 | |
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| 51504 "reference": { | |
| 51505 "median_depth": 18, | |
| 51506 "min_non_zero_depth": 17, | |
| 51507 "percent_coverage": 100.0, | |
| 51508 "kmer_count": 387 | |
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| 51510 }, | |
| 51511 "expected_depths": [ | |
| 51512 17.0 | |
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| 51514 "filter": "PASS", | |
| 51515 "conf": 99999996 | |
| 51516 }, | |
| 51517 "genotype_likelihoods": [ | |
| 51518 -2.6809383483544966, | |
| 51519 -99999999, | |
| 51520 -99999999 | |
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| 51522 "_cls": "Call.VariantCall", | |
| 51523 "genotype": [ | |
| 51524 0, | |
| 51525 0 | |
| 51526 ], | |
| 51527 "variant": "ref-G442E?var_name=GGG761130GAA&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442E" | |
| 51528 }, | |
| 51529 "rpoB_L452A-CTG761160GCA": { | |
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| 51539 "reference": { | |
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| 51541 "min_non_zero_depth": 14, | |
| 51542 "percent_coverage": 100.0, | |
| 51543 "kmer_count": 315 | |
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| 51545 }, | |
| 51546 "expected_depths": [ | |
| 51547 17.0 | |
| 51548 ], | |
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| 51550 "conf": 99999996 | |
| 51551 }, | |
| 51552 "genotype_likelihoods": [ | |
| 51553 -2.8095676992849885, | |
| 51554 -99999999, | |
| 51555 -99999999 | |
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| 51557 "_cls": "Call.VariantCall", | |
| 51558 "genotype": [ | |
| 51559 0, | |
| 51560 0 | |
| 51561 ], | |
| 51562 "variant": "ref-L452A?var_name=CTG761160GCA&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452A" | |
| 51563 }, | |
| 51564 "rpoB_S431T-AGC761097ACA": { | |
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| 51567 "coverage": { | |
| 51568 "alternate": { | |
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| 51570 "min_non_zero_depth": 19, | |
| 51571 "percent_coverage": 22.73, | |
| 51572 "kmer_count": 98 | |
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| 51574 "reference": { | |
| 51575 "median_depth": 19, | |
| 51576 "min_non_zero_depth": 17, | |
| 51577 "percent_coverage": 100.0, | |
| 51578 "kmer_count": 411 | |
| 51579 } | |
| 51580 }, | |
| 51581 "expected_depths": [ | |
| 51582 17.0 | |
| 51583 ], | |
| 51584 "filter": "PASS", | |
| 51585 "conf": 99999996 | |
| 51586 }, | |
| 51587 "genotype_likelihoods": [ | |
| 51588 -2.79216398346472, | |
| 51589 -99999999, | |
| 51590 -99999999 | |
| 51591 ], | |
| 51592 "_cls": "Call.VariantCall", | |
| 51593 "genotype": [ | |
| 51594 0, | |
| 51595 0 | |
| 51596 ], | |
| 51597 "variant": "ref-S431T?var_name=AGC761097ACA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431T" | |
| 51598 }, | |
| 51599 "rpoB_S450E-TCG761154GAA": { | |
| 51600 "info": { | |
| 51601 "contamination_depths": [], | |
| 51602 "coverage": { | |
| 51603 "alternate": { | |
| 51604 "median_depth": 0, | |
| 51605 "min_non_zero_depth": 0, | |
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| 51607 "kmer_count": 0 | |
| 51608 }, | |
| 51609 "reference": { | |
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| 51611 "min_non_zero_depth": 14, | |
| 51612 "percent_coverage": 4.55, | |
| 51613 "kmer_count": 14 | |
| 51614 } | |
| 51615 }, | |
| 51616 "expected_depths": [ | |
| 51617 17.0 | |
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| 52807 17.0 | |
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| 52809 "filter": "LOW_GT_CONF", | |
| 52810 "conf": 0 | |
| 52811 }, | |
| 52812 "genotype_likelihoods": [ | |
| 52813 -99999999, | |
| 52814 -99999999, | |
| 52815 -99999999 | |
| 52816 ], | |
| 52817 "_cls": "Call.VariantCall", | |
| 52818 "genotype": [ | |
| 52819 0, | |
| 52820 0 | |
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| 52822 "variant": "ref-Q141T?var_name=CTG2288819AGT&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141T" | |
| 52823 }, | |
| 52824 "rpoB_S441R-TCG761127AGG": { | |
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| 52830 "min_non_zero_depth": 18, | |
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| 52832 "kmer_count": 18 | |
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| 52836 "min_non_zero_depth": 17, | |
| 52837 "percent_coverage": 100.0, | |
| 52838 "kmer_count": 384 | |
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| 52840 }, | |
| 52841 "expected_depths": [ | |
| 52842 17.0 | |
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| 52845 "conf": 99999996 | |
| 52846 }, | |
| 52847 "genotype_likelihoods": [ | |
| 52848 -2.6237799345145465, | |
| 52849 -99999999, | |
| 52850 -99999999 | |
| 52851 ], | |
| 52852 "_cls": "Call.VariantCall", | |
| 52853 "genotype": [ | |
| 52854 0, | |
| 52855 0 | |
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| 52857 "variant": "ref-S441R?var_name=TCG761127AGG&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441R" | |
| 52858 }, | |
| 52859 "rpoB_N438A-AAC761118GCA": { | |
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| 52875 }, | |
| 52876 "expected_depths": [ | |
| 52877 17.0 | |
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| 52880 "conf": 99999996 | |
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| 52882 "genotype_likelihoods": [ | |
| 52883 -2.6809383483544966, | |
| 52884 -99999999, | |
| 52885 -99999999 | |
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| 52887 "_cls": "Call.VariantCall", | |
| 52888 "genotype": [ | |
| 52889 0, | |
| 52890 0 | |
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| 52892 "variant": "ref-N438A?var_name=AAC761118GCA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438A" | |
| 52893 }, | |
| 52894 "katG_L159P-GAG2155635GGG": { | |
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| 52900 "min_non_zero_depth": 20, | |
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| 52908 "kmer_count": 431 | |
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| 52911 "expected_depths": [ | |
| 52912 17.0 | |
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| 52917 "genotype_likelihoods": [ | |
| 52918 -2.79216398346472, | |
| 52919 -99999999, | |
| 52920 -99999999 | |
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| 52922 "_cls": "Call.VariantCall", | |
| 52923 "genotype": [ | |
| 52924 0, | |
| 52925 0 | |
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| 52927 "variant": "ref-L159P?var_name=GAG2155635GGG&num_alts=5&ref=NC_000962.3&enum=0&gene=katG&mut=L159P" | |
| 52928 }, | |
| 52929 "rpoB_T427D-ACC761085GAT": { | |
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| 52941 "min_non_zero_depth": 14, | |
| 52942 "percent_coverage": 100.0, | |
| 52943 "kmer_count": 367 | |
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| 52945 }, | |
| 52946 "expected_depths": [ | |
| 52947 17.0 | |
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| 52950 "conf": 99999996 | |
| 52951 }, | |
| 52952 "genotype_likelihoods": [ | |
| 52953 -2.6237799345145465, | |
| 52954 -99999999, | |
| 52955 -99999999 | |
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| 52957 "_cls": "Call.VariantCall", | |
| 52958 "genotype": [ | |
| 52959 0, | |
| 52960 0 | |
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| 52962 "variant": "ref-T427D?var_name=ACC761085GAT&num_alts=32&ref=NC_000962.3&enum=0&gene=rpoB&mut=T427D" | |
| 52963 }, | |
| 52964 "rpoB_H445T-CAC761139ACA": { | |
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| 52976 "min_non_zero_depth": 15, | |
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| 52982 17.0 | |
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| 52986 }, | |
| 52987 "genotype_likelihoods": [ | |
| 52988 -2.6237799345145465, | |
| 52989 -99999999, | |
| 52990 -99999999 | |
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| 52992 "_cls": "Call.VariantCall", | |
| 52993 "genotype": [ | |
| 52994 0, | |
| 52995 0 | |
| 52996 ], | |
| 52997 "variant": "ref-H445T?var_name=CAC761139ACA&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445T" | |
| 52998 }, | |
| 52999 "rpoB_S450L-TCG761154TTA": { | |
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| 53004 "median_depth": 0, | |
| 53005 "min_non_zero_depth": 16, | |
| 53006 "percent_coverage": 4.55, | |
| 53007 "kmer_count": 16 | |
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| 53009 "reference": { | |
| 53010 "median_depth": 0, | |
| 53011 "min_non_zero_depth": 14, | |
| 53012 "percent_coverage": 4.55, | |
| 53013 "kmer_count": 14 | |
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| 53015 }, | |
| 53016 "expected_depths": [ | |
| 53017 17.0 | |
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| 53019 "filter": "LOW_GT_CONF", | |
| 53020 "conf": 0 | |
| 53021 }, | |
| 53022 "genotype_likelihoods": [ | |
| 53023 -99999999, | |
| 53024 -99999999, | |
| 53025 -99999999 | |
| 53026 ], | |
| 53027 "_cls": "Call.VariantCall", | |
| 53028 "genotype": [ | |
| 53029 0, | |
| 53030 0 | |
| 53031 ], | |
| 53032 "variant": "ref-S450L?var_name=TCG761154TTA&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450L" | |
| 53033 }, | |
| 53034 "gid_Q125G-CTG4407828GCC": { | |
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| 53040 "min_non_zero_depth": 17, | |
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| 53042 "kmer_count": 17 | |
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| 53044 "reference": { | |
| 53045 "median_depth": 13, | |
| 53046 "min_non_zero_depth": 13, | |
| 53047 "percent_coverage": 100.0, | |
| 53048 "kmer_count": 313 | |
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| 53050 }, | |
| 53051 "expected_depths": [ | |
| 53052 17.0 | |
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| 53055 "conf": 99999996 | |
| 53056 }, | |
| 53057 "genotype_likelihoods": [ | |
| 53058 -3.0037237137259485, | |
| 53059 -99999999, | |
| 53060 -99999999 | |
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| 53062 "_cls": "Call.VariantCall", | |
| 53063 "genotype": [ | |
| 53064 0, | |
| 53065 0 | |
| 53066 ], | |
| 53067 "variant": "ref-Q125G?var_name=CTG4407828GCC&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125G" | |
| 53068 }, | |
| 53069 "rpoB_F425P-TTC761079CCC": { | |
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| 53075 "min_non_zero_depth": 16, | |
| 53076 "percent_coverage": 13.64, | |
| 53077 "kmer_count": 48 | |
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| 53079 "reference": { | |
| 53080 "median_depth": 15, | |
| 53081 "min_non_zero_depth": 14, | |
| 53082 "percent_coverage": 100.0, | |
| 53083 "kmer_count": 344 | |
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| 53085 }, | |
| 53086 "expected_depths": [ | |
| 53087 17.0 | |
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| 53090 "conf": 99999996 | |
| 53091 }, | |
| 53092 "genotype_likelihoods": [ | |
| 53093 -2.6844045563309873, | |
| 53094 -99999999, | |
| 53095 -99999999 | |
| 53096 ], | |
| 53097 "_cls": "Call.VariantCall", | |
| 53098 "genotype": [ | |
| 53099 0, | |
| 53100 0 | |
| 53101 ], | |
| 53102 "variant": "ref-F425P?var_name=TTC761079CCC&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425P" | |
| 53103 }, | |
| 53104 "rpoB_K446C-AAG761142TGC": { | |
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| 53106 "contamination_depths": [], | |
| 53107 "coverage": { | |
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| 53109 "median_depth": 0, | |
| 53110 "min_non_zero_depth": 0, | |
| 53111 "percent_coverage": 0.0, | |
| 53112 "kmer_count": 0 | |
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| 53114 "reference": { | |
| 53115 "median_depth": 17, | |
| 53116 "min_non_zero_depth": 14, | |
| 53117 "percent_coverage": 100.0, | |
| 53118 "kmer_count": 368 | |
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| 53120 }, | |
| 53121 "expected_depths": [ | |
| 53122 17.0 | |
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| 53124 "filter": "PASS", | |
| 53125 "conf": 99999996 | |
| 53126 }, | |
| 53127 "genotype_likelihoods": [ | |
| 53128 -2.6237799345145465, | |
| 53129 -99999999, | |
| 53130 -99999999 | |
| 53131 ], | |
| 53132 "_cls": "Call.VariantCall", | |
| 53133 "genotype": [ | |
| 53134 0, | |
| 53135 0 | |
| 53136 ], | |
| 53137 "variant": "ref-K446C?var_name=AAG761142TGC&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446C" | |
| 53138 }, | |
| 53139 "pncA_I133T-AAT2288843CGT": { | |
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| 53141 "contamination_depths": [], | |
| 53142 "coverage": { | |
| 53143 "alternate": { | |
| 53144 "median_depth": 0, | |
| 53145 "min_non_zero_depth": 15, | |
| 53146 "percent_coverage": 9.09, | |
| 53147 "kmer_count": 30 | |
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| 53149 "reference": { | |
| 53150 "median_depth": 16, | |
| 53151 "min_non_zero_depth": 15, | |
| 53152 "percent_coverage": 100.0, | |
| 53153 "kmer_count": 350 | |
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| 53155 }, | |
| 53156 "expected_depths": [ | |
| 53157 17.0 | |
| 53158 ], | |
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| 53160 "conf": 99999996 | |
| 53161 }, | |
| 53162 "genotype_likelihoods": [ | |
| 53163 -2.62377993451455, | |
| 53164 -99999999, | |
| 53165 -99999999 | |
| 53166 ], | |
| 53167 "_cls": "Call.VariantCall", | |
| 53168 "genotype": [ | |
| 53169 0, | |
| 53170 0 | |
| 53171 ], | |
| 53172 "variant": "ref-I133T?var_name=AAT2288843CGT&num_alts=15&ref=NC_000962.3&enum=0&gene=pncA&mut=I133T" | |
| 53173 }, | |
| 53174 "gyrA_H87D-CAC7560GAC": { | |
| 53175 "info": { | |
| 53176 "contamination_depths": [], | |
| 53177 "coverage": { | |
| 53178 "alternate": { | |
| 53179 "median_depth": 0, | |
| 53180 "min_non_zero_depth": 19, | |
| 53181 "percent_coverage": 9.09, | |
| 53182 "kmer_count": 38 | |
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| 53184 "reference": { | |
| 53185 "median_depth": 18, | |
| 53186 "min_non_zero_depth": 15, | |
| 53187 "percent_coverage": 100.0, | |
| 53188 "kmer_count": 377 | |
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| 53190 }, | |
| 53191 "expected_depths": [ | |
| 53192 17.0 | |
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| 53195 "conf": 99999996 | |
| 53196 }, | |
| 53197 "genotype_likelihoods": [ | |
| 53198 -2.6809383483544966, | |
| 53199 -99999999, | |
| 53200 -99999999 | |
| 53201 ], | |
| 53202 "_cls": "Call.VariantCall", | |
| 53203 "genotype": [ | |
| 53204 0, | |
| 53205 0 | |
| 53206 ], | |
| 53207 "variant": "ref-H87D?var_name=CAC7560GAC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87D" | |
| 53208 }, | |
| 53209 "rpoB_N437V-AAC761115GTC": { | |
| 53210 "info": { | |
| 53211 "contamination_depths": [], | |
| 53212 "coverage": { | |
| 53213 "alternate": { | |
| 53214 "median_depth": 0, | |
| 53215 "min_non_zero_depth": 17, | |
| 53216 "percent_coverage": 27.27, | |
| 53217 "kmer_count": 102 | |
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| 53219 "reference": { | |
| 53220 "median_depth": 18, | |
| 53221 "min_non_zero_depth": 17, | |
| 53222 "percent_coverage": 100.0, | |
| 53223 "kmer_count": 408 | |
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| 53225 }, | |
| 53226 "expected_depths": [ | |
| 53227 17.0 | |
| 53228 ], | |
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| 53230 "conf": 99999996 | |
| 53231 }, | |
| 53232 "genotype_likelihoods": [ | |
| 53233 -2.6809383483544966, | |
| 53234 -99999999, | |
| 53235 -99999999 | |
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| 53237 "_cls": "Call.VariantCall", | |
| 53238 "genotype": [ | |
| 53239 0, | |
| 53240 0 | |
| 53241 ], | |
| 53242 "variant": "ref-N437V?var_name=AAC761115GTC&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437V" | |
| 53243 }, | |
| 53244 "gyrA_Y93G-TAC7578GGT": { | |
| 53245 "info": { | |
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| 53247 "coverage": { | |
| 53248 "alternate": { | |
| 53249 "median_depth": 0, | |
| 53250 "min_non_zero_depth": 0, | |
| 53251 "percent_coverage": 0.0, | |
| 53252 "kmer_count": 0 | |
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| 53254 "reference": { | |
| 53255 "median_depth": 19, | |
| 53256 "min_non_zero_depth": 17, | |
| 53257 "percent_coverage": 100.0, | |
| 53258 "kmer_count": 412 | |
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| 53260 }, | |
| 53261 "expected_depths": [ | |
| 53262 17.0 | |
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| 53265 "conf": 99999996 | |
| 53266 }, | |
| 53267 "genotype_likelihoods": [ | |
| 53268 -2.79216398346472, | |
| 53269 -99999999, | |
| 53270 -99999999 | |
| 53271 ], | |
| 53272 "_cls": "Call.VariantCall", | |
| 53273 "genotype": [ | |
| 53274 0, | |
| 53275 0 | |
| 53276 ], | |
| 53277 "variant": "ref-Y93G?var_name=TAC7578GGT&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93G" | |
| 53278 }, | |
| 53279 "gyrA_D89M-GAC7566ATG": { | |
| 53280 "info": { | |
| 53281 "contamination_depths": [], | |
| 53282 "coverage": { | |
| 53283 "alternate": { | |
| 53284 "median_depth": 0, | |
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| 53286 "percent_coverage": 0.0, | |
| 53287 "kmer_count": 0 | |
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| 53289 "reference": { | |
| 53290 "median_depth": 18, | |
| 53291 "min_non_zero_depth": 16, | |
| 53292 "percent_coverage": 100.0, | |
| 53293 "kmer_count": 400 | |
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| 53295 }, | |
| 53296 "expected_depths": [ | |
| 53297 17.0 | |
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| 53300 "conf": 99999996 | |
| 53301 }, | |
| 53302 "genotype_likelihoods": [ | |
| 53303 -2.6809383483544966, | |
| 53304 -99999999, | |
| 53305 -99999999 | |
| 53306 ], | |
| 53307 "_cls": "Call.VariantCall", | |
| 53308 "genotype": [ | |
| 53309 0, | |
| 53310 0 | |
| 53311 ], | |
| 53312 "variant": "ref-D89M?var_name=GAC7566ATG&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89M" | |
| 53313 }, | |
| 53314 "rpoB_Q436I-CAG761112ATA": { | |
| 53315 "info": { | |
| 53316 "contamination_depths": [], | |
| 53317 "coverage": { | |
| 53318 "alternate": { | |
| 53319 "median_depth": 0, | |
| 53320 "min_non_zero_depth": 17, | |
| 53321 "percent_coverage": 22.73, | |
| 53322 "kmer_count": 86 | |
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| 53324 "reference": { | |
| 53325 "median_depth": 19, | |
| 53326 "min_non_zero_depth": 17, | |
| 53327 "percent_coverage": 100.0, | |
| 53328 "kmer_count": 413 | |
| 53329 } | |
| 53330 }, | |
| 53331 "expected_depths": [ | |
| 53332 17.0 | |
| 53333 ], | |
| 53334 "filter": "PASS", | |
| 53335 "conf": 99999996 | |
| 53336 }, | |
| 53337 "genotype_likelihoods": [ | |
| 53338 -2.79216398346472, | |
| 53339 -99999999, | |
| 53340 -99999999 | |
| 53341 ], | |
| 53342 "_cls": "Call.VariantCall", | |
| 53343 "genotype": [ | |
| 53344 0, | |
| 53345 0 | |
| 53346 ], | |
| 53347 "variant": "ref-Q436I?var_name=CAG761112ATA&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436I" | |
| 53348 }, | |
| 53349 "gyrA_S91A-TCG7572GCC": { | |
| 53350 "info": { | |
| 53351 "contamination_depths": [], | |
| 53352 "coverage": { | |
| 53353 "alternate": { | |
| 53354 "median_depth": 0, | |
| 53355 "min_non_zero_depth": 0, | |
| 53356 "percent_coverage": 0.0, | |
| 53357 "kmer_count": 0 | |
| 53358 }, | |
| 53359 "reference": { | |
