- Filename
- 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.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_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34/1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.mutect2.whatshap.phased.bcftools_stats.txt
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- 11.3 KB
- Published
- Feb 04, 2026 1:49 AM
# 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_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.mutect2.whatshap.phased.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 1029_BIHO-T1-TDNA-1_23FC2GLT4_s35_vs_1029_BIHO-N1-BDNA-1_2375WFLT3_s34.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: 10086
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 6189
SN 0 number of MNPs: 624
SN 0 number of indels: 3635
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1485
SN 0 number of multiallelic SNP sites: 79
# 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 4196 2079 2.02 4058 1869 2.17
# 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 6275 4196 2079 7472 0 0 7472
# 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 6275 4196 2079 7472 0 0 7472
# 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 . 5927 4058 1869 3635
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 92 0 .
IDD 0 -58 1 0 .
IDD 0 -57 2 0 .
IDD 0 -54 2 0 .
IDD 0 -51 2 0 .
IDD 0 -49 1 0 .
IDD 0 -48 1 0 .
IDD 0 -47 1 0 .
IDD 0 -45 3 0 .
IDD 0 -42 3 0 .
IDD 0 -41 1 0 .
IDD 0 -40 1 0 .
IDD 0 -39 8 0 .
IDD 0 -38 1 0 .
IDD 0 -37 1 0 .
IDD 0 -36 5 0 .
IDD 0 -35 2 0 .
IDD 0 -34 1 0 .
IDD 0 -33 3 0 .
IDD 0 -32 1 0 .
IDD 0 -30 8 0 .
IDD 0 -29 2 0 .
IDD 0 -28 1 0 .
IDD 0 -27 2 0 .
IDD 0 -25 1 0 .
IDD 0 -24 7 0 .
IDD 0 -22 3 0 .
IDD 0 -21 11 0 .
IDD 0 -20 5 0 .
IDD 0 -19 1 0 .
IDD 0 -18 11 0 .
IDD 0 -17 1 0 .
IDD 0 -16 10 0 .
IDD 0 -15 10 0 .
IDD 0 -14 10 0 .
IDD 0 -13 2 0 .
IDD 0 -12 30 0 .
IDD 0 -11 11 0 .
IDD 0 -10 25 0 .
IDD 0 -9 48 0 .
IDD 0 -8 64 0 .
IDD 0 -7 46 0 .
IDD 0 -6 278 0 .
IDD 0 -5 180 0 .
IDD 0 -4 398 0 .
IDD 0 -3 1655 0 .
IDD 0 -2 887 0 .
IDD 0 -1 1113 0 .
IDD 0 1 980 0 .
IDD 0 2 776 0 .
IDD 0 3 301 0 .
IDD 0 4 139 0 .
IDD 0 5 38 0 .
IDD 0 6 65 0 .
IDD 0 7 12 0 .
IDD 0 8 28 0 .
IDD 0 9 17 0 .
IDD 0 10 22 0 .
IDD 0 11 5 0 .
IDD 0 12 18 0 .
IDD 0 13 8 0 .
IDD 0 14 11 0 .
IDD 0 15 11 0 .
IDD 0 16 9 0 .
IDD 0 17 2 0 .
IDD 0 18 11 0 .
IDD 0 20 2 0 .
IDD 0 21 6 0 .
IDD 0 22 1 0 .
IDD 0 24 4 0 .
IDD 0 26 1 0 .
IDD 0 27 4 0 .
IDD 0 28 1 0 .
IDD 0 29 3 0 .
IDD 0 30 5 0 .
IDD 0 31 2 0 .
IDD 0 32 2 0 .
IDD 0 33 1 0 .
IDD 0 35 1 0 .
IDD 0 36 1 0 .
IDD 0 37 1 0 .
IDD 0 39 4 0 .
IDD 0 40 2 0 .
IDD 0 42 3 0 .
IDD 0 43 1 0 .
IDD 0 49 1 0 .
IDD 0 57 2 0 .
