- Filename
- 1029_BBS1-T1-TDNA-1_23FC2GLT4_s23_vs_1029_BBS1-N1-BDNA-1_2375WFLT3_s23.mutect2.whatshap.phased.bcftools_stats.txt
- Full Path
- s3://natera-rnd-pltf-dev-nextflow-data-01/users/mipeters/semiproductionize/sarek/69814f07/std_run_largest2_smallest2_8a99ba01/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.whatshap.phased.bcftools_stats.txt
- Size
- 10.8 KB
- Published
- Feb 02, 2026 10:30 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.whatshap.phased.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.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: 9114
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 4919
SN 0 number of MNPs: 656
SN 0 number of indels: 3949
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1554
SN 0 number of multiallelic SNP sites: 92
# 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 3000 2022 1.48 2822 1818 1.55
# 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 5022 3000 2022 7647 0 0 7647
# 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 5022 3000 2022 7647 0 0 7647
# 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 . 4640 2822 1818 3949
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 71 0 .
IDD 0 -58 2 0 .
IDD 0 -57 2 0 .
IDD 0 -54 4 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 3 0 .
IDD 0 -42 7 0 .
IDD 0 -40 1 0 .
IDD 0 -39 5 0 .
IDD 0 -38 2 0 .
IDD 0 -36 6 0 .
IDD 0 -35 2 0 .
IDD 0 -34 1 0 .
IDD 0 -33 7 0 .
IDD 0 -32 1 0 .
IDD 0 -31 2 0 .
IDD 0 -30 12 0 .
IDD 0 -29 4 0 .
IDD 0 -28 1 0 .
IDD 0 -27 3 0 .
IDD 0 -24 5 0 .
IDD 0 -22 3 0 .
IDD 0 -21 10 0 .
IDD 0 -20 5 0 .
IDD 0 -19 1 0 .
IDD 0 -18 13 0 .
IDD 0 -17 3 0 .
IDD 0 -16 6 0 .
IDD 0 -15 22 0 .
IDD 0 -14 11 0 .
IDD 0 -13 5 0 .
IDD 0 -12 46 0 .
IDD 0 -11 10 0 .
IDD 0 -10 30 0 .
IDD 0 -9 54 0 .
IDD 0 -8 70 0 .
IDD 0 -7 52 0 .
IDD 0 -6 299 0 .
IDD 0 -5 179 0 .
IDD 0 -4 415 0 .
IDD 0 -3 1821 0 .
IDD 0 -2 866 0 .
IDD 0 -1 1042 0 .
IDD 0 1 987 0 .
IDD 0 2 742 0 .
IDD 0 3 295 0 .
IDD 0 4 144 0 .
IDD 0 5 38 0 .
IDD 0 6 80 0 .
IDD 0 7 11 0 .
IDD 0 8 30 0 .
IDD 0 9 26 0 .
IDD 0 10 26 0 .
IDD 0 11 4 0 .
IDD 0 12 20 0 .
IDD 0 13 5 0 .
IDD 0 14 7 0 .
IDD 0 15 11 0 .
IDD 0 16 8 0 .
IDD 0 17 3 0 .
IDD 0 18 14 0 .
IDD 0 19 3 0 .
IDD 0 20 9 0 .
IDD 0 21 4 0 .
IDD 0 22 4 0 .
IDD 0 23 1 0 .
IDD 0 24 3 0 .
IDD 0 25 3 0 .
IDD 0 26 2 0 .
IDD 0 28 1 0 .
IDD 0 29 2 0 .
IDD 0 30 2 0 .
IDD 0 31 1 0 .
IDD 0 32 3 0 .
IDD 0 33 1 0 .
IDD 0 34 1 0 .
IDD 0 36 2 0 .
IDD 0 39 2 0 .
IDD 0 40 1 0 .
IDD 0 43 3 0 .
IDD 0 45 1 0 .
IDD 0 47 2 0 .
IDD 0 49 1 0 .
IDD 0 51 1 0 .
