- Filename
- 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.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_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09/1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.mutect2.whatshap.phased.bcftools_stats.txt
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- 12.7 KB
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- Feb 03, 2026 10:27 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_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.mutect2.whatshap.phased.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 1029_3N0-T1-TDNA-1_23FC2GLT4_s09_vs_1029_3N0-N1-BDNA-1_2375WFLT3_s09.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: 13661
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 7419
SN 0 number of MNPs: 781
SN 0 number of indels: 5854
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1893
SN 0 number of multiallelic SNP sites: 83
# 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 5062 2454 2.06 4921 2266 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 7516 5062 2454 9835 0 0 9835
# 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 7516 5062 2454 9835 0 0 9835
# 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 . 7187 4921 2266 5854
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 160 0 .
IDD 0 -59 3 0 .
IDD 0 -58 1 0 .
IDD 0 -57 4 0 .
IDD 0 -56 2 0 .
IDD 0 -55 1 0 .
IDD 0 -54 2 0 .
IDD 0 -53 2 0 .
IDD 0 -52 2 0 .
IDD 0 -51 3 0 .
IDD 0 -50 2 0 .
IDD 0 -49 4 0 .
IDD 0 -48 8 0 .
IDD 0 -47 2 0 .
IDD 0 -46 1 0 .
IDD 0 -45 4 0 .
IDD 0 -44 1 0 .
IDD 0 -43 2 0 .
IDD 0 -42 6 0 .
IDD 0 -41 1 0 .
IDD 0 -40 1 0 .
IDD 0 -39 7 0 .
IDD 0 -38 2 0 .
IDD 0 -37 2 0 .
IDD 0 -36 10 0 .
IDD 0 -34 3 0 .
IDD 0 -33 7 0 .
IDD 0 -32 2 0 .
IDD 0 -30 18 0 .
IDD 0 -29 2 0 .
IDD 0 -27 7 0 .
IDD 0 -26 4 0 .
IDD 0 -25 1 0 .
IDD 0 -24 15 0 .
IDD 0 -23 2 0 .
IDD 0 -22 2 0 .
IDD 0 -21 16 0 .
IDD 0 -20 7 0 .
IDD 0 -19 3 0 .
IDD 0 -18 22 0 .
IDD 0 -17 2 0 .
IDD 0 -16 8 0 .
IDD 0 -15 24 0 .
IDD 0 -14 11 0 .
IDD 0 -13 9 0 .
IDD 0 -12 41 0 .
IDD 0 -11 16 0 .
IDD 0 -10 36 0 .
IDD 0 -9 55 0 .
IDD 0 -8 73 0 .
IDD 0 -7 48 0 .
IDD 0 -6 378 0 .
IDD 0 -5 174 0 .
IDD 0 -4 465 0 .
IDD 0 -3 2306 0 .
IDD 0 -2 1109 0 .
IDD 0 -1 1607 0 .
IDD 0 1 1446 0 .
IDD 0 2 816 0 .
IDD 0 3 285 0 .
IDD 0 4 148 0 .
IDD 0 5 47 0 .
IDD 0 6 89 0 .
IDD 0 7 18 0 .
IDD 0 8 30 0 .
IDD 0 9 29 0 .
IDD 0 10 31 0 .
IDD 0 11 10 0 .
IDD 0 12 17 0 .
IDD 0 13 5 0 .
IDD 0 14 9 0 .
IDD 0 15 9 0 .
IDD 0 16 9 0 .
IDD 0 17 4 0 .
IDD 0 18 8 0 .
IDD 0 19 1 0 .
IDD 0 20 3 0 .
IDD 0 21 5 0 .
IDD 0 22 2 0 .
IDD 0 23 1 0 .
IDD 0 24 3 0 .
IDD 0 25 1 0 .
IDD 0 26 2 0 .
IDD 0 27 4 0 .
IDD 0 28 1 0 .
IDD 0 29 5 0 .
IDD 0 30 6 0 .
IDD 0 31 3 0 .
IDD 0 32 1 0 .
IDD 0 33 1 0 .
IDD 0 34 1 0 .
IDD 0 35 2 0 .
IDD 0 36 1 0 .
IDD 0 37 1 0 .
IDD 0 38 1 0 .
IDD 0 39 1 0 .
IDD 0 41 1 0 .
IDD 0 42 1 0 .
IDD 0 43 1 0 .
IDD 0 44 1 0 .
IDD 0 45 2 0 .
IDD 0 46 1 0 .
IDD 0 48 2 0 .
IDD 0 49 1 0 .
IDD 0 52 1 0 .
IDD 0 53 2 0 .
IDD 0 54 1 0 .
IDD 0 55 1 0 .
IDD 0 56 1 0 .
IDD 0 58 2 0 .
