- Filename
- 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.whatshap.phased.bcftools_stats.txt
- Full Path
- s3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_bams__8a99ba01--20260203-171151/reports/raw_qc/bcftools/mutect2/1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36/1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.whatshap.phased.bcftools_stats.txt
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- 13.1 KB
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- Feb 03, 2026 10:26 PM
# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.whatshap.phased.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 1029_BK2H-T1-TDNA-1_23FC2GLT4_s37_vs_1029_BK2H-N1-BDNA-1_2375WFLT3_s36.mutect2.whatshap.phased.vcf.gz
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 2
SN 0 number of records: 20729
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 16206
SN 0 number of MNPs: 754
SN 0 number of indels: 4163
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1665
SN 0 number of multiallelic SNP sites: 86
# TSTV, transitions/transversions:
# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 11486 4818 2.38 11347 4589 2.47
# SiS, Singleton stats:
# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
SiS 0 1 16304 11486 4818 8524 0 0 8524
# AF, Stats by non-reference allele frequency:
# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
AF 0 0.000000 16304 11486 4818 8524 0 0 8524
# QUAL, Stats by quality
# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
QUAL 0 . 15936 11347 4589 4163
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 86 0 .
IDD 0 -56 1 0 .
IDD 0 -54 1 0 .
IDD 0 -53 1 0 .
IDD 0 -51 1 0 .
IDD 0 -48 5 0 .
IDD 0 -47 1 0 .
IDD 0 -46 1 0 .
IDD 0 -45 2 0 .
IDD 0 -43 1 0 .
IDD 0 -42 7 0 .
IDD 0 -40 1 0 .
IDD 0 -39 5 0 .
IDD 0 -38 1 0 .
IDD 0 -36 4 0 .
IDD 0 -35 3 0 .
IDD 0 -33 3 0 .
IDD 0 -31 1 0 .
IDD 0 -30 15 0 .
IDD 0 -29 2 0 .
IDD 0 -28 1 0 .
IDD 0 -27 5 0 .
IDD 0 -26 1 0 .
IDD 0 -24 10 0 .
IDD 0 -23 1 0 .
IDD 0 -22 4 0 .
IDD 0 -21 8 0 .
IDD 0 -20 3 0 .
IDD 0 -19 1 0 .
IDD 0 -18 17 0 .
IDD 0 -17 3 0 .
IDD 0 -16 12 0 .
IDD 0 -15 21 0 .
IDD 0 -14 10 0 .
IDD 0 -13 10 0 .
IDD 0 -12 41 0 .
IDD 0 -11 12 0 .
IDD 0 -10 48 0 .
IDD 0 -9 63 0 .
IDD 0 -8 81 0 .
IDD 0 -7 57 0 .
IDD 0 -6 352 0 .
IDD 0 -5 189 0 .
IDD 0 -4 459 0 .
IDD 0 -3 1870 0 .
IDD 0 -2 1014 0 .
IDD 0 -1 1204 0 .
IDD 0 1 1079 0 .
IDD 0 2 882 0 .
IDD 0 3 360 0 .
IDD 0 4 167 0 .
IDD 0 5 39 0 .
IDD 0 6 104 0 .
IDD 0 7 21 0 .
IDD 0 8 34 0 .
IDD 0 9 29 0 .
IDD 0 10 23 0 .
IDD 0 11 6 0 .
IDD 0 12 27 0 .
IDD 0 13 3 0 .
IDD 0 14 10 0 .
IDD 0 15 11 0 .
IDD 0 16 7 0 .
IDD 0 17 1 0 .
IDD 0 18 10 0 .
IDD 0 19 1 0 .
IDD 0 20 4 0 .
IDD 0 21 8 0 .
IDD 0 22 2 0 .
IDD 0 24 5 0 .
IDD 0 25 2 0 .
IDD 0 26 2 0 .
IDD 0 27 4 0 .
IDD 0 29 2 0 .
IDD 0 30 8 0 .
IDD 0 31 3 0 .
IDD 0 32 1 0 .
IDD 0 33 2 0 .