| 53360 "median_depth": 19, | |
| 53361 "min_non_zero_depth": 18, | |
| 53362 "percent_coverage": 100.0, | |
| 53363 "kmer_count": 413 | |
| 53364 } | |
| 53365 }, | |
| 53366 "expected_depths": [ | |
| 53367 17.0 | |
| 53368 ], | |
| 53369 "filter": "PASS", | |
| 53370 "conf": 99999996 | |
| 53371 }, | |
| 53372 "genotype_likelihoods": [ | |
| 53373 -2.79216398346472, | |
| 53374 -99999999, | |
| 53375 -99999999 | |
| 53376 ], | |
| 53377 "_cls": "Call.VariantCall", | |
| 53378 "genotype": [ | |
| 53379 0, | |
| 53380 0 | |
| 53381 ], | |
| 53382 "variant": "ref-S91A?var_name=TCG7572GCC&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91A" | |
| 53383 }, | |
| 53384 "gid_E173S-CTC4407684AGA": { | |
| 53385 "info": { | |
| 53386 "contamination_depths": [], | |
| 53387 "coverage": { | |
| 53388 "alternate": { | |
| 53389 "median_depth": 0, | |
| 53390 "min_non_zero_depth": 22, | |
| 53391 "percent_coverage": 4.55, | |
| 53392 "kmer_count": 22 | |
| 53393 }, | |
| 53394 "reference": { | |
| 53395 "median_depth": 22, | |
| 53396 "min_non_zero_depth": 21, | |
| 53397 "percent_coverage": 100.0, | |
| 53398 "kmer_count": 484 | |
| 53399 } | |
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| 53401 "expected_depths": [ | |
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| 54009 0, | |
| 54010 0 | |
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| 54290 0 | |
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| 54325 0 | |
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| 54327 "variant": "ref-Y99A?var_name=GTA2288945GGC&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99A" | |
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| 54360 0 | |
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| 54364 "katG_S315T-GCT2155167CGT": { | |
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| 54397 "variant": "ref-S315T?var_name=GCT2155167CGT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315T" | |
| 54398 }, | |
| 54399 "gyrA_P86E-CCG7557GAG": { | |
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| 54432 "variant": "ref-P86E?var_name=CCG7557GAG&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86E" | |
| 54433 }, | |
| 54434 "gyrA_H87Y-CAC7560TAT": { | |
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| 54467 "variant": "ref-H87Y?var_name=CAC7560TAT&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87Y" | |
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| 54469 "gid_E173K-CTC4407684CTT": { | |
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| 54502 "variant": "ref-E173K?var_name=CTC4407684CTT&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173K" | |
| 54503 }, | |
| 54504 "gyrA_S91L-TCG7572CTT": { | |
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| 54573 }, | |
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| 56600 0 | |
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| 56602 "variant": "ref-G426T?var_name=GGC761082ACC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426T" | |
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| 56637 "variant": "ref-H57R?var_name=GTG2289071ACG&num_alts=12&ref=NC_000962.3&enum=0&gene=pncA&mut=H57R" | |
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| 56670 0 | |
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| 56700 -2.8095676992849885 | |
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| 56702 "_cls": "Call.VariantCall", | |
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| 56947 "_cls": "Call.VariantCall", | |
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| 56953 }, | |
| 56954 "rpoB_Q436D-CAG761112GAT": { | |
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| 58127 17.0 | |
| 58128 ], | |
| 58129 "filter": "PASS", | |
| 58130 "conf": 99999996 | |
| 58131 }, | |
| 58132 "genotype_likelihoods": [ | |
| 58133 -2.6237799345145465, | |
| 58134 -99999999, | |
| 58135 -99999999 | |
| 58136 ], | |
| 58137 "_cls": "Call.VariantCall", | |
| 58138 "genotype": [ | |
| 58139 0, | |
| 58140 0 | |
| 58141 ], | |
| 58142 "variant": "ref-L440R?var_name=CTG761124CGG&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440R" | |
| 58143 }, | |
| 58144 "rpoB_S441E-TCG761127GAG": { | |
| 58145 "info": { | |
| 58146 "contamination_depths": [], | |
| 58147 "coverage": { | |
| 58148 "alternate": { | |
| 58149 "median_depth": 0, | |
| 58150 "min_non_zero_depth": 18, | |
| 58151 "percent_coverage": 4.55, | |
| 58152 "kmer_count": 18 | |
| 58153 }, | |
| 58154 "reference": { | |
| 58155 "median_depth": 17, | |
| 58156 "min_non_zero_depth": 17, | |
| 58157 "percent_coverage": 100.0, | |
| 58158 "kmer_count": 384 | |
| 58159 } | |
| 58160 }, | |
| 58161 "expected_depths": [ | |
| 58162 17.0 | |
| 58163 ], | |
| 58164 "filter": "PASS", | |
| 58165 "conf": 99999996 | |
| 58166 }, | |
| 58167 "genotype_likelihoods": [ | |
| 58168 -2.6237799345145465, | |
| 58169 -99999999, | |
| 58170 -99999999 | |
| 58171 ], | |
| 58172 "_cls": "Call.VariantCall", | |
| 58173 "genotype": [ | |
| 58174 0, | |
| 58175 0 | |
| 58176 ], | |
| 58177 "variant": "ref-S441E?var_name=TCG761127GAG&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441E" | |
| 58178 }, | |
| 58179 "gid_S136G-TGA4407795GCC": { | |
| 58180 "info": { | |
| 58181 "contamination_depths": [], | |
| 58182 "coverage": { | |
| 58183 "alternate": { | |
| 58184 "median_depth": 0, | |
| 58185 "min_non_zero_depth": 0, | |
| 58186 "percent_coverage": 0.0, | |
| 58187 "kmer_count": 0 | |
| 58188 }, | |
| 58189 "reference": { | |
| 58190 "median_depth": 15, | |
| 58191 "min_non_zero_depth": 14, | |
| 58192 "percent_coverage": 100.0, | |
| 58193 "kmer_count": 327 | |
| 58194 } | |
| 58195 }, | |
| 58196 "expected_depths": [ | |
| 58197 17.0 | |
| 58198 ], | |
| 58199 "filter": "PASS", | |
| 58200 "conf": 99999996 | |
| 58201 }, | |
| 58202 "genotype_likelihoods": [ | |
| 58203 -2.6844045563309873, | |
| 58204 -99999999, | |
| 58205 -99999999 | |
| 58206 ], | |
| 58207 "_cls": "Call.VariantCall", | |
| 58208 "genotype": [ | |
| 58209 0, | |
| 58210 0 | |
| 58211 ], | |
| 58212 "variant": "ref-S136G?var_name=TGA4407795GCC&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136G" | |
| 58213 }, | |
| 58214 "gyrA_P86L-CCG7557TTG": { | |
| 58215 "info": { | |
| 58216 "contamination_depths": [], | |
| 58217 "coverage": { | |
| 58218 "alternate": { | |
| 58219 "median_depth": 0, | |
| 58220 "min_non_zero_depth": 19, | |
| 58221 "percent_coverage": 4.55, | |
| 58222 "kmer_count": 19 | |
| 58223 }, | |
| 58224 "reference": { | |
| 58225 "median_depth": 16, | |
| 58226 "min_non_zero_depth": 13, | |
| 58227 "percent_coverage": 100.0, | |
| 58228 "kmer_count": 359 | |
| 58229 } | |
| 58230 }, | |
| 58231 "expected_depths": [ | |
| 58232 17.0 | |
| 58233 ], | |
| 58234 "filter": "PASS", | |
| 58235 "conf": 99999996 | |
| 58236 }, | |
| 58237 "genotype_likelihoods": [ | |
| 58238 -2.62377993451455, | |
| 58239 -99999999, | |
| 58240 -99999999 | |
| 58241 ], | |
| 58242 "_cls": "Call.VariantCall", | |
| 58243 "genotype": [ | |
| 58244 0, | |
| 58245 0 | |
| 58246 ], | |
| 58247 "variant": "ref-P86L?var_name=CCG7557TTG&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86L" | |
| 58248 }, | |
| 58249 "gid_V41I-GAC4408080GAT": { | |
| 58250 "info": { | |
| 58251 "contamination_depths": [], | |
| 58252 "coverage": { | |
| 58253 "alternate": { | |
| 58254 "median_depth": 0, | |
| 58255 "min_non_zero_depth": 17, | |
| 58256 "percent_coverage": 8.7, | |
| 58257 "kmer_count": 37 | |
| 58258 }, | |
| 58259 "reference": { | |
| 58260 "median_depth": 18, | |
| 58261 "min_non_zero_depth": 17, | |
| 58262 "percent_coverage": 100.0, | |
| 58263 "kmer_count": 424 | |
| 58264 } | |
| 58265 }, | |
| 58266 "expected_depths": [ | |
| 58267 17.0 | |
| 58268 ], | |
| 58269 "filter": "PASS", | |
| 58270 "conf": 99999996 | |
| 58271 }, | |
| 58272 "genotype_likelihoods": [ | |
| 58273 -2.6809383483544966, | |
| 58274 -99999999, | |
| 58275 -99999999 | |
| 58276 ], | |
| 58277 "_cls": "Call.VariantCall", | |
| 58278 "genotype": [ | |
| 58279 0, | |
| 58280 0 | |
| 58281 ], | |
| 58282 "variant": "ref-V41I?var_name=GAC4408080GAT&num_alts=31&ref=NC_000962.3&enum=0&gene=gid&mut=V41I" | |
| 58283 }, | |
| 58284 "pncA_V21G-TAC2289179ACC": { | |
| 58285 "info": { | |
| 58286 "contamination_depths": [], | |
| 58287 "coverage": { | |
| 58288 "alternate": { | |
| 58289 "median_depth": 0, | |
| 58290 "min_non_zero_depth": 17, | |
| 58291 "percent_coverage": 4.55, | |
| 58292 "kmer_count": 17 | |
| 58293 }, | |
| 58294 "reference": { | |
| 58295 "median_depth": 19, | |
| 58296 "min_non_zero_depth": 17, | |
| 58297 "percent_coverage": 100.0, | |
| 58298 "kmer_count": 427 | |
| 58299 } | |
| 58300 }, | |
| 58301 "expected_depths": [ | |
| 58302 17.0 | |
| 58303 ], | |
| 58304 "filter": "PASS", | |
| 58305 "conf": 99999996 | |
| 58306 }, | |
| 58307 "genotype_likelihoods": [ | |
| 58308 -2.79216398346472, | |
| 58309 -99999999, | |
| 58310 -99999999 | |
| 58311 ], | |
| 58312 "_cls": "Call.VariantCall", | |
| 58313 "genotype": [ | |
| 58314 0, | |
| 58315 0 | |
| 58316 ], | |
| 58317 "variant": "ref-V21G?var_name=TAC2289179ACC&num_alts=5&ref=NC_000962.3&enum=0&gene=pncA&mut=V21G" | |
| 58318 }, | |
| 58319 "gyrA_D94Y-GAC7581TAC": { | |
| 58320 "info": { | |
| 58321 "contamination_depths": [], | |
| 58322 "coverage": { | |
| 58323 "alternate": { | |
| 58324 "median_depth": 0, | |
| 58325 "min_non_zero_depth": 17, | |
| 58326 "percent_coverage": 9.09, | |
| 58327 "kmer_count": 34 | |
| 58328 }, | |
| 58329 "reference": { | |
| 58330 "median_depth": 19, | |
| 58331 "min_non_zero_depth": 17, | |
| 58332 "percent_coverage": 100.0, | |
| 58333 "kmer_count": 406 | |
| 58334 } | |
| 58335 }, | |
| 58336 "expected_depths": [ | |
| 58337 17.0 | |
| 58338 ], | |
| 58339 "filter": "PASS", | |
| 58340 "conf": 99999996 | |
| 58341 }, | |
| 58342 "genotype_likelihoods": [ | |
| 58343 -2.79216398346472, | |
| 58344 -99999999, | |
| 58345 -99999999 | |
| 58346 ], | |
| 58347 "_cls": "Call.VariantCall", | |
| 58348 "genotype": [ | |
| 58349 0, | |
| 58350 0 | |
| 58351 ], | |
| 58352 "variant": "ref-D94Y?var_name=GAC7581TAC&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94Y" | |
| 58353 }, | |
| 58354 "rpoB_A451K-GCG761157AAG": { | |
| 58355 "info": { | |
| 58356 "contamination_depths": [], | |
| 58357 "coverage": { | |
| 58358 "alternate": { | |
| 58359 "median_depth": 0, | |
| 58360 "min_non_zero_depth": 15, | |
| 58361 "percent_coverage": 4.55, | |
| 58362 "kmer_count": 15 | |
| 58363 }, | |
| 58364 "reference": { | |
| 58365 "median_depth": 14, | |
| 58366 "min_non_zero_depth": 14, | |
| 58367 "percent_coverage": 100.0, | |
| 58368 "kmer_count": 319 | |
| 58369 } | |
| 58370 }, | |
| 58371 "expected_depths": [ | |
| 58372 17.0 | |
| 58373 ], | |
| 58374 "filter": "PASS", | |
| 58375 "conf": 99999996 | |
| 58376 }, | |
| 58377 "genotype_likelihoods": [ | |
| 58378 -2.8095676992849885, | |
| 58379 -99999999, | |
| 58380 -99999999 | |
| 58381 ], | |
| 58382 "_cls": "Call.VariantCall", | |
| 58383 "genotype": [ | |
| 58384 0, | |
| 58385 0 | |
| 58386 ], | |
| 58387 "variant": "ref-A451K?var_name=GCG761157AAG&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451K" | |
| 58388 }, | |
| 58389 "rpoB_T444H-ACC761136CAC": { | |
| 58390 "info": { | |
| 58391 "contamination_depths": [], | |
| 58392 "coverage": { | |
| 58393 "alternate": { | |
| 58394 "median_depth": 0, | |
| 58395 "min_non_zero_depth": 16, | |
| 58396 "percent_coverage": 4.55, | |
| 58397 "kmer_count": 16 | |
| 58398 }, | |
| 58399 "reference": { | |
| 58400 "median_depth": 17, | |
| 58401 "min_non_zero_depth": 16, | |
| 58402 "percent_coverage": 100.0, | |
| 58403 "kmer_count": 380 | |
| 58404 } | |
| 58405 }, | |
| 58406 "expected_depths": [ | |
| 58407 17.0 | |
| 58408 ], | |
| 58409 "filter": "PASS", | |
| 58410 "conf": 99999996 | |
| 58411 }, | |
| 58412 "genotype_likelihoods": [ | |
| 58413 -2.6237799345145465, | |
| 58414 -99999999, | |
| 58415 -99999999 | |
| 58416 ], | |
| 58417 "_cls": "Call.VariantCall", | |
| 58418 "genotype": [ | |
| 58419 0, | |
| 58420 0 | |
| 58421 ], | |
| 58422 "variant": "ref-T444H?var_name=ACC761136CAC&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444H" | |
| 58423 }, | |
| 58424 "rpoB_G442C-GGG761130TGC": { | |
| 58425 "info": { | |
| 58426 "contamination_depths": [], | |
| 58427 "coverage": { | |
| 58428 "alternate": { | |
| 58429 "median_depth": 0, | |
| 58430 "min_non_zero_depth": 0, | |
| 58431 "percent_coverage": 0.0, | |
| 58432 "kmer_count": 0 | |
| 58433 }, | |
| 58434 "reference": { | |
| 58435 "median_depth": 18, | |
| 58436 "min_non_zero_depth": 17, | |
| 58437 "percent_coverage": 100.0, | |
| 58438 "kmer_count": 387 | |
| 58439 } | |
| 58440 }, | |
| 58441 "expected_depths": [ | |
| 58442 17.0 | |
| 58443 ], | |
| 58444 "filter": "PASS", | |
| 58445 "conf": 99999996 | |
| 58446 }, | |
| 58447 "genotype_likelihoods": [ | |
| 58448 -2.6809383483544966, | |
| 58449 -99999999, | |
| 58450 -99999999 | |
| 58451 ], | |
| 58452 "_cls": "Call.VariantCall", | |
| 58453 "genotype": [ | |
| 58454 0, | |
| 58455 0 | |
| 58456 ], | |
| 58457 "variant": "ref-G442C?var_name=GGG761130TGC&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442C" | |
| 58458 }, | |
| 58459 "pncA_V125G-GAC2288867TCC": { | |
| 58460 "info": { | |
| 58461 "contamination_depths": [], | |
| 58462 "coverage": { | |
| 58463 "alternate": { | |
| 58464 "median_depth": 0, | |
| 58465 "min_non_zero_depth": 16, | |
| 58466 "percent_coverage": 27.27, | |
| 58467 "kmer_count": 100 | |
| 58468 }, | |
| 58469 "reference": { | |
| 58470 "median_depth": 16, | |
| 58471 "min_non_zero_depth": 15, | |
| 58472 "percent_coverage": 100.0, | |
| 58473 "kmer_count": 352 | |
| 58474 } | |
| 58475 }, | |
| 58476 "expected_depths": [ | |
| 58477 17.0 | |
| 58478 ], | |
| 58479 "filter": "PASS", | |
| 58480 "conf": 99999996 | |
| 58481 }, | |
| 58482 "genotype_likelihoods": [ | |
| 58483 -2.62377993451455, | |
| 58484 -99999999, | |
| 58485 -99999999 | |
| 58486 ], | |
| 58487 "_cls": "Call.VariantCall", | |
| 58488 "genotype": [ | |
| 58489 0, | |
| 58490 0 | |
| 58491 ], | |
| 58492 "variant": "ref-V125G?var_name=GAC2288867TCC&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=V125G" | |
| 58493 }, | |
| 58494 "gyrA_P86D-CCG7557GAT": { | |
| 58495 "info": { | |
| 58496 "contamination_depths": [], | |
| 58497 "coverage": { | |
| 58498 "alternate": { | |
| 58499 "median_depth": 0, | |
| 58500 "min_non_zero_depth": 0, | |
| 58501 "percent_coverage": 0.0, | |
| 58502 "kmer_count": 0 | |
| 58503 }, | |
| 58504 "reference": { | |
| 58505 "median_depth": 16, | |
| 58506 "min_non_zero_depth": 13, | |
| 58507 "percent_coverage": 100.0, | |
| 58508 "kmer_count": 359 | |
| 58509 } | |
| 58510 }, | |
| 58511 "expected_depths": [ | |
| 58512 17.0 | |
| 58513 ], | |
| 58514 "filter": "PASS", | |
| 58515 "conf": 99999996 | |
| 58516 }, | |
| 58517 "genotype_likelihoods": [ | |
| 58518 -2.62377993451455, | |
| 58519 -99999999, | |
| 58520 -99999999 | |
| 58521 ], | |
| 58522 "_cls": "Call.VariantCall", | |
| 58523 "genotype": [ | |
| 58524 0, | |
| 58525 0 | |
| 58526 ], | |
| 58527 "variant": "ref-P86D?var_name=CCG7557GAT&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86D" | |
| 58528 }, | |
| 58529 "katG_W191R-CCA2155539TCG": { | |
| 58530 "info": { | |
| 58531 "contamination_depths": [], | |
| 58532 "coverage": { | |
| 58533 "alternate": { | |
| 58534 "median_depth": 0, | |
| 58535 "min_non_zero_depth": 0, | |
| 58536 "percent_coverage": 0.0, | |
| 58537 "kmer_count": 0 | |
| 58538 }, | |
| 58539 "reference": { | |
| 58540 "median_depth": 27, | |
| 58541 "min_non_zero_depth": 26, | |
| 58542 "percent_coverage": 100.0, | |
| 58543 "kmer_count": 596 | |
| 58544 } | |
| 58545 }, | |
| 58546 "expected_depths": [ | |
| 58547 17.0 | |
| 58548 ], | |
| 58549 "filter": "PASS", | |
| 58550 "conf": 99999994 | |
| 58551 }, | |
| 58552 "genotype_likelihoods": [ | |
| 58553 -5.3441116708218335, | |
| 58554 -99999999, | |
| 58555 -99999999 | |
| 58556 ], | |
| 58557 "_cls": "Call.VariantCall", | |
| 58558 "genotype": [ | |
| 58559 0, | |
| 58560 0 | |
| 58561 ], | |
| 58562 "variant": "ref-W191R?var_name=CCA2155539TCG&num_alts=3&ref=NC_000962.3&enum=0&gene=katG&mut=W191R" | |
| 58563 }, | |
| 58564 "rpoB_T444L-ACC761136CTA": { | |
| 58565 "info": { | |
| 58566 "contamination_depths": [], | |
| 58567 "coverage": { | |
| 58568 "alternate": { | |
| 58569 "median_depth": 0, | |
| 58570 "min_non_zero_depth": 0, | |
| 58571 "percent_coverage": 0.0, | |
| 58572 "kmer_count": 0 | |
| 58573 }, | |
| 58574 "reference": { | |
| 58575 "median_depth": 17, | |
| 58576 "min_non_zero_depth": 16, | |
| 58577 "percent_coverage": 100.0, | |
| 58578 "kmer_count": 380 | |
| 58579 } | |
| 58580 }, | |
| 58581 "expected_depths": [ | |
| 58582 17.0 | |
| 58583 ], | |
| 58584 "filter": "PASS", | |
| 58585 "conf": 99999996 | |
| 58586 }, | |
| 58587 "genotype_likelihoods": [ | |
| 58588 -2.6237799345145465, | |
| 58589 -99999999, | |
| 58590 -99999999 | |
| 58591 ], | |
| 58592 "_cls": "Call.VariantCall", | |
| 58593 "genotype": [ | |
| 58594 0, | |
| 58595 0 | |
| 58596 ], | |
| 58597 "variant": "ref-T444L?var_name=ACC761136CTA&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444L" | |
| 58598 }, | |
| 58599 "gyrA_Y93P-TAC7578CCC": { | |
| 58600 "info": { | |
| 58601 "contamination_depths": [], | |
| 58602 "coverage": { | |
| 58603 "alternate": { | |
| 58604 "median_depth": 0, | |
| 58605 "min_non_zero_depth": 17, | |
| 58606 "percent_coverage": 4.55, | |
| 58607 "kmer_count": 17 | |
| 58608 }, | |
| 58609 "reference": { | |
| 58610 "median_depth": 19, | |
| 58611 "min_non_zero_depth": 17, | |
| 58612 "percent_coverage": 100.0, | |
| 58613 "kmer_count": 412 | |
| 58614 } | |
| 58615 }, | |
| 58616 "expected_depths": [ | |
| 58617 17.0 | |
| 58618 ], | |
| 58619 "filter": "PASS", | |
| 58620 "conf": 99999996 | |
| 58621 }, | |
| 58622 "genotype_likelihoods": [ | |
| 58623 -2.79216398346472, | |
| 58624 -99999999, | |
| 58625 -99999999 | |
| 58626 ], | |
| 58627 "_cls": "Call.VariantCall", | |
| 58628 "genotype": [ | |
| 58629 0, | |
| 58630 0 | |
| 58631 ], | |
| 58632 "variant": "ref-Y93P?var_name=TAC7578CCC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93P" | |
| 58633 }, | |
| 58634 "rpoB_S431N-AGC761097AAC": { | |
| 58635 "info": { | |
| 58636 "contamination_depths": [], | |
| 58637 "coverage": { | |
| 58638 "alternate": { | |
| 58639 "median_depth": 0, | |
| 58640 "min_non_zero_depth": 19, | |
| 58641 "percent_coverage": 27.27, | |
| 58642 "kmer_count": 118 | |
| 58643 }, | |
| 58644 "reference": { | |
| 58645 "median_depth": 19, | |
| 58646 "min_non_zero_depth": 17, | |
| 58647 "percent_coverage": 100.0, | |
| 58648 "kmer_count": 411 | |
| 58649 } | |
| 58650 }, | |
| 58651 "expected_depths": [ | |
| 58652 17.0 | |
| 58653 ], | |
| 58654 "filter": "PASS", | |
| 58655 "conf": 99999996 | |
| 58656 }, | |
| 58657 "genotype_likelihoods": [ | |
| 58658 -2.79216398346472, | |
| 58659 -99999999, | |
| 58660 -99999999 | |
| 58661 ], | |
| 58662 "_cls": "Call.VariantCall", | |
| 58663 "genotype": [ | |
| 58664 0, | |
| 58665 0 | |
| 58666 ], | |
| 58667 "variant": "ref-S431N?var_name=AGC761097AAC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431N" | |
| 58668 }, | |
| 58669 "gyrA_D89L-GAC7566CTG": { | |
| 58670 "info": { | |
| 58671 "contamination_depths": [], | |
| 58672 "coverage": { | |