IDD 0 54 1 0 .
IDD 0 57 1 0 .
IDD 0 58 1 0 .
IDD 0 60 26 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 235
ST 0 A>G 644
ST 0 A>T 217
ST 0 C>A 287
ST 0 C>G 255
ST 0 C>T 869
ST 0 G>A 850
ST 0 G>C 291
ST 0 G>T 298
ST 0 T>A 207
ST 0 T>C 637
ST 0 T>G 232
# 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 14 0 0.000000 1 0.010972
DP 0 15 0 0.000000 1 0.010972
DP 0 23 0 0.000000 1 0.010972
DP 0 24 0 0.000000 1 0.010972
DP 0 27 0 0.000000 1 0.010972
DP 0 32 0 0.000000 4 0.043889
DP 0 33 0 0.000000 4 0.043889
DP 0 34 0 0.000000 8 0.087777
DP 0 35 0 0.000000 8 0.087777
DP 0 36 0 0.000000 4 0.043889
DP 0 38 0 0.000000 1 0.010972
DP 0 39 0 0.000000 2 0.021944
DP 0 40 0 0.000000 2 0.021944
DP 0 41 0 0.000000 3 0.032916
DP 0 42 0 0.000000 2 0.021944
DP 0 43 0 0.000000 1 0.010972
DP 0 45 0 0.000000 6 0.065833
DP 0 46 0 0.000000 1 0.010972
DP 0 47 0 0.000000 2 0.021944
DP 0 48 0 0.000000 1 0.010972
DP 0 51 0 0.000000 1 0.010972
DP 0 52 0 0.000000 1 0.010972
DP 0 53 0 0.000000 1 0.010972
DP 0 55 0 0.000000 1 0.010972
DP 0 56 0 0.000000 1 0.010972
DP 0 57 0 0.000000 1 0.010972
DP 0 58 0 0.000000 2 0.021944
DP 0 60 0 0.000000 1 0.010972
DP 0 61 0 0.000000 1 0.010972
DP 0 64 0 0.000000 2 0.021944
DP 0 66 0 0.000000 1 0.010972
DP 0 68 0 0.000000 1 0.010972
DP 0 69 0 0.000000 2 0.021944
DP 0 71 0 0.000000 3 0.032916
DP 0 72 0 0.000000 1 0.010972
DP 0 73 0 0.000000 3 0.032916
DP 0 74 0 0.000000 1 0.010972
DP 0 75 0 0.000000 1 0.010972
DP 0 76 0 0.000000 2 0.021944
DP 0 77 0 0.000000 1 0.010972
DP 0 78 0 0.000000 1 0.010972
DP 0 80 0 0.000000 1 0.010972
DP 0 81 0 0.000000 1 0.010972
DP 0 83 0 0.000000 1 0.010972
DP 0 84 0 0.000000 2 0.021944
DP 0 93 0 0.000000 1 0.010972
DP 0 94 0 0.000000 1 0.010972
DP 0 96 0 0.000000 1 0.010972
DP 0 98 0 0.000000 1 0.010972
DP 0 106 0 0.000000 4 0.043889
DP 0 109 0 0.000000 1 0.010972
DP 0 111 0 0.000000 1 0.010972
DP 0 118 0 0.000000 1 0.010972
DP 0 120 0 0.000000 1 0.010972
DP 0 121 0 0.000000 1 0.010972
DP 0 126 0 0.000000 1 0.010972
DP 0 131 0 0.000000 1 0.010972
DP 0 132 0 0.000000 2 0.021944
DP 0 135 0 0.000000 1 0.010972
DP 0 136 0 0.000000 1 0.010972
DP 0 141 0 0.000000 1 0.010972
DP 0 148 0 0.000000 1 0.010972
DP 0 155 0 0.000000 2 0.021944
DP 0 167 0 0.000000 1 0.010972
DP 0 169 0 0.000000 1 0.010972
DP 0 170 0 0.000000 3 0.032916
DP 0 171 0 0.000000 1 0.010972
