- Filename
- 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.filtered.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_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23/1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.filtered.bcftools_stats.txt
- Size
- 10.7 KB
- Published
- Feb 03, 2026 10:23 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_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.filtered.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.filtered.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: 10068
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 5373
SN 0 number of MNPs: 669
SN 0 number of indels: 4456
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1688
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 3298 2173 1.52 3127 1975 1.58
# 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 5471 3298 2173 8489 0 0 8489
# 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 5471 3298 2173 8489 0 0 8489
# 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 . 5102 3127 1975 4456
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 74 0 .
IDD 0 -57 3 0 .
IDD 0 -54 3 0 .
IDD 0 -53 1 0 .
IDD 0 -52 1 0 .
IDD 0 -51 1 0 .
IDD 0 -50 1 0 .
IDD 0 -48 4 0 .
IDD 0 -47 1 0 .
IDD 0 -46 1 0 .
IDD 0 -45 1 0 .
IDD 0 -43 1 0 .
IDD 0 -42 8 0 .
IDD 0 -41 1 0 .
IDD 0 -40 1 0 .
IDD 0 -39 4 0 .
IDD 0 -38 2 0 .
IDD 0 -36 8 0 .
IDD 0 -35 1 0 .
IDD 0 -34 1 0 .
IDD 0 -33 8 0 .
IDD 0 -32 1 0 .
IDD 0 -31 2 0 .
IDD 0 -30 11 0 .
IDD 0 -29 4 0 .
IDD 0 -28 2 0 .
IDD 0 -27 5 0 .
IDD 0 -25 1 0 .
IDD 0 -24 6 0 .
IDD 0 -22 4 0 .
IDD 0 -21 12 0 .
IDD 0 -20 5 0 .
IDD 0 -19 1 0 .
IDD 0 -18 14 0 .
IDD 0 -17 5 0 .
IDD 0 -16 8 0 .
IDD 0 -15 22 0 .
IDD 0 -14 13 0 .
IDD 0 -13 6 0 .
IDD 0 -12 49 0 .
IDD 0 -11 11 0 .
IDD 0 -10 32 0 .
IDD 0 -9 56 0 .
IDD 0 -8 75 0 .
IDD 0 -7 57 0 .
IDD 0 -6 324 0 .
IDD 0 -5 191 0 .
IDD 0 -4 435 0 .
IDD 0 -3 2002 0 .
IDD 0 -2 955 0 .
IDD 0 -1 1269 0 .
IDD 0 1 1126 0 .
IDD 0 2 810 0 .
IDD 0 3 315 0 .
IDD 0 4 143 0 .
IDD 0 5 46 0 .
IDD 0 6 74 0 .
IDD 0 7 14 0 .
IDD 0 8 31 0 .
IDD 0 9 24 0 .
IDD 0 10 23 0 .
IDD 0 11 7 0 .
IDD 0 12 21 0 .
IDD 0 13 5 0 .
IDD 0 14 6 0 .
IDD 0 15 11 0 .
IDD 0 16 9 0 .
IDD 0 17 2 0 .
IDD 0 18 15 0 .
IDD 0 19 6 0 .
IDD 0 20 10 0 .
IDD 0 21 4 0 .
IDD 0 22 5 0 .
IDD 0 23 3 0 .
IDD 0 24 3 0 .
IDD 0 25 3 0 .
IDD 0 26 2 0 .
IDD 0 28 1 0 .
IDD 0 29 3 0 .
IDD 0 30 3 0 .
IDD 0 31 2 0 .
IDD 0 32 3 0 .
IDD 0 33 1 0 .
IDD 0 34 1 0 .
IDD 0 36 2 0 .
IDD 0 38 1 0 .
IDD 0 39 2 0 .
IDD 0 40 1 0 .
IDD 0 42 1 0 .
IDD 0 43 3 0 .
IDD 0 45 1 0 .
IDD 0 47 1 0 .