| 58673 "alternate": { | |
| 58674 "median_depth": 0, | |
| 58675 "min_non_zero_depth": 0, | |
| 58676 "percent_coverage": 0.0, | |
| 58677 "kmer_count": 0 | |
| 58678 }, | |
| 58679 "reference": { | |
| 58680 "median_depth": 18, | |
| 58681 "min_non_zero_depth": 16, | |
| 58682 "percent_coverage": 100.0, | |
| 58683 "kmer_count": 400 | |
| 58684 } | |
| 58685 }, | |
| 58686 "expected_depths": [ | |
| 58687 17.0 | |
| 58688 ], | |
| 58689 "filter": "PASS", | |
| 58690 "conf": 99999996 | |
| 58691 }, | |
| 58692 "genotype_likelihoods": [ | |
| 58693 -2.6809383483544966, | |
| 58694 -99999999, | |
| 58695 -99999999 | |
| 58696 ], | |
| 58697 "_cls": "Call.VariantCall", | |
| 58698 "genotype": [ | |
| 58699 0, | |
| 58700 0 | |
| 58701 ], | |
| 58702 "variant": "ref-D89L?var_name=GAC7566CTG&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89L" | |
| 58703 }, | |
| 58704 "gyrA_D94V-GAC7581GTG": { | |
| 58705 "info": { | |
| 58706 "contamination_depths": [], | |
| 58707 "coverage": { | |
| 58708 "alternate": { | |
| 58709 "median_depth": 0, | |
| 58710 "min_non_zero_depth": 0, | |
| 58711 "percent_coverage": 0.0, | |
| 58712 "kmer_count": 0 | |
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| 58716 "min_non_zero_depth": 17, | |
| 58717 "percent_coverage": 100.0, | |
| 58718 "kmer_count": 406 | |
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| 58720 }, | |
| 58721 "expected_depths": [ | |
| 58722 17.0 | |
| 58723 ], | |
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| 58726 }, | |
| 58727 "genotype_likelihoods": [ | |
| 58728 -2.79216398346472, | |
| 58729 -99999999, | |
| 58730 -99999999 | |
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| 58732 "_cls": "Call.VariantCall", | |
| 58733 "genotype": [ | |
| 58734 0, | |
| 58735 0 | |
| 58736 ], | |
| 58737 "variant": "ref-D94V?var_name=GAC7581GTG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94V" | |
| 58738 }, | |
| 58739 "katG_W505S-CCA2154597TGA": { | |
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| 58747 "kmer_count": 16 | |
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| 58751 "min_non_zero_depth": 16, | |
| 58752 "percent_coverage": 100.0, | |
| 58753 "kmer_count": 385 | |
| 58754 } | |
| 58755 }, | |
| 58756 "expected_depths": [ | |
| 58757 17.0 | |
| 58758 ], | |
| 58759 "filter": "PASS", | |
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| 58761 }, | |
| 58762 "genotype_likelihoods": [ | |
| 58763 -2.6809383483544966, | |
| 58764 -99999999, | |
| 58765 -99999999 | |
| 58766 ], | |
| 58767 "_cls": "Call.VariantCall", | |
| 58768 "genotype": [ | |
| 58769 0, | |
| 58770 0 | |
| 58771 ], | |
| 58772 "variant": "ref-W505S?var_name=CCA2154597TGA&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505S" | |
| 58773 }, | |
| 58774 "rpoB_M434R-ATG761106AGG": { | |
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| 58786 "min_non_zero_depth": 17, | |
| 58787 "percent_coverage": 100.0, | |
| 58788 "kmer_count": 420 | |
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| 58790 }, | |
| 58791 "expected_depths": [ | |
| 58792 17.0 | |
| 58793 ], | |
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| 58795 "conf": 99999996 | |
| 58796 }, | |
| 58797 "genotype_likelihoods": [ | |
| 58798 -2.79216398346472, | |
| 58799 -99999999, | |
| 58800 -99999999 | |
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| 58802 "_cls": "Call.VariantCall", | |
| 58803 "genotype": [ | |
| 58804 0, | |
| 58805 0 | |
| 58806 ], | |
| 58807 "variant": "ref-M434R?var_name=ATG761106AGG&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434R" | |
| 58808 }, | |
| 58809 "gyrA_I92P-ATC7575CCC": { | |
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| 58815 "min_non_zero_depth": 18, | |
| 58816 "percent_coverage": 4.55, | |
| 58817 "kmer_count": 18 | |
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| 58820 "median_depth": 19, | |
| 58821 "min_non_zero_depth": 18, | |
| 58822 "percent_coverage": 100.0, | |
| 58823 "kmer_count": 414 | |
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| 58825 }, | |
| 58826 "expected_depths": [ | |
| 58827 17.0 | |
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| 58829 "filter": "PASS", | |
| 58830 "conf": 99999996 | |
| 58831 }, | |
| 58832 "genotype_likelihoods": [ | |
| 58833 -2.79216398346472, | |
| 58834 -99999999, | |
| 58835 -99999999 | |
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| 58837 "_cls": "Call.VariantCall", | |
| 58838 "genotype": [ | |
| 58839 0, | |
| 58840 0 | |
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| 58842 "variant": "ref-I92P?var_name=ATC7575CCC&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92P" | |
| 58843 }, | |
| 58844 "gyrA_G88P-GGC7563CCA": { | |
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| 58856 "min_non_zero_depth": 15, | |
| 58857 "percent_coverage": 95.45, | |
| 58858 "kmer_count": 370 | |
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| 58860 }, | |
| 58861 "expected_depths": [ | |
| 58862 17.0 | |
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| 58864 "filter": "LOW_GT_CONF", | |
| 58865 "conf": 0 | |
| 58866 }, | |
| 58867 "genotype_likelihoods": [ | |
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| 58869 -99999999, | |
| 58870 -99999999 | |
| 58871 ], | |
| 58872 "_cls": "Call.VariantCall", | |
| 58873 "genotype": [ | |
| 58874 0, | |
| 58875 0 | |
| 58876 ], | |
| 58877 "variant": "ref-G88P?var_name=GGC7563CCA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88P" | |
| 58878 }, | |
| 58879 "rpoB_M434S-ATG761106AGC": { | |
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| 58893 "kmer_count": 420 | |
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| 58895 }, | |
| 58896 "expected_depths": [ | |
| 58897 17.0 | |
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| 58900 "conf": 99999996 | |
| 58901 }, | |
| 58902 "genotype_likelihoods": [ | |
| 58903 -2.79216398346472, | |
| 58904 -99999999, | |
| 58905 -99999999 | |
| 58906 ], | |
| 58907 "_cls": "Call.VariantCall", | |
| 58908 "genotype": [ | |
| 58909 0, | |
| 58910 0 | |
| 58911 ], | |
| 58912 "variant": "ref-M434S?var_name=ATG761106AGC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434S" | |
| 58913 }, | |
| 58914 "gyrA_H87S-CAC7560TCT": { | |
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| 58921 "percent_coverage": 0.0, | |
| 58922 "kmer_count": 0 | |
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| 58926 "min_non_zero_depth": 15, | |
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| 58928 "kmer_count": 377 | |
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| 58931 "expected_depths": [ | |
| 58932 17.0 | |
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| 58936 }, | |
| 58937 "genotype_likelihoods": [ | |
| 58938 -2.6809383483544966, | |
| 58939 -99999999, | |
| 58940 -99999999 | |
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| 58942 "_cls": "Call.VariantCall", | |
| 58943 "genotype": [ | |
| 58944 0, | |
| 58945 0 | |
| 58946 ], | |
| 58947 "variant": "ref-H87S?var_name=CAC7560TCT&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87S" | |
| 58948 }, | |
| 58949 "gyrA_S91Q-TCG7572CAA": { | |
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| 58967 17.0 | |
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| 58971 }, | |
| 58972 "genotype_likelihoods": [ | |
| 58973 -2.79216398346472, | |
| 58974 -99999999, | |
| 58975 -99999999 | |
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| 58977 "_cls": "Call.VariantCall", | |
| 58978 "genotype": [ | |
| 58979 0, | |
| 58980 0 | |
| 58981 ], | |
| 58982 "variant": "ref-S91Q?var_name=TCG7572CAA&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91Q" | |
| 58983 }, | |
| 58984 "rpoB_T444S-ACC761136AGC": { | |
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| 58990 "min_non_zero_depth": 16, | |
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| 58992 "kmer_count": 16 | |
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| 58994 "reference": { | |
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| 58996 "min_non_zero_depth": 16, | |
| 58997 "percent_coverage": 100.0, | |
| 58998 "kmer_count": 380 | |
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| 59001 "expected_depths": [ | |
| 59002 17.0 | |
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| 59006 }, | |
| 59007 "genotype_likelihoods": [ | |
| 59008 -2.6237799345145465, | |
| 59009 -99999999, | |
| 59010 -99999999 | |
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| 59012 "_cls": "Call.VariantCall", | |
| 59013 "genotype": [ | |
| 59014 0, | |
| 59015 0 | |
| 59016 ], | |
| 59017 "variant": "ref-T444S?var_name=ACC761136AGC&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444S" | |
| 59018 }, | |
| 59019 "pncA_M175V-CAT2288717CAC": { | |
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| 59022 "coverage": { | |
| 59023 "alternate": { | |
| 59024 "median_depth": 0, | |
| 59025 "min_non_zero_depth": 21, | |
| 59026 "percent_coverage": 4.55, | |
| 59027 "kmer_count": 21 | |
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| 59029 "reference": { | |
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| 59031 "min_non_zero_depth": 19, | |
| 59032 "percent_coverage": 100.0, | |
| 59033 "kmer_count": 444 | |
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| 59035 }, | |
| 59036 "expected_depths": [ | |
| 59037 17.0 | |
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| 59041 }, | |
| 59042 "genotype_likelihoods": [ | |
| 59043 -2.9546829129624985, | |
| 59044 -99999999, | |
| 59045 -99999999 | |
| 59046 ], | |
| 59047 "_cls": "Call.VariantCall", | |
| 59048 "genotype": [ | |
| 59049 0, | |
| 59050 0 | |
| 59051 ], | |
| 59052 "variant": "ref-M175V?var_name=CAT2288717CAC&num_alts=8&ref=NC_000962.3&enum=0&gene=pncA&mut=M175V" | |
| 59053 }, | |
| 59054 "rpoB_R448L-CGA761148CTA": { | |
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| 59058 "alternate": { | |
| 59059 "median_depth": 0, | |
| 59060 "min_non_zero_depth": 14, | |
| 59061 "percent_coverage": 4.55, | |
| 59062 "kmer_count": 14 | |
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| 59064 "reference": { | |
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| 59066 "min_non_zero_depth": 14, | |
| 59067 "percent_coverage": 100.0, | |
| 59068 "kmer_count": 346 | |
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| 59070 }, | |
| 59071 "expected_depths": [ | |
| 59072 17.0 | |
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| 59074 "filter": "PASS", | |
| 59075 "conf": 99999996 | |
| 59076 }, | |
| 59077 "genotype_likelihoods": [ | |
| 59078 -2.62377993451455, | |
| 59079 -99999999, | |
| 59080 -99999999 | |
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| 59082 "_cls": "Call.VariantCall", | |
| 59083 "genotype": [ | |
| 59084 0, | |
| 59085 0 | |
| 59086 ], | |
| 59087 "variant": "ref-R448L?var_name=CGA761148CTA&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448L" | |
| 59088 }, | |
| 59089 "gyrA_I92L-ATC7575TTA": { | |
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| 59095 "min_non_zero_depth": 0, | |
| 59096 "percent_coverage": 0.0, | |
| 59097 "kmer_count": 0 | |
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| 59099 "reference": { | |
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| 59101 "min_non_zero_depth": 18, | |
| 59102 "percent_coverage": 100.0, | |
| 59103 "kmer_count": 414 | |
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| 59105 }, | |
| 59106 "expected_depths": [ | |
| 59107 17.0 | |
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| 59110 "conf": 99999996 | |
| 59111 }, | |
| 59112 "genotype_likelihoods": [ | |
| 59113 -2.79216398346472, | |
| 59114 -99999999, | |
| 59115 -99999999 | |
| 59116 ], | |
| 59117 "_cls": "Call.VariantCall", | |
| 59118 "genotype": [ | |
| 59119 0, | |
| 59120 0 | |
| 59121 ], | |
| 59122 "variant": "ref-I92L?var_name=ATC7575TTA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92L" | |
| 59123 }, | |
| 59124 "rrs_C517A-C1472362A": { | |
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| 59127 "coverage": { | |
| 59128 "alternate": { | |
| 59129 "median_depth": 0, | |
| 59130 "min_non_zero_depth": 18, | |
| 59131 "percent_coverage": 9.09, | |
| 59132 "kmer_count": 36 | |
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| 59134 "reference": { | |
| 59135 "median_depth": 18, | |
| 59136 "min_non_zero_depth": 17, | |
| 59137 "percent_coverage": 100.0, | |
| 59138 "kmer_count": 426 | |
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| 59141 "expected_depths": [ | |
| 59142 17.0 | |
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| 59146 }, | |
| 59147 "genotype_likelihoods": [ | |
| 59148 -2.6809383483544966, | |
| 59149 -99999999, | |
| 59150 -99999999 | |
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| 59152 "_cls": "Call.VariantCall", | |
| 59153 "genotype": [ | |
| 59154 0, | |
| 59155 0 | |
| 59156 ], | |
| 59157 "variant": "ref-C517A?var_name=C1472362A&num_alts=12&ref=NC_000962.3&enum=0&gene=rrs&mut=C517A" | |
| 59158 }, | |
| 59159 "gyrA_P86A-CCG7557GCC": { | |
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| 59163 "alternate": { | |
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| 59166 "percent_coverage": 0.0, | |
| 59167 "kmer_count": 0 | |
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| 59169 "reference": { | |
| 59170 "median_depth": 16, | |
| 59171 "min_non_zero_depth": 13, | |
| 59172 "percent_coverage": 100.0, | |
| 59173 "kmer_count": 359 | |
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| 59176 "expected_depths": [ | |
| 59177 17.0 | |
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| 59179 "filter": "PASS", | |
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| 59181 }, | |
| 59182 "genotype_likelihoods": [ | |
| 59183 -2.62377993451455, | |
| 59184 -99999999, | |
| 59185 -99999999 | |
| 59186 ], | |
| 59187 "_cls": "Call.VariantCall", | |
| 59188 "genotype": [ | |
| 59189 0, | |
| 59190 0 | |
| 59191 ], | |
| 59192 "variant": "ref-P86A?var_name=CCG7557GCC&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86A" | |
| 59193 }, | |
| 59194 "gyrA_S91D-TCG7572GAT": { | |
| 59195 "info": { | |
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| 59197 "coverage": { | |
| 59198 "alternate": { | |
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| 59201 "percent_coverage": 0.0, | |
| 59202 "kmer_count": 0 | |
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| 59204 "reference": { | |
| 59205 "median_depth": 19, | |
| 59206 "min_non_zero_depth": 18, | |
| 59207 "percent_coverage": 100.0, | |
| 59208 "kmer_count": 413 | |
| 59209 } | |
| 59210 }, | |
| 59211 "expected_depths": [ | |
| 59212 17.0 | |
| 59213 ], | |
| 59214 "filter": "PASS", | |
| 59215 "conf": 99999996 | |
| 59216 }, | |
| 59217 "genotype_likelihoods": [ | |
| 59218 -2.79216398346472, | |
| 59219 -99999999, | |
| 59220 -99999999 | |
| 59221 ], | |
| 59222 "_cls": "Call.VariantCall", | |
| 59223 "genotype": [ | |
| 59224 0, | |
| 59225 0 | |
| 59226 ], | |
| 59227 "variant": "ref-S91D?var_name=TCG7572GAT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91D" | |
| 59228 }, | |
| 59229 "pncA_V180F-GAC2288702GAA": { | |
| 59230 "info": { | |
| 59231 "contamination_depths": [], | |
| 59232 "coverage": { | |
| 59233 "alternate": { | |
| 59234 "median_depth": 0, | |
| 59235 "min_non_zero_depth": 21, | |
| 59236 "percent_coverage": 4.55, | |
| 59237 "kmer_count": 21 | |
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| 59239 "reference": { | |
| 59240 "median_depth": 20, | |
| 59241 "min_non_zero_depth": 19, | |
| 59242 "percent_coverage": 100.0, | |
| 59243 "kmer_count": 444 | |
| 59244 } | |
| 59245 }, | |
| 59246 "expected_depths": [ | |
| 59247 17.0 | |
| 59248 ], | |
| 59249 "filter": "PASS", | |
| 59250 "conf": 99999996 | |
| 59251 }, | |
| 59252 "genotype_likelihoods": [ | |
| 59253 -2.9546829129624985, | |
| 59254 -99999999, | |
| 59255 -99999999 | |
| 59256 ], | |
| 59257 "_cls": "Call.VariantCall", | |
| 59258 "genotype": [ | |
| 59259 0, | |
| 59260 0 | |
| 59261 ], | |
| 59262 "variant": "ref-V180F?var_name=GAC2288702GAA&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=V180F" | |
| 59263 }, | |
| 59264 "rpoB_G981D-GGC762747GAC": { | |
| 59265 "info": { | |
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| 59267 "coverage": { | |
| 59268 "alternate": { | |
| 59269 "median_depth": 0, | |
| 59270 "min_non_zero_depth": 7, | |
| 59271 "percent_coverage": 4.55, | |
| 59272 "kmer_count": 7 | |
| 59273 }, | |
| 59274 "reference": { | |
| 59275 "median_depth": 6, | |
| 59276 "min_non_zero_depth": 6, | |
| 59277 "percent_coverage": 100.0, | |
| 59278 "kmer_count": 142 | |
| 59279 } | |
| 59280 }, | |
| 59281 "expected_depths": [ | |
| 59282 17.0 | |
| 59283 ], | |
| 59284 "filter": "PASS", | |
| 59285 "conf": 99999992 | |
| 59286 }, | |
| 59287 "genotype_likelihoods": [ | |
| 59288 -6.863304481006136, | |
| 59289 -99999999, | |
| 59290 -99999999 | |
| 59291 ], | |
| 59292 "_cls": "Call.VariantCall", | |
| 59293 "genotype": [ | |
| 59294 0, | |
| 59295 0 | |
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| 59890 0 | |
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| 59928 }, | |
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| 60030 0 | |
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| 60033 }, | |
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| 60100 0 | |
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| 60103 }, | |
| 60104 "gyrA_G88V-GGC7563GTC": { | |
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| 60138 }, | |
| 60139 "rpoB_P439T-CCG761121ACG": { | |
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| 60174 "gid_E173A-CTC4407684GGC": { | |
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| 60202 "_cls": "Call.VariantCall", | |
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| 60205 0 | |
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| 60207 "variant": "ref-E173A?var_name=CTC4407684GGC&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=E173A" | |
| 60208 }, | |
| 60209 "gyrA_A90E-GCG7569GAG": { | |
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| 60237 "_cls": "Call.VariantCall", | |
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| 60240 0 | |
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| 60242 "variant": "ref-A90E?var_name=GCG7569GAG&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90E" | |
| 60243 }, | |
| 60244 "rpoB_G442S-GGG761130TCC": { | |
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| 60272 "_cls": "Call.VariantCall", | |
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| 60277 "variant": "ref-G442S?var_name=GGG761130TCC&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442S" | |
| 60278 }, | |
| 60279 "pncA_Q10N-CTG2289212ATT": { | |
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| 60307 "_cls": "Call.VariantCall", | |
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| 60312 "variant": "ref-Q10N?var_name=CTG2289212ATT&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10N" | |
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| 60337 "genotype_likelihoods": [ | |
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| 60342 "_cls": "Call.VariantCall", | |
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| 60349 "rpoB_K446L-AAG761142CTG": { | |