IDD 0 60 19 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 256
ST 0 A>G 638
ST 0 A>T 192
ST 0 C>A 319
ST 0 C>G 252
ST 0 C>T 1476
ST 0 G>A 1454
ST 0 G>C 285
ST 0 G>T 342
ST 0 T>A 196
ST 0 T>C 628
ST 0 T>G 237
# 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 17 0 0.000000 1 0.009915
DP 0 21 0 0.000000 1 0.009915
DP 0 23 0 0.000000 1 0.009915
DP 0 25 0 0.000000 4 0.039659
DP 0 26 0 0.000000 1 0.009915
DP 0 27 0 0.000000 2 0.019829
DP 0 30 0 0.000000 1 0.009915
DP 0 31 0 0.000000 2 0.019829
DP 0 34 0 0.000000 1 0.009915
DP 0 35 0 0.000000 1 0.009915
DP 0 44 0 0.000000 2 0.019829
DP 0 49 0 0.000000 2 0.019829
DP 0 52 0 0.000000 3 0.029744
DP 0 53 0 0.000000 2 0.019829
DP 0 54 0 0.000000 5 0.049574
DP 0 55 0 0.000000 2 0.019829
DP 0 56 0 0.000000 1 0.009915
DP 0 57 0 0.000000 2 0.019829
DP 0 59 0 0.000000 1 0.009915
DP 0 63 0 0.000000 2 0.019829
DP 0 71 0 0.000000 1 0.009915
DP 0 72 0 0.000000 1 0.009915
DP 0 88 0 0.000000 1 0.009915
DP 0 89 0 0.000000 1 0.009915
DP 0 91 0 0.000000 1 0.009915
DP 0 92 0 0.000000 2 0.019829
DP 0 95 0 0.000000 1 0.009915
DP 0 96 0 0.000000 1 0.009915
DP 0 104 0 0.000000 1 0.009915
DP 0 107 0 0.000000 1 0.009915
DP 0 110 0 0.000000 1 0.009915
DP 0 111 0 0.000000 1 0.009915
DP 0 112 0 0.000000 1 0.009915
DP 0 113 0 0.000000 2 0.019829
DP 0 114 0 0.000000 1 0.009915
DP 0 117 0 0.000000 1 0.009915
DP 0 128 0 0.000000 1 0.009915
DP 0 130 0 0.000000 1 0.009915
DP 0 141 0 0.000000 1 0.009915
DP 0 147 0 0.000000 1 0.009915
DP 0 150 0 0.000000 1 0.009915
DP 0 152 0 0.000000 1 0.009915
DP 0 154 0 0.000000 1 0.009915
DP 0 157 0 0.000000 1 0.009915
DP 0 159 0 0.000000 1 0.009915
DP 0 162 0 0.000000 1 0.009915
DP 0 165 0 0.000000 1 0.009915
DP 0 170 0 0.000000 1 0.009915
DP 0 172 0 0.000000 2 0.019829
DP 0 176 0 0.000000 1 0.009915
DP 0 177 0 0.000000 1 0.009915
DP 0 180 0 0.000000 1 0.009915
DP 0 182 0 0.000000 1 0.009915
DP 0 185 0 0.000000 1 0.009915
DP 0 186 0 0.000000 2 0.019829
DP 0 191 0 0.000000 1 0.009915
DP 0 194 0 0.000000 1 0.009915
DP 0 197 0 0.000000 2 0.019829
DP 0 198 0 0.000000 1 0.009915
DP 0 199 0 0.000000 1 0.009915
DP 0 200 0 0.000000 1 0.009915
DP 0 203 0 0.000000 1 0.009915
DP 0 204 0 0.000000 2 0.019829
DP 0 208 0 0.000000 1 0.009915
DP 0 211 0 0.000000 1 0.009915
DP 0 212 0 0.000000 1 0.009915
DP 0 213 0 0.000000 1 0.009915
DP 0 214 0 0.000000 2 0.019829
DP 0 216 0 0.000000 2 0.019829
DP 0 218 0 0.000000 1 0.009915
DP 0 219 0 0.000000 2 0.019829
DP 0 220 0 0.000000 1 0.009915
DP 0 224 0 0.000000 1 0.009915