IDD 0 51 1 0 .
IDD 0 54 1 0 .
IDD 0 58 1 0 .
IDD 0 59 1 0 .
IDD 0 60 37 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 251
ST 0 A>G 698
ST 0 A>T 232
ST 0 C>A 318
ST 0 C>G 285
ST 0 C>T 964
ST 0 G>A 970
ST 0 G>C 304
ST 0 G>T 329
ST 0 T>A 217
ST 0 T>C 666
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 19 0 0.000000 3 0.029797
DP 0 20 0 0.000000 2 0.019865
DP 0 21 0 0.000000 1 0.009932
DP 0 23 0 0.000000 1 0.009932
DP 0 24 0 0.000000 1 0.009932
DP 0 25 0 0.000000 1 0.009932
DP 0 30 0 0.000000 1 0.009932
DP 0 33 0 0.000000 1 0.009932
DP 0 34 0 0.000000 10 0.099325
DP 0 35 0 0.000000 5 0.049662
DP 0 36 0 0.000000 4 0.039730
DP 0 37 0 0.000000 4 0.039730
DP 0 38 0 0.000000 2 0.019865
DP 0 39 0 0.000000 2 0.019865
DP 0 40 0 0.000000 3 0.029797
DP 0 41 0 0.000000 3 0.029797
DP 0 43 0 0.000000 1 0.009932
DP 0 44 0 0.000000 2 0.019865
DP 0 45 0 0.000000 5 0.049662
DP 0 46 0 0.000000 2 0.019865
DP 0 47 0 0.000000 2 0.019865
DP 0 48 0 0.000000 1 0.009932
DP 0 52 0 0.000000 1 0.009932
DP 0 53 0 0.000000 1 0.009932
DP 0 55 0 0.000000 1 0.009932
DP 0 56 0 0.000000 1 0.009932
DP 0 58 0 0.000000 2 0.019865
DP 0 63 0 0.000000 1 0.009932
DP 0 64 0 0.000000 1 0.009932
DP 0 65 0 0.000000 1 0.009932
DP 0 66 0 0.000000 1 0.009932
DP 0 68 0 0.000000 2 0.019865
DP 0 70 0 0.000000 1 0.009932
DP 0 71 0 0.000000 4 0.039730
DP 0 72 0 0.000000 4 0.039730
DP 0 75 0 0.000000 2 0.019865
DP 0 76 0 0.000000 1 0.009932
DP 0 77 0 0.000000 1 0.009932
DP 0 79 0 0.000000 1 0.009932
DP 0 80 0 0.000000 1 0.009932
DP 0 81 0 0.000000 1 0.009932
DP 0 84 0 0.000000 1 0.009932
DP 0 88 0 0.000000 1 0.009932
DP 0 93 0 0.000000 1 0.009932
DP 0 94 0 0.000000 1 0.009932
DP 0 95 0 0.000000 1 0.009932
DP 0 98 0 0.000000 1 0.009932
DP 0 106 0 0.000000 3 0.029797
DP 0 109 0 0.000000 1 0.009932
DP 0 112 0 0.000000 1 0.009932
DP 0 115 0 0.000000 1 0.009932
DP 0 118 0 0.000000 1 0.009932
DP 0 125 0 0.000000 1 0.009932
DP 0 130 0 0.000000 1 0.009932
DP 0 131 0 0.000000 2 0.019865
DP 0 132 0 0.000000 1 0.009932
DP 0 135 0 0.000000 1 0.009932
DP 0 136 0 0.000000 1 0.009932
DP 0 143 0 0.000000 1 0.009932
DP 0 153 0 0.000000 1 0.009932
DP 0 155 0 0.000000 1 0.009932
DP 0 156 0 0.000000 1 0.009932
DP 0 158 0 0.000000 1 0.009932
DP 0 166 0 0.000000 1 0.009932
DP 0 170 0 0.000000 3 0.029797