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| 60372 "genotype_likelihoods": [ | |
| 60373 -2.6237799345145465, | |
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| 60377 "_cls": "Call.VariantCall", | |
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| 60380 0 | |
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| 60382 "variant": "ref-K446L?var_name=AAG761142CTG&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446L" | |
| 60383 }, | |
| 60384 "rpoB_H445G-CAC761139GGA": { | |
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| 60407 "genotype_likelihoods": [ | |
| 60408 -2.6237799345145465, | |
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| 60412 "_cls": "Call.VariantCall", | |
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| 60417 "variant": "ref-H445G?var_name=CAC761139GGA&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445G" | |
| 60418 }, | |
| 60419 "rpoB_S428G-AGC761088GGG": { | |
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| 60441 }, | |
| 60442 "genotype_likelihoods": [ | |
| 60443 -2.6809383483544966, | |
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| 60447 "_cls": "Call.VariantCall", | |
| 60448 "genotype": [ | |
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| 60450 0 | |
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| 60452 "variant": "ref-S428G?var_name=AGC761088GGG&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428G" | |
| 60453 }, | |
| 60454 "rpoB_M434E-ATG761106GAG": { | |
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| 61958 }, | |
| 61959 "rpoB_F433K-TTC761103AAG": { | |
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| 62028 }, | |
| 62029 "rpoB_Q429T-CAG761091ACA": { | |
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| 62064 "rpoB_L440S-CTG761124TCT": { | |
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| 62097 "variant": "ref-L440S?var_name=CTG761124TCT&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440S" | |
| 62098 }, | |
| 62099 "rpoB_S431P-AGC761097CCA": { | |
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| 62122 "genotype_likelihoods": [ | |
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| 62127 "_cls": "Call.VariantCall", | |
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| 62132 "variant": "ref-S431P?var_name=AGC761097CCA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431P" | |
| 62133 }, | |
| 62134 "inhA_S94A-TCG1674481GCG": { | |
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| 62151 "expected_depths": [ | |
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| 62157 "genotype_likelihoods": [ | |
| 62158 -2.6237799345145465, | |
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| 62162 "_cls": "Call.VariantCall", | |
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| 62167 "variant": "ref-S94A?var_name=TCG1674481GCG&num_alts=4&ref=NC_000962.3&enum=0&gene=inhA&mut=S94A" | |
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| 62169 "gyrA_D89C-GAC7566TGT": { | |
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| 62192 "genotype_likelihoods": [ | |
| 62193 -2.6809383483544966, | |
| 62194 -99999999, | |
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| 62197 "_cls": "Call.VariantCall", | |
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| 62200 0 | |
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| 62202 "variant": "ref-D89C?var_name=GAC7566TGT&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89C" | |
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| 62204 "gid_P93L-CGG4407924AAG": { | |
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| 62222 17.0 | |
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| 62227 "genotype_likelihoods": [ | |
| 62228 -2.6237799345145465, | |
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| 62300 -99999999 | |
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| 62340 0 | |
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| 62342 "variant": "ref-L440V?var_name=CTG761124GTA&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440V" | |
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| 62375 0 | |
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| 62377 "variant": "ref-S428E?var_name=AGC761088GAA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428E" | |
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| 62379 "embB_M306L-ATG4247429CTC": { | |
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| 62402 "genotype_likelihoods": [ | |
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| 62407 "_cls": "Call.VariantCall", | |
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| 62412 "variant": "ref-M306L?var_name=ATG4247429CTC&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306L" | |
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| 62442 "_cls": "Call.VariantCall", | |
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| 62445 0 | |
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| 62480 0 | |
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| 62482 "variant": "ref-G34V?var_name=CCC4408101CAC&num_alts=38&ref=NC_000962.3&enum=0&gene=gid&mut=G34V" | |
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| 62484 "rpoB_N438T-AAC761118ACA": { | |
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| 62506 }, | |
| 62507 "genotype_likelihoods": [ | |
| 62508 -2.6809383483544966, | |
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| 62510 -99999999 | |
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| 62512 "_cls": "Call.VariantCall", | |
| 62513 "genotype": [ | |
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| 62515 0 | |
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| 62517 "variant": "ref-N438T?var_name=AAC761118ACA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438T" | |
| 62518 }, | |
| 62519 "rpoB_Q429W-CAG761091TGG": { | |
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| 62542 "genotype_likelihoods": [ | |
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| 62547 "_cls": "Call.VariantCall", | |
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| 62550 0 | |
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| 62552 "variant": "ref-Q429W?var_name=CAG761091TGG&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429W" | |
| 62553 }, | |
| 62554 "gyrA_D89R-GAC7566AGG": { | |
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| 62582 "_cls": "Call.VariantCall", | |
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| 62585 0 | |
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| 62587 "variant": "ref-D89R?var_name=GAC7566AGG&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89R" | |
| 62588 }, | |
| 62589 "gid_Q125V-CTG4407828GAC": { | |
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| 62612 "genotype_likelihoods": [ | |
| 62613 -3.0037237137259485, | |
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| 62617 "_cls": "Call.VariantCall", | |
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| 62620 0 | |
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| 62622 "variant": "ref-Q125V?var_name=CTG4407828GAC&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125V" | |
| 62623 }, | |
| 62624 "rpoB_L430R-CTG761094CGG": { | |
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| 62641 "expected_depths": [ | |
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| 62647 "genotype_likelihoods": [ | |
| 62648 -2.6809383483544966, | |
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| 62657 "variant": "ref-L430R?var_name=CTG761094CGG&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430R" | |
| 62658 }, | |
| 62659 "rpoB_R448G-CGA761148GGT": { | |
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| 62682 "genotype_likelihoods": [ | |
| 62683 -2.62377993451455, | |
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| 62692 "variant": "ref-R448G?var_name=CGA761148GGT&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R448G" | |
| 62693 }, | |
| 62694 "pncA_V180F-GAC2288702AAA": { | |
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| 62722 "_cls": "Call.VariantCall", | |
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| 62727 "variant": "ref-V180F?var_name=GAC2288702AAA&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=V180F" | |
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| 62729 "rpoB_L443V-TTG761133GTG": { | |
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| 62752 "genotype_likelihoods": [ | |
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| 62755 -99999999 | |
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| 62762 "variant": "ref-L443V?var_name=TTG761133GTG&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443V" | |
| 62763 }, | |
| 62764 "rpoB_H445F-CAC761139TTT": { | |
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| 62782 17.0 | |
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| 62787 "genotype_likelihoods": [ | |
| 62788 -2.6237799345145465, | |
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| 62792 "_cls": "Call.VariantCall", | |
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| 62794 0, | |
| 62795 0 | |
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| 62797 "variant": "ref-H445F?var_name=CAC761139TTT&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445F" | |
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| 62830 0 | |
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| 62900 0 | |
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| 62902 "variant": "ref-T114P?var_name=CGT2288900AGG&num_alts=3&ref=NC_000962.3&enum=0&gene=pncA&mut=T114P" | |
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| 62904 "rpoB_V359A-GTG760881GCG": { | |
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| 62922 17.0 | |
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| 62935 0 | |
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| 62937 "variant": "ref-V359A?var_name=GTG760881GCG&num_alts=3&ref=NC_000962.3&enum=0&gene=rpoB&mut=V359A" | |
| 62938 }, | |
| 62939 "rpoB_L430R-CTG761094CGC": { | |
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| 62957 17.0 | |
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| 62970 0 | |
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| 62973 }, | |
| 62974 "gyrA_G88L-GGC7563CTG": { | |
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| 63000 -99999999 | |
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| 63004 0, | |
| 63005 0 | |
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| 63007 "variant": "ref-G88L?var_name=GGC7563CTG&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88L" | |
| 63008 }, | |
| 63009 "rpoB_S428V-AGC761088GTG": { | |
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| 63021 "min_non_zero_depth": 14, | |
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| 63027 17.0 | |
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| 63032 "genotype_likelihoods": [ | |
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| 63039 0, | |
| 63040 0 | |
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| 63042 "variant": "ref-S428V?var_name=AGC761088GTG&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428V" | |
| 63043 }, | |
| 63044 "katG_S315T-GCT2155167GGT": { | |
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| 63075 0 | |
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| 63077 "variant": "ref-S315T?var_name=GCT2155167GGT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315T" | |
| 63078 }, | |
| 63079 "gid_S136I-TGA4407795TAT": { | |
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| 63102 "genotype_likelihoods": [ | |
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| 63107 "_cls": "Call.VariantCall", | |
| 63108 "genotype": [ | |
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| 63110 0 | |
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| 63112 "variant": "ref-S136I?var_name=TGA4407795TAT&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136I" | |
| 63113 }, | |
| 63114 "rpoB_R447S-CGC761145TCC": { | |
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| 63126 "min_non_zero_depth": 14, | |
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| 63137 "genotype_likelihoods": [ | |
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| 63142 "_cls": "Call.VariantCall", | |
| 63143 "genotype": [ | |
| 63144 0, | |
| 63145 0 | |
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| 63147 "variant": "ref-R447S?var_name=CGC761145TCC&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447S" | |
| 63148 }, | |
| 63149 "gid_P93L-CGG4407924TAA": { | |
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| 63161 "min_non_zero_depth": 14, | |
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| 63172 "genotype_likelihoods": [ | |
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| 63177 "_cls": "Call.VariantCall", | |
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| 63179 0, | |
| 63180 0 | |
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| 63182 "variant": "ref-P93L?var_name=CGG4407924TAA&num_alts=15&ref=NC_000962.3&enum=0&gene=gid&mut=P93L" | |
| 63183 }, | |
| 63184 "rpoB_D435A-GAC761109GCG": { | |
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| 63207 "genotype_likelihoods": [ | |
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| 63212 "_cls": "Call.VariantCall", | |
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| 63214 0, | |
| 63215 0 | |
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| 63217 "variant": "ref-D435A?var_name=GAC761109GCG&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435A" | |
| 63218 }, | |
| 63219 "gid_D85A-GTC4407948TGC": { | |
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| 63230 "median_depth": 20, | |
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| 63242 "genotype_likelihoods": [ | |
| 63243 -2.9546829129624985, | |
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| 63249 0, | |
| 63250 0 | |
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| 63252 "variant": "ref-D85A?var_name=GTC4407948TGC&num_alts=17&ref=NC_000962.3&enum=0&gene=gid&mut=D85A" | |
| 63253 }, | |
| 63254 "rpoB_G442E-GGG761130GAG": { | |
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| 63272 17.0 | |
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| 63277 "genotype_likelihoods": [ | |
| 63278 -2.6809383483544966, | |
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| 63280 -99999999 | |
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| 63282 "_cls": "Call.VariantCall", | |
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| 63284 0, | |
| 63285 0 | |
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| 63287 "variant": "ref-G442E?var_name=GGG761130GAG&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442E" | |
| 63288 }, | |
| 63289 "rpoB_L440A-CTG761124GCC": { | |
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| 63306 "expected_depths": [ | |
| 63307 17.0 | |
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| 63312 "genotype_likelihoods": [ | |
| 63313 -2.6237799345145465, | |
| 63314 -99999999, | |
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| 63317 "_cls": "Call.VariantCall", | |
| 63318 "genotype": [ | |
| 63319 0, | |
| 63320 0 | |
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| 63322 "variant": "ref-L440A?var_name=CTG761124GCC&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440A" | |
| 63323 }, | |
| 63324 "pncA_W68R-CCA2289038ACG": { | |
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| 63330 "min_non_zero_depth": 11, | |
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| 63332 "kmer_count": 55 | |
| 63333 }, | |
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| 63336 "min_non_zero_depth": 10, | |
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| 63338 "kmer_count": 238 | |
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| 63341 "expected_depths": [ | |
| 63342 17.0 | |
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| 63345 "conf": 99999995 | |
| 63346 }, | |
| 63347 "genotype_likelihoods": [ | |
| 63348 -3.620294394588841, | |
| 63349 -99999999, | |
| 63350 -99999999 | |
| 63351 ], | |
| 63352 "_cls": "Call.VariantCall", | |
| 63353 "genotype": [ | |
| 63354 0, | |
| 63355 0 | |
| 63356 ], | |
| 63357 "variant": "ref-W68R?var_name=CCA2289038ACG&num_alts=39&ref=NC_000962.3&enum=0&gene=pncA&mut=W68R" | |
| 63358 }, | |
| 63359 "embB_M306A-ATG4247429GCT": { | |
| 63360 "info": { | |
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| 63363 "alternate": { | |
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| 63390 0 | |
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| 63557 "genotype_likelihoods": [ | |
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| 63600 0 | |
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| 63603 }, | |
| 63604 "pncA_Q10L-CTG2289212TAA": { | |
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| 63674 "pncA_T135P-GGT2288837TGG": { | |
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| 63709 "rpoB_P439R-CCG761121CGT": { | |
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| 63849 "rpoB_D435R-GAC761109CGT": { | |
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| 63884 "gyrA_P86R-CCG7557AGG": { | |
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| 63919 "gyrA_G88F-GGC7563TTC": { | |
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| 68640 0 | |
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| 70219 "embB_M306E-ATG4247429GAG": { | |
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| 70247 "_cls": "Call.VariantCall", | |
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| 70254 "rpoB_D435H-GAC761109CAT": { | |
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| 70852 "coverage": { | |
| 70853 "alternate": { | |
| 70854 "median_depth": 0, | |
| 70855 "min_non_zero_depth": 17, | |
| 70856 "percent_coverage": 4.55, | |
| 70857 "kmer_count": 17 | |
| 70858 }, | |
| 70859 "reference": { | |
| 70860 "median_depth": 19, | |
| 70861 "min_non_zero_depth": 17, | |
| 70862 "percent_coverage": 100.0, | |
| 70863 "kmer_count": 412 | |
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| 70865 }, | |
| 70866 "expected_depths": [ | |
| 70867 17.0 | |
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| 70869 "filter": "PASS", | |
| 70870 "conf": 99999996 | |
| 70871 }, | |
| 70872 "genotype_likelihoods": [ | |
| 70873 -2.79216398346472, | |
| 70874 -99999999, | |
| 70875 -99999999 | |
| 70876 ], | |
| 70877 "_cls": "Call.VariantCall", | |
| 70878 "genotype": [ | |
| 70879 0, | |
| 70880 0 | |
| 70881 ], | |
| 70882 "variant": "ref-Y93G?var_name=TAC7578GGC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93G" | |
| 70883 }, | |
| 70884 "rpoB_S428R-AGC761088CGT": { | |
| 70885 "info": { | |
| 70886 "contamination_depths": [], | |
| 70887 "coverage": { | |
| 70888 "alternate": { | |
| 70889 "median_depth": 0, | |
| 70890 "min_non_zero_depth": 0, | |
| 70891 "percent_coverage": 0.0, | |
| 70892 "kmer_count": 0 | |
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| 70894 "reference": { | |
| 70895 "median_depth": 18, | |
| 70896 "min_non_zero_depth": 14, | |
| 70897 "percent_coverage": 100.0, | |
| 70898 "kmer_count": 382 | |
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| 70900 }, | |
| 70901 "expected_depths": [ | |
| 70902 17.0 | |
| 70903 ], | |
| 70904 "filter": "PASS", | |
| 70905 "conf": 99999996 | |
| 70906 }, | |
| 70907 "genotype_likelihoods": [ | |