DP 0 172 0 0.000000 1 0.010972
DP 0 173 0 0.000000 1 0.010972
DP 0 174 0 0.000000 1 0.010972
DP 0 175 0 0.000000 1 0.010972
DP 0 176 0 0.000000 2 0.021944
DP 0 178 0 0.000000 1 0.010972
DP 0 183 0 0.000000 1 0.010972
DP 0 193 0 0.000000 1 0.010972
DP 0 210 0 0.000000 1 0.010972
DP 0 214 0 0.000000 1 0.010972
DP 0 218 0 0.000000 1 0.010972
DP 0 222 0 0.000000 1 0.010972
DP 0 223 0 0.000000 1 0.010972
DP 0 230 0 0.000000 1 0.010972
DP 0 232 0 0.000000 2 0.021944
DP 0 244 0 0.000000 1 0.010972
DP 0 246 0 0.000000 4 0.043889
DP 0 247 0 0.000000 1 0.010972
DP 0 248 0 0.000000 1 0.010972
DP 0 250 0 0.000000 1 0.010972
DP 0 265 0 0.000000 1 0.010972
DP 0 268 0 0.000000 1 0.010972
DP 0 271 0 0.000000 1 0.010972
DP 0 272 0 0.000000 1 0.010972
DP 0 277 0 0.000000 1 0.010972
DP 0 279 0 0.000000 1 0.010972
DP 0 280 0 0.000000 1 0.010972
DP 0 284 0 0.000000 1 0.010972
DP 0 285 0 0.000000 1 0.010972
DP 0 286 0 0.000000 1 0.010972
DP 0 287 0 0.000000 2 0.021944
DP 0 289 0 0.000000 2 0.021944
DP 0 293 0 0.000000 1 0.010972
DP 0 294 0 0.000000 1 0.010972
DP 0 296 0 0.000000 1 0.010972
DP 0 297 0 0.000000 1 0.010972
DP 0 299 0 0.000000 2 0.021944
DP 0 300 0 0.000000 1 0.010972
DP 0 301 0 0.000000 1 0.010972
DP 0 303 0 0.000000 1 0.010972
DP 0 305 0 0.000000 2 0.021944
DP 0 307 0 0.000000 1 0.010972
DP 0 308 0 0.000000 2 0.021944
DP 0 309 0 0.000000 1 0.010972
DP 0 310 0 0.000000 2 0.021944
DP 0 316 0 0.000000 1 0.010972
DP 0 318 0 0.000000 2 0.021944
DP 0 321 0 0.000000 1 0.010972
DP 0 326 0 0.000000 1 0.010972
DP 0 327 0 0.000000 1 0.010972
DP 0 329 0 0.000000 1 0.010972
DP 0 331 0 0.000000 2 0.021944
DP 0 333 0 0.000000 1 0.010972
DP 0 334 0 0.000000 1 0.010972
DP 0 337 0 0.000000 1 0.010972
DP 0 338 0 0.000000 1 0.010972
DP 0 341 0 0.000000 1 0.010972
DP 0 346 0 0.000000 1 0.010972
DP 0 354 0 0.000000 1 0.010972
DP 0 355 0 0.000000 1 0.010972
DP 0 356 0 0.000000 1 0.010972
DP 0 357 0 0.000000 2 0.021944
DP 0 358 0 0.000000 1 0.010972
DP 0 359 0 0.000000 2 0.021944
DP 0 361 0 0.000000 3 0.032916
DP 0 364 0 0.000000 1 0.010972
DP 0 370 0 0.000000 2 0.021944
DP 0 373 0 0.000000 1 0.010972
DP 0 374 0 0.000000 1 0.010972
DP 0 376 0 0.000000 1 0.010972
DP 0 379 0 0.000000 1 0.010972
DP 0 380 0 0.000000 1 0.010972
DP 0 382 0 0.000000 2 0.021944
DP 0 383 0 0.000000 1 0.010972
DP 0 384 0 0.000000 2 0.021944