IDD 0 60 55 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 278
ST 0 A>G 819
ST 0 A>T 331
ST 0 C>A 303
ST 0 C>G 303
ST 0 C>T 1696
ST 0 G>A 1719
ST 0 G>C 335
ST 0 G>T 334
ST 0 T>A 309
ST 0 T>C 828
ST 0 T>G 261
# 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 11 0 0.000000 1 0.007320
DP 0 17 0 0.000000 5 0.036601
DP 0 18 0 0.000000 2 0.014640
DP 0 22 0 0.000000 1 0.007320
DP 0 23 0 0.000000 2 0.014640
DP 0 26 0 0.000000 2 0.014640
DP 0 27 0 0.000000 1 0.007320
DP 0 28 0 0.000000 4 0.029280
DP 0 31 0 0.000000 4 0.029280
DP 0 32 0 0.000000 1 0.007320
DP 0 33 0 0.000000 3 0.021960
DP 0 34 0 0.000000 2 0.014640
DP 0 37 0 0.000000 1 0.007320
DP 0 38 0 0.000000 1 0.007320
DP 0 39 0 0.000000 1 0.007320
DP 0 40 0 0.000000 1 0.007320
DP 0 42 0 0.000000 3 0.021960
DP 0 43 0 0.000000 3 0.021960
DP 0 44 0 0.000000 1 0.007320
DP 0 46 0 0.000000 3 0.021960
DP 0 47 0 0.000000 5 0.036601
DP 0 48 0 0.000000 2 0.014640
DP 0 49 0 0.000000 2 0.014640
DP 0 50 0 0.000000 4 0.029280
DP 0 51 0 0.000000 1 0.007320
DP 0 53 0 0.000000 3 0.021960
DP 0 54 0 0.000000 3 0.021960
DP 0 55 0 0.000000 1 0.007320
DP 0 57 0 0.000000 3 0.021960
DP 0 59 0 0.000000 4 0.029280
DP 0 60 0 0.000000 4 0.029280
DP 0 61 0 0.000000 1 0.007320
DP 0 62 0 0.000000 1 0.007320
DP 0 63 0 0.000000 2 0.014640
DP 0 65 0 0.000000 1 0.007320
DP 0 66 0 0.000000 1 0.007320
DP 0 69 0 0.000000 1 0.007320
DP 0 75 0 0.000000 1 0.007320
DP 0 83 0 0.000000 1 0.007320
DP 0 86 0 0.000000 2 0.014640
DP 0 87 0 0.000000 1 0.007320
DP 0 89 0 0.000000 1 0.007320
DP 0 94 0 0.000000 1 0.007320
DP 0 105 0 0.000000 1 0.007320
DP 0 118 0 0.000000 2 0.014640
DP 0 120 0 0.000000 1 0.007320
DP 0 125 0 0.000000 1 0.007320
DP 0 126 0 0.000000 2 0.014640
DP 0 128 0 0.000000 1 0.007320
DP 0 134 0 0.000000 1 0.007320
DP 0 139 0 0.000000 1 0.007320
DP 0 140 0 0.000000 1 0.007320
DP 0 141 0 0.000000 3 0.021960
DP 0 142 0 0.000000 1 0.007320
DP 0 147 0 0.000000 1 0.007320
DP 0 149 0 0.000000 2 0.014640
DP 0 150 0 0.000000 1 0.007320
DP 0 151 0 0.000000 1 0.007320
DP 0 152 0 0.000000 1 0.007320
DP 0 154 0 0.000000 1 0.007320
DP 0 156 0 0.000000 1 0.007320
DP 0 160 0 0.000000 2 0.014640
DP 0 165 0 0.000000 1 0.007320
DP 0 166 0 0.000000 1 0.007320
DP 0 170 0 0.000000 1 0.007320
DP 0 173 0 0.000000 1 0.007320
DP 0 175 0 0.000000 1 0.007320
DP 0 179 0 0.000000 1 0.007320
DP 0 181 0 0.000000 2 0.014640
DP 0 183 0 0.000000 1 0.007320
DP 0 184 0 0.000000 1 0.007320
DP 0 194 0 0.000000 1 0.007320
DP 0 195 0 0.000000 1 0.007320
DP 0 197 0 0.000000 1 0.007320
DP 0 199 0 0.000000 4 0.029280
DP 0 200 0 0.000000 1 0.007320
DP 0 205 0 0.000000 1 0.007320
DP 0 206 0 0.000000 1 0.007320
DP 0 207 0 0.000000 1 0.007320
DP 0 209 0 0.000000 1 0.007320
DP 0 217 0 0.000000 1 0.007320
DP 0 220 0 0.000000 3 0.021960
DP 0 221 0 0.000000 2 0.014640
DP 0 224 0 0.000000 1 0.007320
DP 0 228 0 0.000000 3 0.021960