| 70908 -2.6809383483544966, | |
| 70909 -99999999, | |
| 70910 -99999999 | |
| 70911 ], | |
| 70912 "_cls": "Call.VariantCall", | |
| 70913 "genotype": [ | |
| 70914 0, | |
| 70915 0 | |
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| 70917 "variant": "ref-S428R?var_name=AGC761088CGT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428R" | |
| 70918 }, | |
| 70919 "katG_W505G-CCA2154597GCC": { | |
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| 70924 "median_depth": 0, | |
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| 70926 "percent_coverage": 0.0, | |
| 70927 "kmer_count": 0 | |
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| 70930 "median_depth": 18, | |
| 70931 "min_non_zero_depth": 16, | |
| 70932 "percent_coverage": 100.0, | |
| 70933 "kmer_count": 385 | |
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| 70935 }, | |
| 70936 "expected_depths": [ | |
| 70937 17.0 | |
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| 70939 "filter": "PASS", | |
| 70940 "conf": 99999996 | |
| 70941 }, | |
| 70942 "genotype_likelihoods": [ | |
| 70943 -2.6809383483544966, | |
| 70944 -99999999, | |
| 70945 -99999999 | |
| 70946 ], | |
| 70947 "_cls": "Call.VariantCall", | |
| 70948 "genotype": [ | |
| 70949 0, | |
| 70950 0 | |
| 70951 ], | |
| 70952 "variant": "ref-W505G?var_name=CCA2154597GCC&num_alts=4&ref=NC_000962.3&enum=0&gene=katG&mut=W505G" | |
| 70953 }, | |
| 70954 "pncA_Y99L-GTA2288945AAG": { | |
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| 70956 "contamination_depths": [], | |
| 70957 "coverage": { | |
| 70958 "alternate": { | |
| 70959 "median_depth": 0, | |
| 70960 "min_non_zero_depth": 16, | |
| 70961 "percent_coverage": 9.09, | |
| 70962 "kmer_count": 32 | |
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| 70965 "median_depth": 16, | |
| 70966 "min_non_zero_depth": 16, | |
| 70967 "percent_coverage": 100.0, | |
| 70968 "kmer_count": 362 | |
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| 70970 }, | |
| 70971 "expected_depths": [ | |
| 70972 17.0 | |
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| 70974 "filter": "PASS", | |
| 70975 "conf": 99999996 | |
| 70976 }, | |
| 70977 "genotype_likelihoods": [ | |
| 70978 -2.62377993451455, | |
| 70979 -99999999, | |
| 70980 -99999999 | |
| 70981 ], | |
| 70982 "_cls": "Call.VariantCall", | |
| 70983 "genotype": [ | |
| 70984 0, | |
| 70985 0 | |
| 70986 ], | |
| 70987 "variant": "ref-Y99L?var_name=GTA2288945AAG&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99L" | |
| 70988 }, | |
| 70989 "rpoB_N437S-AAC761115AGC": { | |
| 70990 "info": { | |
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| 70993 "alternate": { | |
| 70994 "median_depth": 0, | |
| 70995 "min_non_zero_depth": 17, | |
| 70996 "percent_coverage": 27.27, | |
| 70997 "kmer_count": 102 | |
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| 70999 "reference": { | |
| 71000 "median_depth": 18, | |
| 71001 "min_non_zero_depth": 17, | |
| 71002 "percent_coverage": 100.0, | |
| 71003 "kmer_count": 408 | |
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| 71005 }, | |
| 71006 "expected_depths": [ | |
| 71007 17.0 | |
| 71008 ], | |
| 71009 "filter": "PASS", | |
| 71010 "conf": 99999996 | |
| 71011 }, | |
| 71012 "genotype_likelihoods": [ | |
| 71013 -2.6809383483544966, | |
| 71014 -99999999, | |
| 71015 -99999999 | |
| 71016 ], | |
| 71017 "_cls": "Call.VariantCall", | |
| 71018 "genotype": [ | |
| 71019 0, | |
| 71020 0 | |
| 71021 ], | |
| 71022 "variant": "ref-N437S?var_name=AAC761115AGC&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437S" | |
| 71023 }, | |
| 71024 "rpoB_P439G-CCG761121GGT": { | |
| 71025 "info": { | |
| 71026 "contamination_depths": [], | |
| 71027 "coverage": { | |
| 71028 "alternate": { | |
| 71029 "median_depth": 0, | |
| 71030 "min_non_zero_depth": 17, | |
| 71031 "percent_coverage": 13.64, | |
| 71032 "kmer_count": 53 | |
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| 71034 "reference": { | |
| 71035 "median_depth": 17, | |
| 71036 "min_non_zero_depth": 17, | |
| 71037 "percent_coverage": 100.0, | |
| 71038 "kmer_count": 390 | |
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| 71040 }, | |
| 71041 "expected_depths": [ | |
| 71042 17.0 | |
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| 71044 "filter": "PASS", | |
| 71045 "conf": 99999996 | |
| 71046 }, | |
| 71047 "genotype_likelihoods": [ | |
| 71048 -2.6237799345145465, | |
| 71049 -99999999, | |
| 71050 -99999999 | |
| 71051 ], | |
| 71052 "_cls": "Call.VariantCall", | |
| 71053 "genotype": [ | |
| 71054 0, | |
| 71055 0 | |
| 71056 ], | |
| 71057 "variant": "ref-P439G?var_name=CCG761121GGT&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439G" | |
| 71058 }, | |
| 71059 "gyrA_D94C-GAC7581TGC": { | |
| 71060 "info": { | |
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| 71063 "alternate": { | |
| 71064 "median_depth": 0, | |
| 71065 "min_non_zero_depth": 17, | |
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| 71069 "reference": { | |
| 71070 "median_depth": 19, | |
| 71071 "min_non_zero_depth": 17, | |
| 71072 "percent_coverage": 100.0, | |
| 71073 "kmer_count": 406 | |
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| 71075 }, | |
| 71076 "expected_depths": [ | |
| 71077 17.0 | |
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| 71079 "filter": "PASS", | |
| 71080 "conf": 99999996 | |
| 71081 }, | |
| 71082 "genotype_likelihoods": [ | |
| 71083 -2.79216398346472, | |
| 71084 -99999999, | |
| 71085 -99999999 | |
| 71086 ], | |
| 71087 "_cls": "Call.VariantCall", | |
| 71088 "genotype": [ | |
| 71089 0, | |
| 71090 0 | |
| 71091 ], | |
| 71092 "variant": "ref-D94C?var_name=GAC7581TGC&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94C" | |
| 71093 }, | |
| 71094 "rpoB_D435E-GAC761109GAG": { | |
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| 71098 "alternate": { | |
| 71099 "median_depth": 0, | |
| 71100 "min_non_zero_depth": 19, | |
| 71101 "percent_coverage": 4.55, | |
| 71102 "kmer_count": 19 | |
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| 71108 "kmer_count": 416 | |
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| 71111 "expected_depths": [ | |
| 71112 17.0 | |
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| 71115 "conf": 99999996 | |
| 71116 }, | |
| 71117 "genotype_likelihoods": [ | |
| 71118 -2.79216398346472, | |
| 71119 -99999999, | |
| 71120 -99999999 | |
| 71121 ], | |
| 71122 "_cls": "Call.VariantCall", | |
| 71123 "genotype": [ | |
| 71124 0, | |
| 71125 0 | |
| 71126 ], | |
| 71127 "variant": "ref-D435E?var_name=GAC761109GAG&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435E" | |
| 71128 }, | |
| 71129 "gyrA_G88R-GGC7563CGA": { | |
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| 71137 "kmer_count": 0 | |
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| 71140 "median_depth": 18, | |
| 71141 "min_non_zero_depth": 15, | |
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| 71143 "kmer_count": 370 | |
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| 71146 "expected_depths": [ | |
| 71147 17.0 | |
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| 71149 "filter": "LOW_GT_CONF", | |
| 71150 "conf": 0 | |
| 71151 }, | |
| 71152 "genotype_likelihoods": [ | |
| 71153 -99999999, | |
| 71154 -99999999, | |
| 71155 -99999999 | |
| 71156 ], | |
| 71157 "_cls": "Call.VariantCall", | |
| 71158 "genotype": [ | |
| 71159 0, | |
| 71160 0 | |
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| 71162 "variant": "ref-G88R?var_name=GGC7563CGA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88R" | |
| 71163 }, | |
| 71164 "pncA_L151S-CAA2288789AGA": { | |
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| 71170 "min_non_zero_depth": 10, | |
| 71171 "percent_coverage": 4.55, | |
| 71172 "kmer_count": 10 | |
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| 71174 "reference": { | |
| 71175 "median_depth": 13, | |
| 71176 "min_non_zero_depth": 10, | |
| 71177 "percent_coverage": 100.0, | |
| 71178 "kmer_count": 285 | |
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| 71181 "expected_depths": [ | |
| 71182 17.0 | |
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| 71184 "filter": "PASS", | |
| 71185 "conf": 99999996 | |
| 71186 }, | |
| 71187 "genotype_likelihoods": [ | |
| 71188 -3.0037237137259485, | |
| 71189 -99999999, | |
| 71190 -99999999 | |
| 71191 ], | |
| 71192 "_cls": "Call.VariantCall", | |
| 71193 "genotype": [ | |
| 71194 0, | |
| 71195 0 | |
| 71196 ], | |
| 71197 "variant": "ref-L151S?var_name=CAA2288789AGA&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=L151S" | |
| 71198 }, | |
| 71199 "gyrA_D89A-GAC7566GCC": { | |
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| 71204 "median_depth": 0, | |
| 71205 "min_non_zero_depth": 19, | |
| 71206 "percent_coverage": 4.55, | |
| 71207 "kmer_count": 19 | |
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| 71210 "median_depth": 18, | |
| 71211 "min_non_zero_depth": 16, | |
| 71212 "percent_coverage": 100.0, | |
| 71213 "kmer_count": 400 | |
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| 71216 "expected_depths": [ | |
| 71217 17.0 | |
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| 71219 "filter": "PASS", | |
| 71220 "conf": 99999996 | |
| 71221 }, | |
| 71222 "genotype_likelihoods": [ | |
| 71223 -2.6809383483544966, | |
| 71224 -99999999, | |
| 71225 -99999999 | |
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| 71227 "_cls": "Call.VariantCall", | |
| 71228 "genotype": [ | |
| 71229 0, | |
| 71230 0 | |
| 71231 ], | |
| 71232 "variant": "ref-D89A?var_name=GAC7566GCC&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89A" | |
| 71233 }, | |
| 71234 "rpoB_Q432N-CAA761100AAT": { | |
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| 71242 "kmer_count": 93 | |
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| 71247 "percent_coverage": 100.0, | |
| 71248 "kmer_count": 417 | |
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| 71251 "expected_depths": [ | |
| 71252 17.0 | |
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| 71254 "filter": "PASS", | |
| 71255 "conf": 99999996 | |
| 71256 }, | |
| 71257 "genotype_likelihoods": [ | |
| 71258 -2.79216398346472, | |
| 71259 -99999999, | |
| 71260 -99999999 | |
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| 71262 "_cls": "Call.VariantCall", | |
| 71263 "genotype": [ | |
| 71264 0, | |
| 71265 0 | |
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| 71267 "variant": "ref-Q432N?var_name=CAA761100AAT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432N" | |
| 71268 }, | |
| 71269 "rpoB_L452R-CTG761160AGA": { | |
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| 71279 "reference": { | |
| 71280 "median_depth": 14, | |
| 71281 "min_non_zero_depth": 14, | |
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| 71283 "kmer_count": 315 | |
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| 71286 "expected_depths": [ | |
| 71287 17.0 | |
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| 71290 "conf": 99999996 | |
| 71291 }, | |
| 71292 "genotype_likelihoods": [ | |
| 71293 -2.8095676992849885, | |
| 71294 -99999999, | |
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| 71297 "_cls": "Call.VariantCall", | |
| 71298 "genotype": [ | |
| 71299 0, | |
| 71300 0 | |
| 71301 ], | |
| 71302 "variant": "ref-L452R?var_name=CTG761160AGA&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452R" | |
| 71303 }, | |
| 71304 "rpoB_G426D-GGC761082GAC": { | |
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| 71310 "min_non_zero_depth": 18, | |
| 71311 "percent_coverage": 8.0, | |
| 71312 "kmer_count": 36 | |
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| 71314 "reference": { | |
| 71315 "median_depth": 17, | |
| 71316 "min_non_zero_depth": 14, | |
| 71317 "percent_coverage": 92.0, | |
| 71318 "kmer_count": 373 | |
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| 71320 }, | |
| 71321 "expected_depths": [ | |
| 71322 17.0 | |
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| 71324 "filter": "LOW_GT_CONF", | |
| 71325 "conf": 0 | |
| 71326 }, | |
| 71327 "genotype_likelihoods": [ | |
| 71328 -99999999, | |
| 71329 -99999999, | |
| 71330 -99999999 | |
| 71331 ], | |
| 71332 "_cls": "Call.VariantCall", | |
| 71333 "genotype": [ | |
| 71334 0, | |
| 71335 0 | |
| 71336 ], | |
| 71337 "variant": "ref-G426D?var_name=GGC761082GAC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426D" | |
| 71338 }, | |
| 71339 "gyrA_A90R-GCG7569AGG": { | |
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| 71345 "min_non_zero_depth": 20, | |
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| 71347 "kmer_count": 20 | |
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| 71351 "min_non_zero_depth": 18, | |
| 71352 "percent_coverage": 100.0, | |
| 71353 "kmer_count": 410 | |
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| 71355 }, | |
| 71356 "expected_depths": [ | |
| 71357 17.0 | |
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| 71359 "filter": "PASS", | |
| 71360 "conf": 99999996 | |
| 71361 }, | |
| 71362 "genotype_likelihoods": [ | |
| 71363 -2.79216398346472, | |
| 71364 -99999999, | |
| 71365 -99999999 | |
| 71366 ], | |
| 71367 "_cls": "Call.VariantCall", | |
| 71368 "genotype": [ | |
| 71369 0, | |
| 71370 0 | |
| 71371 ], | |
| 71372 "variant": "ref-A90R?var_name=GCG7569AGG&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90R" | |
| 71373 }, | |
| 71374 "rpoB_L443Q-TTG761133CAG": { | |
| 71375 "info": { | |
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| 71377 "coverage": { | |
| 71378 "alternate": { | |
| 71379 "median_depth": 0, | |
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| 71382 "kmer_count": 0 | |
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| 71384 "reference": { | |
| 71385 "median_depth": 18, | |
| 71386 "min_non_zero_depth": 17, | |
| 71387 "percent_coverage": 95.45, | |
| 71388 "kmer_count": 369 | |
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| 71390 }, | |
| 71391 "expected_depths": [ | |
| 71392 17.0 | |
| 71393 ], | |
| 71394 "filter": "LOW_GT_CONF", | |
| 71395 "conf": 0 | |
| 71396 }, | |
| 71397 "genotype_likelihoods": [ | |
| 71398 -99999999, | |
| 71399 -99999999, | |
| 71400 -99999999 | |
| 71401 ], | |
| 71402 "_cls": "Call.VariantCall", | |
| 71403 "genotype": [ | |
| 71404 0, | |
| 71405 0 | |
| 71406 ], | |
| 71407 "variant": "ref-L443Q?var_name=TTG761133CAG&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443Q" | |
| 71408 }, | |
| 71409 "gyrA_P86R-CCG7557CGA": { | |
| 71410 "info": { | |
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| 71414 "median_depth": 0, | |
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| 71417 "kmer_count": 0 | |
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| 71986 "expected_depths": [ | |
| 71987 17.0 | |
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| 71992 "genotype_likelihoods": [ | |
| 71993 -2.79216398346472, | |
| 71994 -99999999, | |
| 71995 -99999999 | |
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| 71997 "_cls": "Call.VariantCall", | |
| 71998 "genotype": [ | |
| 71999 0, | |
| 72000 0 | |
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| 72002 "variant": "ref-I92R?var_name=ATC7575AGG&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92R" | |
| 72003 }, | |
| 72004 "gyrA_P86C-CCG7557TGT": { | |
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| 72012 "kmer_count": 0 | |
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| 72014 "reference": { | |
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| 72016 "min_non_zero_depth": 13, | |
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| 72022 17.0 | |
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| 72026 }, | |
| 72027 "genotype_likelihoods": [ | |
| 72028 -2.62377993451455, | |
| 72029 -99999999, | |
| 72030 -99999999 | |
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| 72032 "_cls": "Call.VariantCall", | |
| 72033 "genotype": [ | |
| 72034 0, | |
| 72035 0 | |
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| 72037 "variant": "ref-P86C?var_name=CCG7557TGT&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86C" | |
| 72038 }, | |
| 72039 "rpoB_T444N-ACC761136AAT": { | |
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| 72051 "min_non_zero_depth": 16, | |
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| 72053 "kmer_count": 380 | |
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| 72057 17.0 | |
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| 72062 "genotype_likelihoods": [ | |
| 72063 -2.6237799345145465, | |
| 72064 -99999999, | |
| 72065 -99999999 | |
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| 72067 "_cls": "Call.VariantCall", | |
| 72068 "genotype": [ | |
| 72069 0, | |
| 72070 0 | |
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| 72072 "variant": "ref-T444N?var_name=ACC761136AAT&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444N" | |
| 72073 }, | |
| 72074 "rpoB_A451D-GCG761157GAC": { | |
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| 72086 "min_non_zero_depth": 14, | |
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| 72088 "kmer_count": 319 | |
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| 72090 }, | |
| 72091 "expected_depths": [ | |
| 72092 17.0 | |
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| 72096 }, | |
| 72097 "genotype_likelihoods": [ | |
| 72098 -2.8095676992849885, | |
| 72099 -99999999, | |
| 72100 -99999999 | |
| 72101 ], | |
| 72102 "_cls": "Call.VariantCall", | |
| 72103 "genotype": [ | |
| 72104 0, | |
| 72105 0 | |
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| 72107 "variant": "ref-A451D?var_name=GCG761157GAC&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451D" | |
| 72108 }, | |
| 72109 "gid_S136G-TGA4407795TCC": { | |
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| 72121 "min_non_zero_depth": 14, | |
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| 72123 "kmer_count": 327 | |
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| 72126 "expected_depths": [ | |
| 72127 17.0 | |
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| 72131 }, | |
| 72132 "genotype_likelihoods": [ | |
| 72133 -2.6844045563309873, | |
| 72134 -99999999, | |
| 72135 -99999999 | |
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| 72137 "_cls": "Call.VariantCall", | |
| 72138 "genotype": [ | |
| 72139 0, | |
| 72140 0 | |
| 72141 ], | |
| 72142 "variant": "ref-S136G?var_name=TGA4407795TCC&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136G" | |
| 72143 }, | |
| 72144 "gyrA_G88R-GGC7563CGT": { | |
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| 72156 "min_non_zero_depth": 15, | |
| 72157 "percent_coverage": 95.45, | |
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| 72161 "expected_depths": [ | |
| 72162 17.0 | |
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| 72164 "filter": "LOW_GT_CONF", | |
| 72165 "conf": 0 | |
| 72166 }, | |
| 72167 "genotype_likelihoods": [ | |
| 72168 -99999999, | |
| 72169 -99999999, | |
| 72170 -99999999 | |
| 72171 ], | |
| 72172 "_cls": "Call.VariantCall", | |
| 72173 "genotype": [ | |
| 72174 0, | |
| 72175 0 | |
| 72176 ], | |
| 72177 "variant": "ref-G88R?var_name=GGC7563CGT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88R" | |