DP 0 227 0 0.000000 1 0.009915
DP 0 231 0 0.000000 1 0.009915
DP 0 237 0 0.000000 1 0.009915
DP 0 238 0 0.000000 1 0.009915
DP 0 240 0 0.000000 1 0.009915
DP 0 241 0 0.000000 1 0.009915
DP 0 245 0 0.000000 1 0.009915
DP 0 246 0 0.000000 1 0.009915
DP 0 248 0 0.000000 2 0.019829
DP 0 249 0 0.000000 1 0.009915
DP 0 252 0 0.000000 2 0.019829
DP 0 254 0 0.000000 2 0.019829
DP 0 259 0 0.000000 1 0.009915
DP 0 260 0 0.000000 2 0.019829
DP 0 265 0 0.000000 1 0.009915
DP 0 269 0 0.000000 2 0.019829
DP 0 271 0 0.000000 1 0.009915
DP 0 277 0 0.000000 1 0.009915
DP 0 281 0 0.000000 2 0.019829
DP 0 282 0 0.000000 1 0.009915
DP 0 288 0 0.000000 3 0.029744
DP 0 292 0 0.000000 1 0.009915
DP 0 293 0 0.000000 1 0.009915
DP 0 294 0 0.000000 1 0.009915
DP 0 296 0 0.000000 1 0.009915
DP 0 298 0 0.000000 1 0.009915
DP 0 299 0 0.000000 1 0.009915
DP 0 300 0 0.000000 1 0.009915
DP 0 301 0 0.000000 1 0.009915
DP 0 302 0 0.000000 1 0.009915
DP 0 308 0 0.000000 1 0.009915
DP 0 309 0 0.000000 2 0.019829
DP 0 311 0 0.000000 1 0.009915
DP 0 312 0 0.000000 1 0.009915
DP 0 313 0 0.000000 1 0.009915
DP 0 318 0 0.000000 1 0.009915
DP 0 319 0 0.000000 1 0.009915
DP 0 320 0 0.000000 1 0.009915
DP 0 321 0 0.000000 1 0.009915
DP 0 322 0 0.000000 2 0.019829
DP 0 323 0 0.000000 1 0.009915
DP 0 324 0 0.000000 1 0.009915
DP 0 325 0 0.000000 3 0.029744
DP 0 326 0 0.000000 1 0.009915
DP 0 328 0 0.000000 3 0.029744
DP 0 329 0 0.000000 1 0.009915
DP 0 330 0 0.000000 2 0.019829
DP 0 333 0 0.000000 2 0.019829
DP 0 334 0 0.000000 1 0.009915
DP 0 335 0 0.000000 3 0.029744
DP 0 343 0 0.000000 2 0.019829
DP 0 344 0 0.000000 2 0.019829
DP 0 346 0 0.000000 4 0.039659
DP 0 347 0 0.000000 2 0.019829
DP 0 349 0 0.000000 1 0.009915
DP 0 350 0 0.000000 2 0.019829
DP 0 351 0 0.000000 2 0.019829
DP 0 353 0 0.000000 2 0.019829
DP 0 355 0 0.000000 1 0.009915
DP 0 356 0 0.000000 2 0.019829
DP 0 360 0 0.000000 1 0.009915
DP 0 362 0 0.000000 4 0.039659
DP 0 364 0 0.000000 1 0.009915
DP 0 370 0 0.000000 1 0.009915
DP 0 374 0 0.000000 2 0.019829
DP 0 376 0 0.000000 2 0.019829
DP 0 377 0 0.000000 2 0.019829
DP 0 379 0 0.000000 1 0.009915
DP 0 381 0 0.000000 1 0.009915
DP 0 383 0 0.000000 2 0.019829
DP 0 384 0 0.000000 3 0.029744
DP 0 386 0 0.000000 1 0.009915
DP 0 387 0 0.000000 1 0.009915
DP 0 389 0 0.000000 2 0.019829
DP 0 390 0 0.000000 4 0.039659
DP 0 391 0 0.000000 1 0.009915
DP 0 392 0 0.000000 2 0.019829
DP 0 393 0 0.000000 1 0.009915
DP 0 394 0 0.000000 2 0.019829
DP 0 395 0 0.000000 1 0.009915
DP 0 397 0 0.000000 1 0.009915