DP 0 229 0 0.000000 1 0.007320
DP 0 231 0 0.000000 1 0.007320
DP 0 232 0 0.000000 1 0.007320
DP 0 236 0 0.000000 1 0.007320
DP 0 242 0 0.000000 1 0.007320
DP 0 247 0 0.000000 1 0.007320
DP 0 249 0 0.000000 1 0.007320
DP 0 253 0 0.000000 1 0.007320
DP 0 255 0 0.000000 2 0.014640
DP 0 258 0 0.000000 1 0.007320
DP 0 260 0 0.000000 2 0.014640
DP 0 261 0 0.000000 2 0.014640
DP 0 262 0 0.000000 1 0.007320
DP 0 269 0 0.000000 1 0.007320
DP 0 270 0 0.000000 1 0.007320
DP 0 271 0 0.000000 1 0.007320
DP 0 273 0 0.000000 1 0.007320
DP 0 274 0 0.000000 1 0.007320
DP 0 277 0 0.000000 2 0.014640
DP 0 279 0 0.000000 2 0.014640
DP 0 280 0 0.000000 1 0.007320
DP 0 283 0 0.000000 1 0.007320
DP 0 284 0 0.000000 2 0.014640
DP 0 287 0 0.000000 3 0.021960
DP 0 288 0 0.000000 1 0.007320
DP 0 289 0 0.000000 1 0.007320
DP 0 290 0 0.000000 3 0.021960
DP 0 292 0 0.000000 1 0.007320
DP 0 293 0 0.000000 2 0.014640
DP 0 294 0 0.000000 3 0.021960
DP 0 295 0 0.000000 3 0.021960
DP 0 297 0 0.000000 1 0.007320
DP 0 298 0 0.000000 1 0.007320
DP 0 301 0 0.000000 1 0.007320
DP 0 305 0 0.000000 1 0.007320
DP 0 307 0 0.000000 2 0.014640
DP 0 309 0 0.000000 2 0.014640
DP 0 310 0 0.000000 1 0.007320
DP 0 312 0 0.000000 2 0.014640
DP 0 313 0 0.000000 2 0.014640
DP 0 316 0 0.000000 2 0.014640
DP 0 319 0 0.000000 1 0.007320
DP 0 320 0 0.000000 1 0.007320
DP 0 324 0 0.000000 2 0.014640
DP 0 326 0 0.000000 1 0.007320
DP 0 329 0 0.000000 1 0.007320
DP 0 330 0 0.000000 1 0.007320
DP 0 331 0 0.000000 1 0.007320
DP 0 332 0 0.000000 1 0.007320
DP 0 333 0 0.000000 1 0.007320
DP 0 335 0 0.000000 1 0.007320
DP 0 336 0 0.000000 2 0.014640
DP 0 338 0 0.000000 1 0.007320
DP 0 341 0 0.000000 3 0.021960
DP 0 343 0 0.000000 1 0.007320
DP 0 345 0 0.000000 1 0.007320
DP 0 346 0 0.000000 1 0.007320
DP 0 350 0 0.000000 1 0.007320
DP 0 352 0 0.000000 1 0.007320
DP 0 354 0 0.000000 1 0.007320
DP 0 355 0 0.000000 1 0.007320
DP 0 356 0 0.000000 1 0.007320
DP 0 357 0 0.000000 2 0.014640
DP 0 358 0 0.000000 1 0.007320
DP 0 359 0 0.000000 1 0.007320
DP 0 362 0 0.000000 1 0.007320
DP 0 364 0 0.000000 4 0.029280
DP 0 365 0 0.000000 2 0.014640
DP 0 366 0 0.000000 1 0.007320
DP 0 367 0 0.000000 1 0.007320
DP 0 368 0 0.000000 2 0.014640
DP 0 369 0 0.000000 4 0.029280
DP 0 371 0 0.000000 1 0.007320
DP 0 372 0 0.000000 1 0.007320
DP 0 374 0 0.000000 2 0.014640
DP 0 375 0 0.000000 1 0.007320
DP 0 376 0 0.000000 1 0.007320
DP 0 377 0 0.000000 3 0.021960
DP 0 378 0 0.000000 1 0.007320
DP 0 379 0 0.000000 1 0.007320
DP 0 380 0 0.000000 1 0.007320
DP 0 384 0 0.000000 2 0.014640
DP 0 386 0 0.000000 1 0.007320
DP 0 387 0 0.000000 2 0.014640
DP 0 388 0 0.000000 2 0.014640
DP 0 389 0 0.000000 3 0.021960
DP 0 390 0 0.000000 1 0.007320
DP 0 391 0 0.000000 1 0.007320
DP 0 392 0 0.000000 1 0.007320
DP 0 393 0 0.000000 2 0.014640
DP 0 394 0 0.000000 1 0.007320
DP 0 396 0 0.000000 2 0.014640