IDD 0 34 1 0 .
IDD 0 36 1 0 .
IDD 0 37 1 0 .
IDD 0 39 2 0 .
IDD 0 42 1 0 .
IDD 0 44 1 0 .
IDD 0 45 2 0 .
IDD 0 48 1 0 .
IDD 0 51 1 0 .
IDD 0 57 1 0 .
IDD 0 60 16 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 509
ST 0 A>G 2094
ST 0 A>T 382
ST 0 C>A 710
ST 0 C>G 764
ST 0 C>T 3486
ST 0 G>A 3684
ST 0 G>C 793
ST 0 G>T 739
ST 0 T>A 405
ST 0 T>C 2222
ST 0 T>G 516
# DP, Depth distribution
# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)
DP 0 18 0 0.000000 1 0.004824
DP 0 19 0 0.000000 1 0.004824
DP 0 20 0 0.000000 1 0.004824
DP 0 22 0 0.000000 1 0.004824
DP 0 23 0 0.000000 2 0.009648
DP 0 25 0 0.000000 1 0.004824
DP 0 26 0 0.000000 1 0.004824
DP 0 27 0 0.000000 3 0.014472
DP 0 28 0 0.000000 1 0.004824
DP 0 29 0 0.000000 2 0.009648
DP 0 30 0 0.000000 1 0.004824
DP 0 31 0 0.000000 2 0.009648
DP 0 32 0 0.000000 1 0.004824
DP 0 33 0 0.000000 1 0.004824
DP 0 38 0 0.000000 1 0.004824
DP 0 40 0 0.000000 1 0.004824
DP 0 42 0 0.000000 1 0.004824
DP 0 45 0 0.000000 1 0.004824
DP 0 53 0 0.000000 1 0.004824
DP 0 55 0 0.000000 1 0.004824
DP 0 56 0 0.000000 1 0.004824
DP 0 59 0 0.000000 2 0.009648
DP 0 60 0 0.000000 1 0.004824
DP 0 61 0 0.000000 2 0.009648
DP 0 62 0 0.000000 1 0.004824
DP 0 64 0 0.000000 3 0.014472
DP 0 65 0 0.000000 2 0.009648
DP 0 66 0 0.000000 1 0.004824
DP 0 69 0 0.000000 1 0.004824
DP 0 70 0 0.000000 2 0.009648
DP 0 71 0 0.000000 1 0.004824
DP 0 73 0 0.000000 1 0.004824
DP 0 74 0 0.000000 1 0.004824
DP 0 75 0 0.000000 1 0.004824
DP 0 76 0 0.000000 3 0.014472
DP 0 77 0 0.000000 2 0.009648
DP 0 82 0 0.000000 1 0.004824
DP 0 84 0 0.000000 1 0.004824
DP 0 86 0 0.000000 1 0.004824
DP 0 88 0 0.000000 2 0.009648
DP 0 91 0 0.000000 1 0.004824
DP 0 93 0 0.000000 1 0.004824
DP 0 95 0 0.000000 1 0.004824
DP 0 96 0 0.000000 1 0.004824
DP 0 100 0 0.000000 1 0.004824
DP 0 103 0 0.000000 2 0.009648
DP 0 106 0 0.000000 1 0.004824
DP 0 107 0 0.000000 1 0.004824
DP 0 112 0 0.000000 2 0.009648
DP 0 114 0 0.000000 1 0.004824
DP 0 115 0 0.000000 1 0.004824
DP 0 118 0 0.000000 1 0.004824
DP 0 129 0 0.000000 2 0.009648
DP 0 134 0 0.000000 1 0.004824
DP 0 139 0 0.000000 1 0.004824
DP 0 141 0 0.000000 1 0.004824
DP 0 148 0 0.000000 1 0.004824
DP 0 149 0 0.000000 4 0.019297
DP 0 151 0 0.000000 1 0.004824
DP 0 154 0 0.000000 1 0.004824
DP 0 157 0 0.000000 1 0.004824
DP 0 162 0 0.000000 1 0.004824
DP 0 166 0 0.000000 1 0.004824
DP 0 168 0 0.000000 1 0.004824