DP 0 385 0 0.000000 4 0.043889
DP 0 386 0 0.000000 1 0.010972
DP 0 388 0 0.000000 2 0.021944
DP 0 389 0 0.000000 1 0.010972
DP 0 390 0 0.000000 2 0.021944
DP 0 391 0 0.000000 1 0.010972
DP 0 393 0 0.000000 1 0.010972
DP 0 394 0 0.000000 1 0.010972
DP 0 396 0 0.000000 1 0.010972
DP 0 397 0 0.000000 2 0.021944
DP 0 398 0 0.000000 1 0.010972
DP 0 399 0 0.000000 1 0.010972
DP 0 402 0 0.000000 1 0.010972
DP 0 403 0 0.000000 1 0.010972
DP 0 404 0 0.000000 2 0.021944
DP 0 405 0 0.000000 3 0.032916
DP 0 406 0 0.000000 1 0.010972
DP 0 407 0 0.000000 2 0.021944
DP 0 408 0 0.000000 2 0.021944
DP 0 409 0 0.000000 2 0.021944
DP 0 410 0 0.000000 2 0.021944
DP 0 411 0 0.000000 1 0.010972
DP 0 415 0 0.000000 1 0.010972
DP 0 417 0 0.000000 1 0.010972
DP 0 419 0 0.000000 1 0.010972
DP 0 423 0 0.000000 1 0.010972
DP 0 424 0 0.000000 1 0.010972
DP 0 426 0 0.000000 1 0.010972
DP 0 428 0 0.000000 4 0.043889
DP 0 429 0 0.000000 2 0.021944
DP 0 432 0 0.000000 2 0.021944
DP 0 434 0 0.000000 1 0.010972
DP 0 437 0 0.000000 1 0.010972
DP 0 438 0 0.000000 1 0.010972
DP 0 439 0 0.000000 2 0.021944
DP 0 440 0 0.000000 1 0.010972
DP 0 442 0 0.000000 1 0.010972
DP 0 443 0 0.000000 1 0.010972
DP 0 446 0 0.000000 4 0.043889
DP 0 449 0 0.000000 1 0.010972
DP 0 452 0 0.000000 1 0.010972
DP 0 453 0 0.000000 1 0.010972
DP 0 454 0 0.000000 1 0.010972
DP 0 455 0 0.000000 1 0.010972
DP 0 457 0 0.000000 1 0.010972
DP 0 459 0 0.000000 2 0.021944
DP 0 461 0 0.000000 1 0.010972
DP 0 462 0 0.000000 2 0.021944
DP 0 466 0 0.000000 3 0.032916
DP 0 467 0 0.000000 4 0.043889
DP 0 468 0 0.000000 1 0.010972
DP 0 469 0 0.000000 2 0.021944
DP 0 470 0 0.000000 1 0.010972
DP 0 471 0 0.000000 3 0.032916
DP 0 472 0 0.000000 2 0.021944
DP 0 475 0 0.000000 1 0.010972
DP 0 476 0 0.000000 2 0.021944
DP 0 477 0 0.000000 1 0.010972
DP 0 478 0 0.000000 1 0.010972
DP 0 480 0 0.000000 1 0.010972
DP 0 482 0 0.000000 1 0.010972
DP 0 483 0 0.000000 2 0.021944
DP 0 484 0 0.000000 2 0.021944
DP 0 488 0 0.000000 1 0.010972
DP 0 489 0 0.000000 2 0.021944
DP 0 490 0 0.000000 1 0.010972
DP 0 491 0 0.000000 1 0.010972
DP 0 493 0 0.000000 2 0.021944
DP 0 494 0 0.000000 3 0.032916
DP 0 495 0 0.000000 2 0.021944
DP 0 497 0 0.000000 1 0.010972
DP 0 498 0 0.000000 4 0.043889
DP 0 499 0 0.000000 1 0.010972
DP 0 500 0 0.000000 2 0.021944
DP 0 >500 0 0.000000 8783 96.368225