| 72178 }, | |
| 72179 "katG_S315K-GCT2155167CTT": { | |
| 72180 "info": { | |
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| 72184 "median_depth": 0, | |
| 72185 "min_non_zero_depth": 17, | |
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| 72189 "reference": { | |
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| 72192 "percent_coverage": 4.55, | |
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| 72196 "expected_depths": [ | |
| 72197 17.0 | |
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| 72199 "filter": "LOW_GT_CONF", | |
| 72200 "conf": 0 | |
| 72201 }, | |
| 72202 "genotype_likelihoods": [ | |
| 72203 -99999999, | |
| 72204 -99999999, | |
| 72205 -99999999 | |
| 72206 ], | |
| 72207 "_cls": "Call.VariantCall", | |
| 72208 "genotype": [ | |
| 72209 0, | |
| 72210 0 | |
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| 72212 "variant": "ref-S315K?var_name=GCT2155167CTT&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315K" | |
| 72213 }, | |
| 72214 "rpoB_L452P-CTG761160CCA": { | |
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| 72232 17.0 | |
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| 72236 }, | |
| 72237 "genotype_likelihoods": [ | |
| 72238 -2.8095676992849885, | |
| 72239 -99999999, | |
| 72240 -99999999 | |
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| 72242 "_cls": "Call.VariantCall", | |
| 72243 "genotype": [ | |
| 72244 0, | |
| 72245 0 | |
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| 72247 "variant": "ref-L452P?var_name=CTG761160CCA&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452P" | |
| 72248 }, | |
| 72249 "embB_M306D-ATG4247429GAC": { | |
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| 72253 "alternate": { | |
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| 72260 "median_depth": 14, | |
| 72261 "min_non_zero_depth": 8, | |
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| 72267 17.0 | |
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| 72278 "genotype": [ | |
| 72279 0, | |
| 72280 0 | |
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| 72282 "variant": "ref-M306D?var_name=ATG4247429GAC&num_alts=4&ref=NC_000962.3&enum=0&gene=embB&mut=M306D" | |
| 72283 }, | |
| 72284 "rpoB_S431G-AGC761097GGA": { | |
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| 72302 17.0 | |
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| 72307 "genotype_likelihoods": [ | |
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| 72313 "genotype": [ | |
| 72314 0, | |
| 72315 0 | |
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| 72317 "variant": "ref-S431G?var_name=AGC761097GGA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431G" | |
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| 72319 "rpoB_G426S-GGC761082AGC": { | |
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| 72340 "conf": 0 | |
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| 72342 "genotype_likelihoods": [ | |
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| 72345 -99999999 | |
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| 72347 "_cls": "Call.VariantCall", | |
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| 72350 0 | |
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| 72352 "variant": "ref-G426S?var_name=GGC761082AGC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=G426S" | |
| 72353 }, | |
| 72354 "gyrA_P86D-CCG7557GAC": { | |
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| 72372 17.0 | |
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| 72377 "genotype_likelihoods": [ | |
| 72378 -2.62377993451455, | |
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| 72382 "_cls": "Call.VariantCall", | |
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| 72384 0, | |
| 72385 0 | |
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| 72387 "variant": "ref-P86D?var_name=CCG7557GAC&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86D" | |
| 72388 }, | |
| 72389 "rpoB_Q436P-CAG761112CCC": { | |
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| 72412 "genotype_likelihoods": [ | |
| 72413 -2.79216398346472, | |
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| 72420 0 | |
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| 72422 "variant": "ref-Q436P?var_name=CAG761112CCC&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436P" | |
| 72423 }, | |
| 72424 "rpoB_P439I-CCG761121ATA": { | |
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| 72442 17.0 | |
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| 72447 "genotype_likelihoods": [ | |
| 72448 -2.6237799345145465, | |
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| 72455 0 | |
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| 72457 "variant": "ref-P439I?var_name=CCG761121ATA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439I" | |
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| 72459 "gyrA_H85P-CAC7554CCA": { | |
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| 72477 17.0 | |
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| 72482 "genotype_likelihoods": [ | |
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| 72490 0 | |
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| 72492 "variant": "ref-H85P?var_name=CAC7554CCA&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85P" | |
| 72493 }, | |
| 72494 "pncA_S32I-GCT2289146GAT": { | |
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| 72522 "_cls": "Call.VariantCall", | |
| 72523 "genotype": [ | |
| 72524 0, | |
| 72525 0 | |
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| 72527 "variant": "ref-S32I?var_name=GCT2289146GAT&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=S32I" | |
| 72528 }, | |
| 72529 "gid_Q125S-CTG4407828TGA": { | |
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| 72546 "expected_depths": [ | |
| 72547 17.0 | |
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| 73680 0 | |
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| 73702 17.0 | |
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| 73710 -99999999 | |
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| 73714 0, | |
| 73715 0 | |
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| 73717 "variant": "ref-T427G?var_name=ACC761085GGA&num_alts=32&ref=NC_000962.3&enum=0&gene=rpoB&mut=T427G" | |
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| 73750 0 | |
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| 73772 17.0 | |
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| 73782 "_cls": "Call.VariantCall", | |
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| 73784 0, | |
| 73785 0 | |
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| 73787 "variant": "ref-L151S?var_name=CAA2288789CGA&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=L151S" | |
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| 73807 17.0 | |
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| 73819 0, | |
| 73820 0 | |
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| 73822 "variant": "ref-A451G?var_name=GCG761157GGA&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451G" | |
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| 73850 -99999999 | |
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| 73854 0, | |
| 73855 0 | |
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| 73857 "variant": "ref-T444S?var_name=ACC761136TCT&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444S" | |
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| 73883 -2.6809383483544966, | |
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| 73889 0, | |
| 73890 0 | |
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| 73892 "variant": "ref-S428V?var_name=AGC761088GTA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428V" | |
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| 73917 "genotype_likelihoods": [ | |
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| 73924 0, | |
| 73925 0 | |
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| 73927 "variant": "ref-Q10I?var_name=CTG2289212GAT&num_alts=9&ref=NC_000962.3&enum=0&gene=pncA&mut=Q10I" | |
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| 73929 "rpoB_K446S-AAG761142AGC": { | |
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| 73947 17.0 | |
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| 73959 0, | |
| 73960 0 | |
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| 73962 "variant": "ref-K446S?var_name=AAG761142AGC&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446S" | |
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| 73964 "rpoB_S428L-AGC761088CTG": { | |
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| 73982 17.0 | |
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| 73988 -2.6809383483544966, | |
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| 73990 -99999999 | |
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| 73992 "_cls": "Call.VariantCall", | |
| 73993 "genotype": [ | |
| 73994 0, | |
| 73995 0 | |
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| 73997 "variant": "ref-S428L?var_name=AGC761088CTG&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428L" | |
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| 73999 "rpoB_M434C-ATG761106TGT": { | |
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| 74030 0 | |
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| 74032 "variant": "ref-M434C?var_name=ATG761106TGT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434C" | |
| 74033 }, | |
| 74034 "rpoB_L443T-TTG761133ACT": { | |
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| 74057 "genotype_likelihoods": [ | |
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| 74065 0 | |
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| 74067 "variant": "ref-L443T?var_name=TTG761133ACT&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443T" | |
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| 74069 "rpoB_K446R-AAG761142AGG": { | |
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| 74092 "genotype_likelihoods": [ | |
| 74093 -2.6237799345145465, | |
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| 74097 "_cls": "Call.VariantCall", | |
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| 74099 0, | |
| 74100 0 | |
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| 74102 "variant": "ref-K446R?var_name=AAG761142AGG&num_alts=43&ref=NC_000962.3&enum=0&gene=rpoB&mut=K446R" | |
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| 74104 "rpoB_L430H-CTG761094CAC": { | |
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| 74127 "genotype_likelihoods": [ | |
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| 74129 -99999999, | |
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| 74132 "_cls": "Call.VariantCall", | |
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| 74137 "variant": "ref-L430H?var_name=CTG761094CAC&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430H" | |
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| 74139 "rpoB_P439E-CCG761121GAA": { | |
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| 74162 "genotype_likelihoods": [ | |
| 74163 -2.6237799345145465, | |
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| 74167 "_cls": "Call.VariantCall", | |
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| 74172 "variant": "ref-P439E?var_name=CCG761121GAA&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=P439E" | |
| 74173 }, | |
| 74174 "rpoB_F433L-TTC761103CTT": { | |
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| 74197 "genotype_likelihoods": [ | |
| 74198 -2.79216398346472, | |
| 74199 -99999999, | |
| 74200 -99999999 | |
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| 74202 "_cls": "Call.VariantCall", | |
| 74203 "genotype": [ | |
| 74204 0, | |
| 74205 0 | |
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| 74207 "variant": "ref-F433L?var_name=TTC761103CTT&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=F433L" | |
| 74208 }, | |
| 74209 "rpoB_S450G-TCG761154GGT": { | |
| 74210 "info": { | |
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| 74230 "conf": 0 | |
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| 74232 "genotype_likelihoods": [ | |
| 74233 -99999999, | |
| 74234 -99999999, | |
| 74235 -99999999 | |
| 74236 ], | |
| 74237 "_cls": "Call.VariantCall", | |
| 74238 "genotype": [ | |
| 74239 0, | |
| 74240 0 | |
| 74241 ], | |
| 74242 "variant": "ref-S450G?var_name=TCG761154GGT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450G" | |
| 74243 }, | |
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| 77110 0 | |
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| 77674 "gyrA_H85E-CAC7554GAA": { | |
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| 79414 -99999999, | |
| 79415 -99999999 | |
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| 79420 0 | |
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| 79490 0 | |
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| 79739 "rpoB_P439E-CCG761121GAG": { | |
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| 79971 }, | |
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| 79974 -99999999, | |
| 79975 -99999999 | |
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| 79979 0, | |
| 79980 0 | |
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| 79982 "variant": "ref-A90T?var_name=GCG7569ACT&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=A90T" | |
| 79983 }, | |
| 79984 "rpoB_D435V-GAC761109GTC": { | |
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| 80000 }, | |
| 80001 "expected_depths": [ | |
| 80002 17.0 | |
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| 80006 }, | |
| 80007 "genotype_likelihoods": [ | |
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| 80009 -99999999, | |
| 80010 -99999999 | |
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| 80012 "_cls": "Call.VariantCall", | |
| 80013 "genotype": [ | |
| 80014 0, | |
| 80015 0 | |
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| 80018 }, | |
| 80019 "rpoB_S450Q-TCG761154CAA": { | |
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| 80035 }, | |
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| 80044 -99999999, | |
| 80045 -99999999 | |
| 80046 ], | |
| 80047 "_cls": "Call.VariantCall", | |
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| 80050 0 | |
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| 80053 }, | |
| 80054 "rpoB_D435K-GAC761109AAA": { | |
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| 80084 0, | |
| 80085 0 | |
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| 80087 "variant": "ref-D435K?var_name=GAC761109AAA&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435K" | |
| 80088 }, | |
| 80089 "rpoB_S428N-AGC761088AAC": { | |
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| 80101 "min_non_zero_depth": 14, | |
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| 80103 "kmer_count": 382 | |
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| 80105 }, | |
| 80106 "expected_depths": [ | |
| 80107 17.0 | |
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| 80111 }, | |
| 80112 "genotype_likelihoods": [ | |
| 80113 -2.6809383483544966, | |
| 80114 -99999999, | |
| 80115 -99999999 | |
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| 80117 "_cls": "Call.VariantCall", | |
| 80118 "genotype": [ | |
| 80119 0, | |
| 80120 0 | |
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| 80122 "variant": "ref-S428N?var_name=AGC761088AAC&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428N" | |
| 80123 }, | |
| 80124 "rpoB_S428H-AGC761088CAT": { | |
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| 80134 "reference": { | |
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| 80147 "genotype_likelihoods": [ | |
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| 80149 -99999999, | |
| 80150 -99999999 | |
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| 80152 "_cls": "Call.VariantCall", | |
| 80153 "genotype": [ | |
| 80154 0, | |
| 80155 0 | |
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| 80157 "variant": "ref-S428H?var_name=AGC761088CAT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428H" | |
| 80158 }, | |
| 80159 "rpoB_T444D-ACC761136GAT": { | |
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| 80171 "min_non_zero_depth": 16, | |
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| 80176 "expected_depths": [ | |
| 80177 17.0 | |
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| 80182 "genotype_likelihoods": [ | |
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| 80187 "_cls": "Call.VariantCall", | |
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| 80189 0, | |
| 80190 0 | |
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| 80192 "variant": "ref-T444D?var_name=ACC761136GAT&num_alts=37&ref=NC_000962.3&enum=0&gene=rpoB&mut=T444D" | |
| 80193 }, | |
| 80194 "rpoB_S441A-TCG761127GCC": { | |
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| 80212 17.0 | |
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| 80216 }, | |
| 80217 "genotype_likelihoods": [ | |
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| 80219 -99999999, | |
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| 80222 "_cls": "Call.VariantCall", | |
| 80223 "genotype": [ | |
| 80224 0, | |
| 80225 0 | |
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| 80227 "variant": "ref-S441A?var_name=TCG761127GCC&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441A" | |
| 80228 }, | |
| 80229 "pncA_Y99F-GTA2288945GAA": { | |
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| 80235 "min_non_zero_depth": 16, | |
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| 80237 "kmer_count": 48 | |
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| 80239 "reference": { | |
| 80240 "median_depth": 16, | |
| 80241 "min_non_zero_depth": 16, | |
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| 80252 "genotype_likelihoods": [ | |
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| 80254 -99999999, | |
| 80255 -99999999 | |
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| 80257 "_cls": "Call.VariantCall", | |
| 80258 "genotype": [ | |
| 80259 0, | |
| 80260 0 | |
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| 80262 "variant": "ref-Y99F?var_name=GTA2288945GAA&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=Y99F" | |
| 80263 }, | |
| 80264 "pncA_Q141L-CTG2288819CAG": { | |
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| 80276 "min_non_zero_depth": 14, | |
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| 80290 -99999999 | |
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| 80292 "_cls": "Call.VariantCall", | |
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| 80294 0, | |
| 80295 0 | |
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| 80297 "variant": "ref-Q141L?var_name=CTG2288819CAG&num_alts=11&ref=NC_000962.3&enum=0&gene=pncA&mut=Q141L" | |
| 80298 }, | |
| 80299 "rpoB_D435W-GAC761109TGG": { | |
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| 80313 "kmer_count": 416 | |
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| 80316 "expected_depths": [ | |
| 80317 17.0 | |
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| 80321 }, | |
| 80322 "genotype_likelihoods": [ | |
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| 80325 -99999999 | |