DP 0 398 0 0.000000 3 0.021960
DP 0 399 0 0.000000 2 0.014640
DP 0 400 0 0.000000 6 0.043921
DP 0 401 0 0.000000 1 0.007320
DP 0 402 0 0.000000 2 0.014640
DP 0 403 0 0.000000 2 0.014640
DP 0 404 0 0.000000 1 0.007320
DP 0 405 0 0.000000 1 0.007320
DP 0 406 0 0.000000 2 0.014640
DP 0 407 0 0.000000 1 0.007320
DP 0 409 0 0.000000 3 0.021960
DP 0 410 0 0.000000 2 0.014640
DP 0 411 0 0.000000 2 0.014640
DP 0 412 0 0.000000 2 0.014640
DP 0 415 0 0.000000 1 0.007320
DP 0 418 0 0.000000 1 0.007320
DP 0 419 0 0.000000 2 0.014640
DP 0 421 0 0.000000 3 0.021960
DP 0 422 0 0.000000 2 0.014640
DP 0 423 0 0.000000 2 0.014640
DP 0 424 0 0.000000 2 0.014640
DP 0 425 0 0.000000 2 0.014640
DP 0 426 0 0.000000 2 0.014640
DP 0 427 0 0.000000 1 0.007320
DP 0 428 0 0.000000 2 0.014640
DP 0 430 0 0.000000 2 0.014640
DP 0 432 0 0.000000 4 0.029280
DP 0 433 0 0.000000 3 0.021960
DP 0 434 0 0.000000 1 0.007320
DP 0 435 0 0.000000 3 0.021960
DP 0 436 0 0.000000 2 0.014640
DP 0 438 0 0.000000 1 0.007320
DP 0 439 0 0.000000 3 0.021960
DP 0 440 0 0.000000 2 0.014640
DP 0 441 0 0.000000 2 0.014640
DP 0 442 0 0.000000 1 0.007320
DP 0 443 0 0.000000 3 0.021960
DP 0 444 0 0.000000 1 0.007320
DP 0 445 0 0.000000 1 0.007320
DP 0 446 0 0.000000 1 0.007320
DP 0 447 0 0.000000 1 0.007320
DP 0 448 0 0.000000 4 0.029280
DP 0 449 0 0.000000 2 0.014640
DP 0 450 0 0.000000 2 0.014640
DP 0 451 0 0.000000 2 0.014640
DP 0 452 0 0.000000 1 0.007320
DP 0 453 0 0.000000 3 0.021960
DP 0 454 0 0.000000 2 0.014640
DP 0 455 0 0.000000 4 0.029280
DP 0 456 0 0.000000 5 0.036601
DP 0 457 0 0.000000 4 0.029280
DP 0 458 0 0.000000 4 0.029280
DP 0 459 0 0.000000 4 0.029280
DP 0 460 0 0.000000 1 0.007320
DP 0 461 0 0.000000 1 0.007320
DP 0 462 0 0.000000 2 0.014640
DP 0 463 0 0.000000 2 0.014640
DP 0 464 0 0.000000 2 0.014640
DP 0 465 0 0.000000 4 0.029280
DP 0 466 0 0.000000 3 0.021960
DP 0 467 0 0.000000 1 0.007320
DP 0 468 0 0.000000 3 0.021960
DP 0 469 0 0.000000 2 0.014640
DP 0 470 0 0.000000 6 0.043921
DP 0 471 0 0.000000 1 0.007320
DP 0 472 0 0.000000 3 0.021960
DP 0 473 0 0.000000 2 0.014640
DP 0 474 0 0.000000 2 0.014640
DP 0 475 0 0.000000 4 0.029280
DP 0 476 0 0.000000 4 0.029280
DP 0 477 0 0.000000 4 0.029280
DP 0 478 0 0.000000 2 0.014640
DP 0 479 0 0.000000 4 0.029280
DP 0 480 0 0.000000 3 0.021960
DP 0 481 0 0.000000 2 0.014640
DP 0 482 0 0.000000 2 0.014640
DP 0 483 0 0.000000 2 0.014640
DP 0 484 0 0.000000 4 0.029280
DP 0 485 0 0.000000 3 0.021960
DP 0 486 0 0.000000 3 0.021960
DP 0 487 0 0.000000 3 0.021960
DP 0 489 0 0.000000 3 0.021960
DP 0 490 0 0.000000 3 0.021960
DP 0 491 0 0.000000 2 0.014640
DP 0 492 0 0.000000 1 0.007320
DP 0 493 0 0.000000 3 0.021960
DP 0 494 0 0.000000 5 0.036601
DP 0 496 0 0.000000 1 0.007320
DP 0 498 0 0.000000 4 0.029280
DP 0 499 0 0.000000 4 0.029280
DP 0 500 0 0.000000 2 0.014640
DP 0 >500 0 0.000000 13160 96.332626