DP 0 171 0 0.000000 1 0.009932
DP 0 172 0 0.000000 2 0.019865
DP 0 173 0 0.000000 1 0.009932
DP 0 174 0 0.000000 2 0.019865
DP 0 176 0 0.000000 2 0.019865
DP 0 177 0 0.000000 1 0.009932
DP 0 193 0 0.000000 1 0.009932
DP 0 200 0 0.000000 1 0.009932
DP 0 201 0 0.000000 1 0.009932
DP 0 214 0 0.000000 1 0.009932
DP 0 216 0 0.000000 1 0.009932
DP 0 228 0 0.000000 1 0.009932
DP 0 233 0 0.000000 1 0.009932
DP 0 236 0 0.000000 1 0.009932
DP 0 243 0 0.000000 1 0.009932
DP 0 246 0 0.000000 1 0.009932
DP 0 248 0 0.000000 3 0.029797
DP 0 249 0 0.000000 1 0.009932
DP 0 250 0 0.000000 1 0.009932
DP 0 252 0 0.000000 1 0.009932
DP 0 264 0 0.000000 1 0.009932
DP 0 267 0 0.000000 1 0.009932
DP 0 268 0 0.000000 1 0.009932
DP 0 272 0 0.000000 1 0.009932
DP 0 274 0 0.000000 2 0.019865
DP 0 276 0 0.000000 1 0.009932
DP 0 280 0 0.000000 2 0.019865
DP 0 283 0 0.000000 1 0.009932
DP 0 284 0 0.000000 1 0.009932
DP 0 294 0 0.000000 1 0.009932
DP 0 296 0 0.000000 1 0.009932
DP 0 298 0 0.000000 1 0.009932
DP 0 303 0 0.000000 2 0.019865
DP 0 307 0 0.000000 1 0.009932
DP 0 308 0 0.000000 2 0.019865
DP 0 309 0 0.000000 1 0.009932
DP 0 314 0 0.000000 1 0.009932
DP 0 317 0 0.000000 1 0.009932
DP 0 318 0 0.000000 1 0.009932
DP 0 319 0 0.000000 1 0.009932
DP 0 322 0 0.000000 1 0.009932
DP 0 324 0 0.000000 1 0.009932
DP 0 325 0 0.000000 1 0.009932
DP 0 327 0 0.000000 2 0.019865
DP 0 328 0 0.000000 1 0.009932
DP 0 331 0 0.000000 1 0.009932
DP 0 333 0 0.000000 1 0.009932
DP 0 334 0 0.000000 1 0.009932
DP 0 337 0 0.000000 1 0.009932
DP 0 339 0 0.000000 1 0.009932
DP 0 342 0 0.000000 1 0.009932
DP 0 354 0 0.000000 3 0.029797
DP 0 355 0 0.000000 1 0.009932
DP 0 356 0 0.000000 1 0.009932
DP 0 357 0 0.000000 1 0.009932
DP 0 358 0 0.000000 1 0.009932
DP 0 359 0 0.000000 2 0.019865
DP 0 360 0 0.000000 1 0.009932
DP 0 362 0 0.000000 1 0.009932
DP 0 363 0 0.000000 2 0.019865
DP 0 365 0 0.000000 2 0.019865
DP 0 367 0 0.000000 1 0.009932
DP 0 371 0 0.000000 1 0.009932
DP 0 372 0 0.000000 1 0.009932
DP 0 373 0 0.000000 1 0.009932
DP 0 374 0 0.000000 1 0.009932
DP 0 375 0 0.000000 1 0.009932
DP 0 378 0 0.000000 1 0.009932
DP 0 380 0 0.000000 1 0.009932
DP 0 381 0 0.000000 1 0.009932
DP 0 384 0 0.000000 1 0.009932
DP 0 387 0 0.000000 1 0.009932
DP 0 388 0 0.000000 1 0.009932
DP 0 389 0 0.000000 1 0.009932