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| 80327 "_cls": "Call.VariantCall", | |
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| 80329 0, | |
| 80330 0 | |
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| 80332 "variant": "ref-D435W?var_name=GAC761109TGG&num_alts=26&ref=NC_000962.3&enum=0&gene=rpoB&mut=D435W" | |
| 80333 }, | |
| 80334 "gid_S136R-TGA4407795TCG": { | |
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| 80344 "reference": { | |
| 80345 "median_depth": 15, | |
| 80346 "min_non_zero_depth": 14, | |
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| 80348 "kmer_count": 327 | |
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| 80350 }, | |
| 80351 "expected_depths": [ | |
| 80352 17.0 | |
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| 80356 }, | |
| 80357 "genotype_likelihoods": [ | |
| 80358 -2.6844045563309873, | |
| 80359 -99999999, | |
| 80360 -99999999 | |
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| 80362 "_cls": "Call.VariantCall", | |
| 80363 "genotype": [ | |
| 80364 0, | |
| 80365 0 | |
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| 80367 "variant": "ref-S136R?var_name=TGA4407795TCG&num_alts=68&ref=NC_000962.3&enum=0&gene=gid&mut=S136R" | |
| 80368 }, | |
| 80369 "gyrA_S91V-TCG7572GTA": { | |
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| 80373 "alternate": { | |
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| 80381 "min_non_zero_depth": 18, | |
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| 80385 }, | |
| 80386 "expected_depths": [ | |
| 80387 17.0 | |
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| 80392 "genotype_likelihoods": [ | |
| 80393 -2.79216398346472, | |
| 80394 -99999999, | |
| 80395 -99999999 | |
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| 80397 "_cls": "Call.VariantCall", | |
| 80398 "genotype": [ | |
| 80399 0, | |
| 80400 0 | |
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| 80402 "variant": "ref-S91V?var_name=TCG7572GTA&num_alts=11&ref=NC_000962.3&enum=0&gene=gyrA&mut=S91V" | |
| 80403 }, | |
| 80404 "gyrA_I92G-ATC7575GGT": { | |
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| 80416 "min_non_zero_depth": 18, | |
| 80417 "percent_coverage": 100.0, | |
| 80418 "kmer_count": 414 | |
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| 80421 "expected_depths": [ | |
| 80422 17.0 | |
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| 80425 "conf": 99999996 | |
| 80426 }, | |
| 80427 "genotype_likelihoods": [ | |
| 80428 -2.79216398346472, | |
| 80429 -99999999, | |
| 80430 -99999999 | |
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| 80432 "_cls": "Call.VariantCall", | |
| 80433 "genotype": [ | |
| 80434 0, | |
| 80435 0 | |
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| 80437 "variant": "ref-I92G?var_name=ATC7575GGT&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=I92G" | |
| 80438 }, | |
| 80439 "pncA_L27P-CAG2289161CGG": { | |
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| 80447 "kmer_count": 19 | |
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| 80451 "min_non_zero_depth": 17, | |
| 80452 "percent_coverage": 100.0, | |
| 80453 "kmer_count": 380 | |
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| 80456 "expected_depths": [ | |
| 80457 17.0 | |
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| 80461 }, | |
| 80462 "genotype_likelihoods": [ | |
| 80463 -2.6237799345145465, | |
| 80464 -99999999, | |
| 80465 -99999999 | |
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| 80467 "_cls": "Call.VariantCall", | |
| 80468 "genotype": [ | |
| 80469 0, | |
| 80470 0 | |
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| 80472 "variant": "ref-L27P?var_name=CAG2289161CGG&num_alts=5&ref=NC_000962.3&enum=0&gene=pncA&mut=L27P" | |
| 80473 }, | |
| 80474 "gyrA_D94M-GAC7581ATG": { | |
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| 80488 "kmer_count": 406 | |
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| 80491 "expected_depths": [ | |
| 80492 17.0 | |
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| 80495 "conf": 99999996 | |
| 80496 }, | |
| 80497 "genotype_likelihoods": [ | |
| 80498 -2.79216398346472, | |
| 80499 -99999999, | |
| 80500 -99999999 | |
| 80501 ], | |
| 80502 "_cls": "Call.VariantCall", | |
| 80503 "genotype": [ | |
| 80504 0, | |
| 80505 0 | |
| 80506 ], | |
| 80507 "variant": "ref-D94M?var_name=GAC7581ATG&num_alts=4&ref=NC_000962.3&enum=0&gene=gyrA&mut=D94M" | |
| 80508 }, | |
| 80509 "gyrA_H87I-CAC7560ATT": { | |
| 80510 "info": { | |
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| 80517 "kmer_count": 0 | |
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| 80519 "reference": { | |
| 80520 "median_depth": 18, | |
| 80521 "min_non_zero_depth": 15, | |
| 80522 "percent_coverage": 100.0, | |
| 80523 "kmer_count": 377 | |
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| 80526 "expected_depths": [ | |
| 80527 17.0 | |
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| 80529 "filter": "PASS", | |
| 80530 "conf": 99999996 | |
| 80531 }, | |
| 80532 "genotype_likelihoods": [ | |
| 80533 -2.6809383483544966, | |
| 80534 -99999999, | |
| 80535 -99999999 | |
| 80536 ], | |
| 80537 "_cls": "Call.VariantCall", | |
| 80538 "genotype": [ | |
| 80539 0, | |
| 80540 0 | |
| 80541 ], | |
| 80542 "variant": "ref-H87I?var_name=CAC7560ATT&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87I" | |
| 80543 }, | |
| 80544 "pncA_F81V-GAA2288999CAC": { | |
| 80545 "info": { | |
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| 80547 "coverage": { | |
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| 83375 0 | |
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| 83397 17.0 | |
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| 83402 "genotype_likelihoods": [ | |
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| 83404 -99999999, | |
| 83405 -99999999 | |
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| 83407 "_cls": "Call.VariantCall", | |
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| 83410 0 | |
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| 83550 0 | |
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| 83589 "rpoB_S431G-AGC761097GGT": { | |
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| 83655 0 | |
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| 83659 "gyrA_D94T-GAC7581ACC": { | |
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| 83729 "rpoB_L443N-TTG761133AAC": { | |
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| 83764 "rpoB_S441N-TCG761127AAT": { | |
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| 85637 17.0 | |
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| 85649 0, | |
| 85650 0 | |
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| 85720 0 | |
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| 85722 "variant": "ref-Y93L?var_name=TAC7578TTA&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=Y93L" | |
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| 85790 0 | |
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| 85864 "katG_V633A-GAC2154213GGC": { | |
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| 85899 "gyrA_H87E-CAC7560GAG": { | |
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| 85934 "gyrA_G88E-GGC7563GAG": { | |
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| 85967 "variant": "ref-G88E?var_name=GGC7563GAG&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88E" | |
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| 85969 "pncA_Q10E-CTG2289212CTC": { | |
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| 86004 "gyrA_A90R-GCG7569CGC": { | |
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| 86074 "gid_L79S-CAA4407966AGA": { | |
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| 86143 }, | |
| 86144 "rpoB_N437V-AAC761115GTT": { | |
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| 86178 }, | |
| 86179 "rpoB_R448E-CGA761148GAA": { | |
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| 88590 0 | |
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| 88625 0 | |
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| 88725 -99999999 | |
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| 88732 "variant": "ref-G88R?var_name=GGC7563AGA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88R" | |
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| 88769 "gyrA_H85D-CAC7554GAT": { | |
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| 88800 0 | |
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| 88802 "variant": "ref-H85D?var_name=CAC7554GAT&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85D" | |
| 88803 }, | |
| 88804 "gyrA_P86K-CCG7557AAA": { | |
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| 88837 "variant": "ref-P86K?var_name=CCG7557AAA&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86K" | |
| 88838 }, | |
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| 88873 }, | |
| 88874 "gyrA_H87R-CAC7560CGC": { | |
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| 88909 "rpoB_T444D-ACC761136GAC": { | |
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| 88944 "rpoB_L452D-CTG761160GAT": { | |
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| 88977 "variant": "ref-L452D?var_name=CTG761160GAT&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452D" | |
| 88978 }, | |
| 88979 "rpoB_G442V-GGG761130GTT": { | |
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| 89007 "_cls": "Call.VariantCall", | |
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| 89010 0 | |
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| 89012 "variant": "ref-G442V?var_name=GGG761130GTT&num_alts=19&ref=NC_000962.3&enum=0&gene=rpoB&mut=G442V" | |
| 89013 }, | |
| 89014 "rrs_G515T-G1472360T": { | |
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| 89048 }, | |
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| 95857 17.0 | |
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| 95870 0 | |
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| 95874 "katG_S315P-GCT2155167CGG": { | |
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| 95900 -99999999 | |
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| 95907 "variant": "ref-S315P?var_name=GCT2155167CGG&num_alts=1&ref=NC_000962.3&enum=0&gene=katG&mut=S315P" | |
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| 95942 "variant": "ref-A200E?var_name=CGC4407603TTC&num_alts=16&ref=NC_000962.3&enum=0&gene=gid&mut=A200E" | |
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| 95944 "rpoB_M434V-ATG761106GTG": { | |
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| 95962 17.0 | |
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| 95975 0 | |
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| 95977 "variant": "ref-M434V?var_name=ATG761106GTG&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434V" | |
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| 95979 "rpoB_S428K-AGC761088AAA": { | |
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| 95997 17.0 | |
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| 96002 "genotype_likelihoods": [ | |
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| 96007 "_cls": "Call.VariantCall", | |
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| 96009 0, | |
| 96010 0 | |
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| 96012 "variant": "ref-S428K?var_name=AGC761088AAA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=S428K" | |
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| 96014 "rpoB_F425I-TTC761079ATA": { | |
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| 96045 0 | |
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| 96047 "variant": "ref-F425I?var_name=TTC761079ATA&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425I" | |
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| 96049 "rpoB_Q429H-CAG761091CAT": { | |
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| 96080 0 | |
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| 96082 "variant": "ref-Q429H?var_name=CAG761091CAT&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429H" | |
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| 96084 "rpoB_L430C-CTG761094TGT": { | |
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| 96107 "genotype_likelihoods": [ | |
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| 96114 0, | |
| 96115 0 | |
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| 96117 "variant": "ref-L430C?var_name=CTG761094TGT&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430C" | |
| 96118 }, | |
| 96119 "gyrA_P86S-CCG7557TCT": { | |
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| 96142 "genotype_likelihoods": [ | |
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| 96147 "_cls": "Call.VariantCall", | |
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| 96150 0 | |
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| 96152 "variant": "ref-P86S?var_name=CCG7557TCT&num_alts=6&ref=NC_000962.3&enum=0&gene=gyrA&mut=P86S" | |
| 96153 }, | |
| 96154 "rpoB_S450T-TCG761154ACC": { | |
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| 96182 "_cls": "Call.VariantCall", | |
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| 96184 0, | |
| 96185 0 | |
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| 96187 "variant": "ref-S450T?var_name=TCG761154ACC&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450T" | |
| 96188 }, | |
| 96189 "rpoB_N437R-AAC761115AGG": { | |
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| 96212 "genotype_likelihoods": [ | |
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| 96220 0 | |
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| 96222 "variant": "ref-N437R?var_name=AAC761115AGG&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437R" | |
| 96223 }, | |
| 96224 "rpoB_F425K-TTC761079AAA": { | |
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| 96247 "genotype_likelihoods": [ | |
| 96248 -2.6844045563309873, | |
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| 96252 "_cls": "Call.VariantCall", | |
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| 96255 0 | |
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| 96257 "variant": "ref-F425K?var_name=TTC761079AAA&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=F425K" | |
| 96258 }, | |
| 96259 "gid_H48Q-ATG4408059TTG": { | |
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| 96282 "genotype_likelihoods": [ | |
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| 96287 "_cls": "Call.VariantCall", | |
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| 96290 0 | |
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| 96292 "variant": "ref-H48Q?var_name=ATG4408059TTG&num_alts=18&ref=NC_000962.3&enum=0&gene=gid&mut=H48Q" | |
| 96293 }, | |
| 96294 "rpoB_L430A-CTG761094GCA": { | |
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| 96312 17.0 | |
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| 96316 }, | |
| 96317 "genotype_likelihoods": [ | |
| 96318 -2.6809383483544966, | |
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| 96320 -99999999 | |
| 96321 ], | |
| 96322 "_cls": "Call.VariantCall", | |
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| 96324 0, | |
| 96325 0 | |
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| 96327 "variant": "ref-L430A?var_name=CTG761094GCA&num_alts=34&ref=NC_000962.3&enum=0&gene=rpoB&mut=L430A" | |
| 96328 }, | |
| 96329 "rpoB_Q436E-CAG761112GAA": { | |
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| 96352 "genotype_likelihoods": [ | |
| 96353 -2.79216398346472, | |
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| 96357 "_cls": "Call.VariantCall", | |
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| 96360 0 | |
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| 96362 "variant": "ref-Q436E?var_name=CAG761112GAA&num_alts=47&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q436E" | |
| 96363 }, | |
| 96364 "rpoB_S450A-TCG761154GCT": { | |
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| 96380 }, | |
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| 96387 "genotype_likelihoods": [ | |
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| 96389 -99999999, | |
| 96390 -99999999 | |
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| 96392 "_cls": "Call.VariantCall", | |
| 96393 "genotype": [ | |
| 96394 0, | |
| 96395 0 | |
| 96396 ], | |
| 96397 "variant": "ref-S450A?var_name=TCG761154GCT&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=S450A" | |
| 96398 }, | |
| 96399 "gyrA_G88D-GGC7563GAT": { | |
| 96400 "info": { | |
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| 96410 "median_depth": 18, | |
| 96411 "min_non_zero_depth": 15, | |
| 96412 "percent_coverage": 95.45, | |
| 96413 "kmer_count": 370 | |
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| 96422 "genotype_likelihoods": [ | |
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| 96424 -99999999, | |
| 96425 -99999999 | |
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| 96427 "_cls": "Call.VariantCall", | |
| 96428 "genotype": [ | |
| 96429 0, | |
| 96430 0 | |
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| 96500 0 | |
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| 96604 0, | |
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| 96640 0 | |
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| 96675 0 | |
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| 96679 "gyrA_G88S-GGC7563AGT": { | |
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| 96957 "variant": "ref-H445R?var_name=CAC761139CGT&num_alts=7&ref=NC_000962.3&enum=0&gene=rpoB&mut=H445R" | |
| 96958 }, | |
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| 96989 0, | |
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| 101007 "genotype_likelihoods": [ | |
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| 101015 0 | |
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| 101048 "genotype": [ | |
| 101049 0, | |
| 101050 0 | |
| 101051 ], | |
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| 101053 }, | |
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| 101076 }, | |
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| 101085 0 | |
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| 101088 }, | |
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| 101120 0 | |
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| 101123 }, | |
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| 101155 0 | |
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| 101158 }, | |
| 101159 "rpoB_S441P-TCG761127CCC": { | |
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| 101190 0 | |
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| 101193 }, | |
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| 101224 0, | |
| 101225 0 | |
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| 101227 "variant": "ref-R447Q?var_name=CGC761145CAA&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447Q" | |
| 101228 }, | |
| 101229 "rpoB_F425G-TTC761079GGG": { | |
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| 101260 0 | |
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| 101263 }, | |
| 101264 "pncA_D136N-ATC2288834GTT": { | |
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| 101295 0 | |