DP 0 170 0 0.000000 2 0.009648
DP 0 174 0 0.000000 1 0.004824
DP 0 176 0 0.000000 2 0.009648
DP 0 178 0 0.000000 2 0.009648
DP 0 180 0 0.000000 1 0.004824
DP 0 181 0 0.000000 1 0.004824
DP 0 185 0 0.000000 1 0.004824
DP 0 186 0 0.000000 1 0.004824
DP 0 187 0 0.000000 1 0.004824
DP 0 188 0 0.000000 1 0.004824
DP 0 189 0 0.000000 3 0.014472
DP 0 190 0 0.000000 1 0.004824
DP 0 194 0 0.000000 1 0.004824
DP 0 197 0 0.000000 1 0.004824
DP 0 202 0 0.000000 2 0.009648
DP 0 206 0 0.000000 2 0.009648
DP 0 207 0 0.000000 2 0.009648
DP 0 214 0 0.000000 3 0.014472
DP 0 216 0 0.000000 1 0.004824
DP 0 219 0 0.000000 1 0.004824
DP 0 221 0 0.000000 1 0.004824
DP 0 229 0 0.000000 1 0.004824
DP 0 231 0 0.000000 1 0.004824
DP 0 237 0 0.000000 1 0.004824
DP 0 238 0 0.000000 1 0.004824
DP 0 239 0 0.000000 1 0.004824
DP 0 241 0 0.000000 1 0.004824
DP 0 243 0 0.000000 1 0.004824
DP 0 244 0 0.000000 1 0.004824
DP 0 246 0 0.000000 1 0.004824
DP 0 247 0 0.000000 2 0.009648
DP 0 248 0 0.000000 1 0.004824
DP 0 251 0 0.000000 1 0.004824
DP 0 252 0 0.000000 1 0.004824
DP 0 258 0 0.000000 1 0.004824
DP 0 261 0 0.000000 2 0.009648
DP 0 263 0 0.000000 2 0.009648
DP 0 266 0 0.000000 1 0.004824
DP 0 269 0 0.000000 1 0.004824
DP 0 271 0 0.000000 1 0.004824
DP 0 273 0 0.000000 1 0.004824
DP 0 274 0 0.000000 1 0.004824
DP 0 275 0 0.000000 1 0.004824
DP 0 276 0 0.000000 1 0.004824
DP 0 277 0 0.000000 4 0.019297
DP 0 280 0 0.000000 2 0.009648
DP 0 281 0 0.000000 1 0.004824
DP 0 284 0 0.000000 2 0.009648
DP 0 286 0 0.000000 1 0.004824
DP 0 287 0 0.000000 2 0.009648
DP 0 291 0 0.000000 2 0.009648
DP 0 292 0 0.000000 1 0.004824
DP 0 294 0 0.000000 3 0.014472
DP 0 295 0 0.000000 1 0.004824
DP 0 296 0 0.000000 1 0.004824
DP 0 297 0 0.000000 1 0.004824
DP 0 298 0 0.000000 1 0.004824
DP 0 300 0 0.000000 2 0.009648
DP 0 301 0 0.000000 1 0.004824
DP 0 305 0 0.000000 3 0.014472
DP 0 306 0 0.000000 2 0.009648
DP 0 307 0 0.000000 1 0.004824
DP 0 308 0 0.000000 2 0.009648
DP 0 309 0 0.000000 2 0.009648
DP 0 310 0 0.000000 3 0.014472
DP 0 314 0 0.000000 1 0.004824
DP 0 315 0 0.000000 1 0.004824
DP 0 317 0 0.000000 1 0.004824
DP 0 318 0 0.000000 3 0.014472
DP 0 319 0 0.000000 1 0.004824
DP 0 320 0 0.000000 1 0.004824
DP 0 322 0 0.000000 2 0.009648
DP 0 324 0 0.000000 1 0.004824
DP 0 326 0 0.000000 1 0.004824
DP 0 327 0 0.000000 1 0.004824
DP 0 329 0 0.000000 2 0.009648