DP 0 398 0 0.000000 1 0.009915
DP 0 399 0 0.000000 1 0.009915
DP 0 400 0 0.000000 4 0.039659
DP 0 401 0 0.000000 2 0.019829
DP 0 402 0 0.000000 1 0.009915
DP 0 403 0 0.000000 1 0.009915
DP 0 404 0 0.000000 2 0.019829
DP 0 405 0 0.000000 1 0.009915
DP 0 406 0 0.000000 2 0.019829
DP 0 407 0 0.000000 1 0.009915
DP 0 410 0 0.000000 1 0.009915
DP 0 411 0 0.000000 2 0.019829
DP 0 412 0 0.000000 5 0.049574
DP 0 413 0 0.000000 2 0.019829
DP 0 414 0 0.000000 2 0.019829
DP 0 415 0 0.000000 2 0.019829
DP 0 416 0 0.000000 3 0.029744
DP 0 417 0 0.000000 4 0.039659
DP 0 418 0 0.000000 2 0.019829
DP 0 419 0 0.000000 2 0.019829
DP 0 420 0 0.000000 4 0.039659
DP 0 422 0 0.000000 2 0.019829
DP 0 424 0 0.000000 1 0.009915
DP 0 426 0 0.000000 2 0.019829
DP 0 427 0 0.000000 2 0.019829
DP 0 429 0 0.000000 2 0.019829
DP 0 432 0 0.000000 3 0.029744
DP 0 433 0 0.000000 1 0.009915
DP 0 434 0 0.000000 1 0.009915
DP 0 435 0 0.000000 1 0.009915
DP 0 436 0 0.000000 1 0.009915
DP 0 437 0 0.000000 2 0.019829
DP 0 438 0 0.000000 3 0.029744
DP 0 440 0 0.000000 1 0.009915
DP 0 441 0 0.000000 3 0.029744
DP 0 442 0 0.000000 2 0.019829
DP 0 443 0 0.000000 3 0.029744
DP 0 444 0 0.000000 3 0.029744
DP 0 445 0 0.000000 1 0.009915
DP 0 450 0 0.000000 3 0.029744
DP 0 452 0 0.000000 1 0.009915
DP 0 453 0 0.000000 3 0.029744
DP 0 455 0 0.000000 2 0.019829
DP 0 456 0 0.000000 2 0.019829
DP 0 457 0 0.000000 3 0.029744
DP 0 458 0 0.000000 2 0.019829
DP 0 459 0 0.000000 3 0.029744
DP 0 461 0 0.000000 3 0.029744
DP 0 464 0 0.000000 2 0.019829
DP 0 465 0 0.000000 2 0.019829
DP 0 466 0 0.000000 1 0.009915
DP 0 467 0 0.000000 1 0.009915
DP 0 468 0 0.000000 3 0.029744
DP 0 469 0 0.000000 1 0.009915
DP 0 472 0 0.000000 1 0.009915
DP 0 474 0 0.000000 3 0.029744
DP 0 475 0 0.000000 1 0.009915
DP 0 476 0 0.000000 2 0.019829
DP 0 477 0 0.000000 2 0.019829
DP 0 478 0 0.000000 4 0.039659
DP 0 479 0 0.000000 2 0.019829
DP 0 480 0 0.000000 1 0.009915
DP 0 481 0 0.000000 1 0.009915
DP 0 484 0 0.000000 1 0.009915
DP 0 485 0 0.000000 7 0.069403
DP 0 486 0 0.000000 5 0.049574
DP 0 487 0 0.000000 3 0.029744
DP 0 488 0 0.000000 1 0.009915
DP 0 489 0 0.000000 1 0.009915
DP 0 490 0 0.000000 2 0.019829
DP 0 491 0 0.000000 2 0.019829
DP 0 492 0 0.000000 3 0.029744
DP 0 493 0 0.000000 3 0.029744
DP 0 494 0 0.000000 1 0.009915
DP 0 495 0 0.000000 3 0.029744
DP 0 496 0 0.000000 1 0.009915
DP 0 497 0 0.000000 3 0.029744
DP 0 498 0 0.000000 1 0.009915
DP 0 499 0 0.000000 2 0.019829
DP 0 500 0 0.000000 1 0.009915
DP 0 >500 0 0.000000 9695 96.123339