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| 101297 "variant": "ref-D136N?var_name=ATC2288834GTT&num_alts=18&ref=NC_000962.3&enum=0&gene=pncA&mut=D136N" | |
| 101298 }, | |
| 101299 "rpoB_L440A-CTG761124GCT": { | |
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| 101327 "_cls": "Call.VariantCall", | |
| 101328 "genotype": [ | |
| 101329 0, | |
| 101330 0 | |
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| 101332 "variant": "ref-L440A?var_name=CTG761124GCT&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440A" | |
| 101333 }, | |
| 101334 "rpoB_Q429V-CAG761091GTC": { | |
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| 101362 "_cls": "Call.VariantCall", | |
| 101363 "genotype": [ | |
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| 101365 0 | |
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| 101367 "variant": "ref-Q429V?var_name=CAG761091GTC&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429V" | |
| 101368 }, | |
| 101369 "pncA_L151S-CAA2288789ACT": { | |
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| 101381 "min_non_zero_depth": 10, | |
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| 101392 "genotype_likelihoods": [ | |
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| 101397 "_cls": "Call.VariantCall", | |
| 101398 "genotype": [ | |
| 101399 0, | |
| 101400 0 | |
| 101401 ], | |
| 101402 "variant": "ref-L151S?var_name=CAA2288789ACT&num_alts=6&ref=NC_000962.3&enum=0&gene=pncA&mut=L151S" | |
| 101403 }, | |
| 101404 "embA_C-12T-C4243221T": { | |
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| 101410 "min_non_zero_depth": 13, | |
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| 101416 "min_non_zero_depth": 11, | |
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| 101427 "genotype_likelihoods": [ | |
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| 101435 0 | |
| 101436 ], | |
| 101437 "variant": "ref-C-12T?var_name=C4243221T&num_alts=15&ref=NC_000962.3&enum=0&gene=embA&mut=C-12T" | |
| 101438 }, | |
| 101439 "gid_S149R-GCT4407756TCT": { | |
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| 101447 "kmer_count": 50 | |
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| 101451 "min_non_zero_depth": 14, | |
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| 101462 "genotype_likelihoods": [ | |
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| 101467 "_cls": "Call.VariantCall", | |
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| 101470 0 | |
| 101471 ], | |
| 101472 "variant": "ref-S149R?var_name=GCT4407756TCT&num_alts=7&ref=NC_000962.3&enum=0&gene=gid&mut=S149R" | |
| 101473 }, | |
| 101474 "rpoB_L452W-CTG761160TGG": { | |
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| 101497 "genotype_likelihoods": [ | |
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| 101499 -99999999, | |
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| 101502 "_cls": "Call.VariantCall", | |
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| 101505 0 | |
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| 101507 "variant": "ref-L452W?var_name=CTG761160TGG&num_alts=13&ref=NC_000962.3&enum=0&gene=rpoB&mut=L452W" | |
| 101508 }, | |
| 101509 "rpoB_M434A-ATG761106GCG": { | |
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| 101531 }, | |
| 101532 "genotype_likelihoods": [ | |
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| 101534 -99999999, | |
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| 101537 "_cls": "Call.VariantCall", | |
| 101538 "genotype": [ | |
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| 101540 0 | |
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| 101542 "variant": "ref-M434A?var_name=ATG761106GCG&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434A" | |
| 101543 }, | |
| 101544 "gid_P93L-CGG4407924TAG": { | |
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| 101559 } | |
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| 101566 }, | |
| 101567 "genotype_likelihoods": [ | |
| 101568 -2.6237799345145465, | |
| 101569 -99999999, | |
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| 101571 ], | |
| 101572 "_cls": "Call.VariantCall", | |
| 101573 "genotype": [ | |
| 101574 0, | |
| 101575 0 | |
| 101576 ], | |
| 101577 "variant": "ref-P93L?var_name=CGG4407924TAG&num_alts=15&ref=NC_000962.3&enum=0&gene=gid&mut=P93L" | |
| 101578 }, | |
| 101579 "gyrA_H87V-CAC7560GTC": { | |
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| 101587 "kmer_count": 19 | |
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| 101591 "min_non_zero_depth": 15, | |
| 101592 "percent_coverage": 100.0, | |
| 101593 "kmer_count": 377 | |
| 101594 } | |
| 101595 }, | |
| 101596 "expected_depths": [ | |
| 101597 17.0 | |
| 101598 ], | |
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| 101600 "conf": 99999996 | |
| 101601 }, | |
| 101602 "genotype_likelihoods": [ | |
| 101603 -2.6809383483544966, | |
| 101604 -99999999, | |
| 101605 -99999999 | |
| 101606 ], | |
| 101607 "_cls": "Call.VariantCall", | |
| 101608 "genotype": [ | |
| 101609 0, | |
| 101610 0 | |
| 101611 ], | |
| 101612 "variant": "ref-H87V?var_name=CAC7560GTC&num_alts=7&ref=NC_000962.3&enum=0&gene=gyrA&mut=H87V" | |
| 101613 }, | |
| 101614 "rpoB_R447L-CGC761145TTA": { | |
| 101615 "info": { | |
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| 104467 17.0 | |
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| 104502 17.0 | |
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| 104510 -99999999 | |
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| 104517 "variant": "ref-S441A?var_name=TCG761127GCA&num_alts=22&ref=NC_000962.3&enum=0&gene=rpoB&mut=S441A" | |
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| 104549 0, | |
| 104550 0 | |
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| 104552 "variant": "ref-G34V?var_name=CCC4408101TAC&num_alts=38&ref=NC_000962.3&enum=0&gene=gid&mut=G34V" | |
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| 104554 "gid_Q125N-CTG4407828GTT": { | |
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| 104578 -3.0037237137259485, | |
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| 104584 0, | |
| 104585 0 | |
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| 104587 "variant": "ref-Q125N?var_name=CTG4407828GTT&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125N" | |
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| 104589 "gyrA_D89V-GAC7566GTC": { | |
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| 104619 0, | |
| 104620 0 | |
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| 104622 "variant": "ref-D89V?var_name=GAC7566GTC&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89V" | |
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| 104624 "gid_R118L-GCG4407849TAA": { | |
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| 104657 "variant": "ref-R118L?var_name=GCG4407849TAA&num_alts=14&ref=NC_000962.3&enum=0&gene=gid&mut=R118L" | |
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| 104659 "rpoB_S431V-AGC761097GTC": { | |
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| 104689 0, | |
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| 104692 "variant": "ref-S431V?var_name=AGC761097GTC&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=S431V" | |
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| 104694 "pncA_W68R-CCA2289038CCT": { | |
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| 104724 0, | |
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| 104727 "variant": "ref-W68R?var_name=CCA2289038CCT&num_alts=39&ref=NC_000962.3&enum=0&gene=pncA&mut=W68R" | |
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| 104729 "gyrA_P86I-CCG7557ATC": { | |
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| 104764 "gyrA_H85I-CAC7554ATA": { | |
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| 104788 -2.6844045563309873, | |
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| 104794 0, | |
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| 104797 "variant": "ref-H85I?var_name=CAC7554ATA&num_alts=5&ref=NC_000962.3&enum=0&gene=gyrA&mut=H85I" | |
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| 104799 "rpoB_Q429C-CAG761091TGC": { | |
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| 104829 0, | |
| 104830 0 | |
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| 104832 "variant": "ref-Q429C?var_name=CAG761091TGC&num_alts=49&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q429C" | |
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| 104834 "rpoB_L443R-TTG761133AGA": { | |
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| 104860 -99999999 | |
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| 104864 0, | |
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| 104867 "variant": "ref-L443R?var_name=TTG761133AGA&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443R" | |
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| 104869 "gyrA_D89T-GAC7566ACT": { | |
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| 104893 -2.6809383483544966, | |
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| 104898 "genotype": [ | |
| 104899 0, | |
| 104900 0 | |
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| 104902 "variant": "ref-D89T?var_name=GAC7566ACT&num_alts=12&ref=NC_000962.3&enum=0&gene=gyrA&mut=D89T" | |
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| 104904 "rpoB_L443D-TTG761133GAT": { | |
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| 104922 17.0 | |
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| 104927 "genotype_likelihoods": [ | |
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| 104929 -99999999, | |
| 104930 -99999999 | |
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| 104932 "_cls": "Call.VariantCall", | |
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| 104934 0, | |
| 104935 0 | |
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| 104937 "variant": "ref-L443D?var_name=TTG761133GAT&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443D" | |
| 104938 }, | |
| 104939 "rpoB_M434E-ATG761106GAA": { | |
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| 104963 -2.79216398346472, | |
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| 104967 "_cls": "Call.VariantCall", | |
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| 104969 0, | |
| 104970 0 | |
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| 104972 "variant": "ref-M434E?var_name=ATG761106GAA&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434E" | |
| 104973 }, | |
| 104974 "rpoB_L440R-CTG761124AGG": { | |
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| 104997 "genotype_likelihoods": [ | |
| 104998 -2.6237799345145465, | |
| 104999 -99999999, | |
| 105000 -99999999 | |
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| 105002 "_cls": "Call.VariantCall", | |
| 105003 "genotype": [ | |
| 105004 0, | |
| 105005 0 | |
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| 105007 "variant": "ref-L440R?var_name=CTG761124AGG&num_alts=25&ref=NC_000962.3&enum=0&gene=rpoB&mut=L440R" | |
| 105008 }, | |
| 105009 "pncA_L4S-CAA2289230GCT": { | |
| 105010 "info": { | |
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| 105591 }, | |
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| 105599 0, | |
| 105600 0 | |
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| 105603 }, | |
| 105604 "rpoB_A451L-GCG761157CTG": { | |
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| 105620 }, | |
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| 105622 17.0 | |
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| 105630 -99999999 | |
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| 105634 0, | |
| 105635 0 | |
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| 105637 "variant": "ref-A451L?var_name=GCG761157CTG&num_alts=41&ref=NC_000962.3&enum=0&gene=rpoB&mut=A451L" | |
| 105638 }, | |
| 105639 "pncA_Y99N-GTA2288945ATT": { | |
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| 105670 0 | |
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| 105705 0 | |
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| 105707 "variant": "ref-G88S?var_name=GGC7563TCA&num_alts=10&ref=NC_000962.3&enum=0&gene=gyrA&mut=G88S" | |
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| 105709 "gid_S70N-GCT4407993GTT": { | |
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| 105740 0 | |
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| 105742 "variant": "ref-S70N?var_name=GCT4407993GTT&num_alts=44&ref=NC_000962.3&enum=0&gene=gid&mut=S70N" | |
| 105743 }, | |
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| 105775 0 | |
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| 105807 "_cls": "Call.VariantCall", | |
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| 105810 0 | |
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| 105845 0 | |
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| 105848 }, | |
| 105849 "rpoB_T427G-ACC761085GGT": { | |
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| 105880 0 | |
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| 105882 "variant": "ref-T427G?var_name=ACC761085GGT&num_alts=32&ref=NC_000962.3&enum=0&gene=rpoB&mut=T427G" | |
| 105883 }, | |
| 105884 "pncA_K48E-CTT2289098TTC": { | |
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| 105917 "variant": "ref-K48E?var_name=CTT2289098TTC&num_alts=16&ref=NC_000962.3&enum=0&gene=pncA&mut=K48E" | |
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| 105950 0 | |
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| 105954 "katG_W505L-CCA2154597TAA": { | |
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| 106012 "genotype_likelihoods": [ | |
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| 106014 -99999999, | |
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| 106020 0 | |
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| 106022 "variant": "ref-R447A?var_name=CGC761145GCC&num_alts=45&ref=NC_000962.3&enum=0&gene=rpoB&mut=R447A" | |
| 106023 }, | |
| 106024 "rpoB_A451T-GCG761157ACT": { | |
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| 106058 }, | |
| 106059 "rpoB_M434P-ATG761106CCG": { | |
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| 106090 0 | |
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| 106092 "variant": "ref-M434P?var_name=ATG761106CCG&num_alts=42&ref=NC_000962.3&enum=0&gene=rpoB&mut=M434P" | |
| 106093 }, | |
| 106094 "rpoB_S428E-AGC761088GAG": { | |
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| 106117 "genotype_likelihoods": [ | |
| 106118 -2.6809383483544966, | |
| 106119 -99999999, | |
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| 106122 "_cls": "Call.VariantCall", | |
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| 106125 0 | |
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| 106128 }, | |
| 106129 "rrs_C905A-C1472750A": { | |
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| 106153 -2.6844045563309873, | |
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| 106754 0, | |
| 106755 0 | |
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| 106934 "gid_E173N-CTC4407684ATT": { | |
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| 107004 "gid_E173C-CTC4407684GCA": { | |
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| 107039 "rpoB_Q432S-CAA761100AGC": { | |
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| 107074 "rpoB_L430E-CTG761094GAG": { | |
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| 107109 "pncA_C138R-ACA2288828CCG": { | |
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| 107142 "variant": "ref-C138R?var_name=ACA2288828CCG&num_alts=18&ref=NC_000962.3&enum=0&gene=pncA&mut=C138R" | |
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| 107144 "inhA_I194T-ATC1674781ACT": { | |
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| 107179 "rpoB_Q432E-CAA761100GAG": { | |
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| 107210 0 | |
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| 107212 "variant": "ref-Q432E?var_name=CAA761100GAG&num_alts=18&ref=NC_000962.3&enum=0&gene=rpoB&mut=Q432E" | |
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| 107214 "gyrA_P86V-CCG7557GTA": { | |
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| 107249 "rpoB_N437G-AAC761115GGA": { | |
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| 107280 0 | |
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| 107282 "variant": "ref-N437G?var_name=AAC761115GGA&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437G" | |
| 107283 }, | |
| 107284 "pncA_T47A-GGT2289101TGC": { | |
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| 107310 -99999999 | |
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| 107314 0, | |
| 107315 0 | |
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| 107319 "rpoB_N438I-AAC761118ATC": { | |
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| 107349 0, | |
| 107350 0 | |
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| 107380 -99999999 | |
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| 107384 0, | |
| 107385 0 | |
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| 107420 0 | |
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| 107422 "variant": "ref-N438G?var_name=AAC761118GGC&num_alts=31&ref=NC_000962.3&enum=0&gene=rpoB&mut=N438G" | |
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| 107424 "katG_W505S-CCA2154597GCT": { | |
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| 107450 -99999999 | |
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| 107452 "_cls": "Call.VariantCall", | |
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| 107455 0 | |
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| 107490 0 | |
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| 107492 "variant": "ref-Q125V?var_name=CTG4407828TAC&num_alts=8&ref=NC_000962.3&enum=0&gene=gid&mut=Q125V" | |
| 107493 }, | |
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| 107529 "gyrA_D94H-GAC7581CAT": { | |
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| 107564 "pncA_Q141T-CTG2288819TGT": { | |
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| 107599 "pncA_D8G-GTC2289218ACC": { | |
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| 107704 "pncA_P54L-CGG2289080TAA": { | |
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| 107772 "variant": "ref-L443A?var_name=TTG761133GCC&num_alts=16&ref=NC_000962.3&enum=0&gene=rpoB&mut=L443A" | |
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| 107774 "rpoB_Q436L-CAG761112CTT": { | |
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| 107808 }, | |
| 107809 "rpoB_N438R-AAC761118CGG": { | |
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| 107843 }, | |
| 107844 "rpoB_P439D-CCG761121GAT": { | |
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| 107874 0, | |
| 107875 0 | |
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| 108124 "rpoB_R447D-CGC761145GAT": { | |
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| 108332 "variant": "ref-N437P?var_name=AAC761115CCT&num_alts=40&ref=NC_000962.3&enum=0&gene=rpoB&mut=N437P" | |
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| 108369 "rpoB_Q436D-CAG761112GAC": { | |
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| 108404 "rpoB_P439A-CCG761121GCC": { | |
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