DP 0 330 0 0.000000 1 0.004824
DP 0 331 0 0.000000 1 0.004824
DP 0 332 0 0.000000 1 0.004824
DP 0 333 0 0.000000 2 0.009648
DP 0 334 0 0.000000 2 0.009648
DP 0 336 0 0.000000 1 0.004824
DP 0 337 0 0.000000 1 0.004824
DP 0 338 0 0.000000 2 0.009648
DP 0 339 0 0.000000 1 0.004824
DP 0 340 0 0.000000 3 0.014472
DP 0 342 0 0.000000 1 0.004824
DP 0 344 0 0.000000 2 0.009648
DP 0 346 0 0.000000 1 0.004824
DP 0 348 0 0.000000 1 0.004824
DP 0 349 0 0.000000 3 0.014472
DP 0 350 0 0.000000 3 0.014472
DP 0 351 0 0.000000 3 0.014472
DP 0 354 0 0.000000 2 0.009648
DP 0 356 0 0.000000 1 0.004824
DP 0 357 0 0.000000 2 0.009648
DP 0 358 0 0.000000 2 0.009648
DP 0 359 0 0.000000 3 0.014472
DP 0 360 0 0.000000 1 0.004824
DP 0 361 0 0.000000 2 0.009648
DP 0 362 0 0.000000 1 0.004824
DP 0 363 0 0.000000 5 0.024121
DP 0 364 0 0.000000 3 0.014472
DP 0 366 0 0.000000 2 0.009648
DP 0 367 0 0.000000 2 0.009648
DP 0 368 0 0.000000 3 0.014472
DP 0 369 0 0.000000 1 0.004824
DP 0 370 0 0.000000 2 0.009648
DP 0 371 0 0.000000 1 0.004824
DP 0 372 0 0.000000 1 0.004824
DP 0 373 0 0.000000 2 0.009648
DP 0 374 0 0.000000 1 0.004824
DP 0 375 0 0.000000 1 0.004824
DP 0 376 0 0.000000 1 0.004824
DP 0 377 0 0.000000 3 0.014472
DP 0 378 0 0.000000 3 0.014472
DP 0 379 0 0.000000 1 0.004824
DP 0 380 0 0.000000 4 0.019297
DP 0 381 0 0.000000 2 0.009648
DP 0 382 0 0.000000 4 0.019297
DP 0 383 0 0.000000 1 0.004824
DP 0 384 0 0.000000 2 0.009648
DP 0 385 0 0.000000 2 0.009648
DP 0 386 0 0.000000 2 0.009648
DP 0 387 0 0.000000 2 0.009648
DP 0 388 0 0.000000 2 0.009648
DP 0 391 0 0.000000 2 0.009648
DP 0 392 0 0.000000 2 0.009648
DP 0 393 0 0.000000 2 0.009648
DP 0 394 0 0.000000 5 0.024121
DP 0 395 0 0.000000 1 0.004824
DP 0 397 0 0.000000 1 0.004824
DP 0 398 0 0.000000 3 0.014472
DP 0 399 0 0.000000 3 0.014472
DP 0 400 0 0.000000 2 0.009648
DP 0 401 0 0.000000 2 0.009648
DP 0 402 0 0.000000 2 0.009648
DP 0 403 0 0.000000 2 0.009648
DP 0 405 0 0.000000 2 0.009648
DP 0 406 0 0.000000 2 0.009648
DP 0 407 0 0.000000 1 0.004824
DP 0 408 0 0.000000 3 0.014472
DP 0 409 0 0.000000 2 0.009648
DP 0 411 0 0.000000 2 0.009648
DP 0 412 0 0.000000 1 0.004824
DP 0 413 0 0.000000 3 0.014472
DP 0 414 0 0.000000 1 0.004824
DP 0 415 0 0.000000 4 0.019297
DP 0 416 0 0.000000 1 0.004824
DP 0 417 0 0.000000 5 0.024121
DP 0 419 0 0.000000 1 0.004824
DP 0 420 0 0.000000 2 0.009648
DP 0 422 0 0.000000 2 0.009648