DP 0 390 0 0.000000 1 0.009932
DP 0 391 0 0.000000 1 0.009932
DP 0 394 0 0.000000 1 0.009932
DP 0 395 0 0.000000 1 0.009932
DP 0 397 0 0.000000 2 0.019865
DP 0 398 0 0.000000 1 0.009932
DP 0 399 0 0.000000 2 0.019865
DP 0 400 0 0.000000 1 0.009932
DP 0 402 0 0.000000 1 0.009932
DP 0 404 0 0.000000 1 0.009932
DP 0 405 0 0.000000 1 0.009932
DP 0 406 0 0.000000 3 0.029797
DP 0 407 0 0.000000 2 0.019865
DP 0 409 0 0.000000 2 0.019865
DP 0 410 0 0.000000 2 0.019865
DP 0 411 0 0.000000 4 0.039730
DP 0 416 0 0.000000 1 0.009932
DP 0 418 0 0.000000 1 0.009932
DP 0 419 0 0.000000 1 0.009932
DP 0 422 0 0.000000 1 0.009932
DP 0 423 0 0.000000 1 0.009932
DP 0 426 0 0.000000 1 0.009932
DP 0 428 0 0.000000 2 0.019865
DP 0 429 0 0.000000 2 0.019865
DP 0 431 0 0.000000 1 0.009932
DP 0 432 0 0.000000 1 0.009932
DP 0 434 0 0.000000 1 0.009932
DP 0 436 0 0.000000 1 0.009932
DP 0 440 0 0.000000 2 0.019865
DP 0 441 0 0.000000 1 0.009932
DP 0 443 0 0.000000 1 0.009932
DP 0 444 0 0.000000 1 0.009932
DP 0 445 0 0.000000 1 0.009932
DP 0 446 0 0.000000 1 0.009932
DP 0 449 0 0.000000 1 0.009932
DP 0 450 0 0.000000 3 0.029797
DP 0 451 0 0.000000 1 0.009932
DP 0 452 0 0.000000 3 0.029797
DP 0 456 0 0.000000 2 0.019865
DP 0 458 0 0.000000 1 0.009932
DP 0 460 0 0.000000 1 0.009932
DP 0 461 0 0.000000 1 0.009932
DP 0 462 0 0.000000 2 0.019865
DP 0 463 0 0.000000 1 0.009932
DP 0 464 0 0.000000 3 0.029797
DP 0 465 0 0.000000 1 0.009932
DP 0 466 0 0.000000 4 0.039730
DP 0 467 0 0.000000 3 0.029797
DP 0 468 0 0.000000 2 0.019865
DP 0 469 0 0.000000 3 0.029797
DP 0 471 0 0.000000 1 0.009932
DP 0 472 0 0.000000 2 0.019865
DP 0 473 0 0.000000 1 0.009932
DP 0 476 0 0.000000 3 0.029797
DP 0 477 0 0.000000 2 0.019865
DP 0 478 0 0.000000 2 0.019865
DP 0 479 0 0.000000 2 0.019865
DP 0 480 0 0.000000 1 0.009932
DP 0 481 0 0.000000 1 0.009932
DP 0 482 0 0.000000 1 0.009932
DP 0 483 0 0.000000 1 0.009932
DP 0 484 0 0.000000 1 0.009932
DP 0 485 0 0.000000 2 0.019865
DP 0 488 0 0.000000 1 0.009932
DP 0 489 0 0.000000 2 0.019865
DP 0 490 0 0.000000 2 0.019865
DP 0 491 0 0.000000 1 0.009932
DP 0 492 0 0.000000 1 0.009932
DP 0 494 0 0.000000 3 0.029797
DP 0 496 0 0.000000 2 0.019865
DP 0 497 0 0.000000 3 0.029797
DP 0 498 0 0.000000 2 0.019865
DP 0 >500 0 0.000000 9749 96.831545