DP 0 423 0 0.000000 3 0.014472
DP 0 424 0 0.000000 2 0.009648
DP 0 425 0 0.000000 1 0.004824
DP 0 426 0 0.000000 2 0.009648
DP 0 427 0 0.000000 7 0.033769
DP 0 428 0 0.000000 3 0.014472
DP 0 429 0 0.000000 4 0.019297
DP 0 430 0 0.000000 1 0.004824
DP 0 431 0 0.000000 3 0.014472
DP 0 432 0 0.000000 4 0.019297
DP 0 433 0 0.000000 1 0.004824
DP 0 434 0 0.000000 2 0.009648
DP 0 435 0 0.000000 4 0.019297
DP 0 436 0 0.000000 5 0.024121
DP 0 437 0 0.000000 2 0.009648
DP 0 438 0 0.000000 4 0.019297
DP 0 439 0 0.000000 3 0.014472
DP 0 440 0 0.000000 4 0.019297
DP 0 441 0 0.000000 3 0.014472
DP 0 442 0 0.000000 5 0.024121
DP 0 443 0 0.000000 6 0.028945
DP 0 444 0 0.000000 3 0.014472
DP 0 445 0 0.000000 3 0.014472
DP 0 446 0 0.000000 1 0.004824
DP 0 447 0 0.000000 1 0.004824
DP 0 448 0 0.000000 4 0.019297
DP 0 449 0 0.000000 4 0.019297
DP 0 450 0 0.000000 3 0.014472
DP 0 451 0 0.000000 3 0.014472
DP 0 452 0 0.000000 3 0.014472
DP 0 453 0 0.000000 4 0.019297
DP 0 454 0 0.000000 3 0.014472
DP 0 455 0 0.000000 1 0.004824
DP 0 456 0 0.000000 3 0.014472
DP 0 457 0 0.000000 3 0.014472
DP 0 458 0 0.000000 1 0.004824
DP 0 459 0 0.000000 7 0.033769
DP 0 460 0 0.000000 1 0.004824
DP 0 461 0 0.000000 2 0.009648
DP 0 462 0 0.000000 2 0.009648
DP 0 463 0 0.000000 1 0.004824
DP 0 464 0 0.000000 2 0.009648
DP 0 465 0 0.000000 3 0.014472
DP 0 466 0 0.000000 2 0.009648
DP 0 467 0 0.000000 2 0.009648
DP 0 468 0 0.000000 2 0.009648
DP 0 469 0 0.000000 1 0.004824
DP 0 470 0 0.000000 3 0.014472
DP 0 471 0 0.000000 1 0.004824
DP 0 472 0 0.000000 1 0.004824
DP 0 473 0 0.000000 7 0.033769
DP 0 474 0 0.000000 3 0.014472
DP 0 475 0 0.000000 3 0.014472
DP 0 476 0 0.000000 1 0.004824
DP 0 477 0 0.000000 1 0.004824
DP 0 479 0 0.000000 4 0.019297
DP 0 480 0 0.000000 7 0.033769
DP 0 481 0 0.000000 1 0.004824
DP 0 483 0 0.000000 6 0.028945
DP 0 484 0 0.000000 6 0.028945
DP 0 485 0 0.000000 1 0.004824
DP 0 486 0 0.000000 3 0.014472
DP 0 487 0 0.000000 5 0.024121
DP 0 488 0 0.000000 1 0.004824
DP 0 489 0 0.000000 3 0.014472
DP 0 490 0 0.000000 5 0.024121
DP 0 491 0 0.000000 2 0.009648
DP 0 493 0 0.000000 2 0.009648
DP 0 494 0 0.000000 4 0.019297
DP 0 495 0 0.000000 4 0.019297
DP 0 496 0 0.000000 1 0.004824
DP 0 497 0 0.000000 3 0.014472
DP 0 498 0 0.000000 3 0.014472
DP 0 499 0 0.000000 4 0.019297
DP 0 500 0 0.000000 3 0.014472
DP 0 >500 0 0.000000 20157 97.240581