- Filename
- 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased.bcftools_stats.txt
- Full Path
- s3://natera-platform-sandbox/users/abshah/sarek/outputs/test_1029_BGFD-variants-3/reports/raw_qc/bcftools/mutect2/1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30/1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased.bcftools_stats.txt
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- 14.4 KB
- Published
- Jan 25, 2026 5:29 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_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.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: 13643
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 8834
SN 0 number of MNPs: 782
SN 0 number of indels: 4571
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1688
SN 0 number of multiallelic SNP sites: 101
# 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 6636 2320 2.86 6387 2130 3.00
# 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 8956 6636 2320 7842 0 0 7842
# 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 8956 6636 2320 7842 0 0 7842
# 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 . 8517 6387 2130 4571
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 98 0 .
IDD 0 -58 6 0 .
IDD 0 -57 3 0 .
IDD 0 -55 3 0 .
IDD 0 -54 2 0 .
IDD 0 -52 1 0 .
IDD 0 -51 5 0 .
IDD 0 -50 2 0 .
IDD 0 -49 2 0 .
IDD 0 -48 1 0 .
IDD 0 -47 1 0 .
IDD 0 -46 1 0 .
IDD 0 -45 5 0 .
IDD 0 -42 6 0 .
IDD 0 -41 1 0 .
IDD 0 -39 3 0 .
IDD 0 -38 4 0 .
IDD 0 -37 2 0 .
IDD 0 -36 10 0 .
IDD 0 -35 1 0 .
IDD 0 -34 3 0 .
IDD 0 -33 6 0 .
IDD 0 -31 1 0 .
IDD 0 -30 8 0 .
IDD 0 -29 2 0 .
IDD 0 -28 1 0 .
IDD 0 -27 12 0 .
IDD 0 -26 1 0 .
IDD 0 -25 1 0 .
IDD 0 -24 16 0 .
IDD 0 -23 3 0 .
IDD 0 -21 14 0 .
IDD 0 -20 7 0 .
IDD 0 -19 1 0 .
IDD 0 -18 20 0 .
IDD 0 -17 4 0 .
IDD 0 -16 5 0 .
IDD 0 -15 21 0 .
IDD 0 -14 16 0 .
IDD 0 -13 9 0 .
IDD 0 -12 58 0 .
IDD 0 -11 11 0 .
IDD 0 -10 28 0 .
IDD 0 -9 52 0 .
IDD 0 -8 70 0 .
IDD 0 -7 37 0 .
IDD 0 -6 271 0 .
IDD 0 -5 162 0 .
IDD 0 -4 396 0 .
IDD 0 -3 1593 0 .
IDD 0 -2 976 0 .
IDD 0 -1 1142 0 .
IDD 0 1 1094 0 .
IDD 0 2 768 0 .
IDD 0 3 263 0 .
IDD 0 4 142 0 .
IDD 0 5 58 0 .
IDD 0 6 73 0 .
IDD 0 7 30 0 .
IDD 0 8 28 0 .
IDD 0 9 32 0 .
IDD 0 10 24 0 .
IDD 0 11 16 0 .
IDD 0 12 15 0 .
IDD 0 13 8 0 .
IDD 0 14 17 0 .
IDD 0 15 10 0 .
IDD 0 16 11 0 .
IDD 0 17 7 0 .
IDD 0 18 6 0 .
IDD 0 19 3 0 .
IDD 0 20 9 0 .
IDD 0 21 7 0 .
IDD 0 22 3 0 .
IDD 0 23 6 0 .
IDD 0 24 1 0 .
IDD 0 25 3 0 .
IDD 0 27 5 0 .
IDD 0 28 1 0 .
IDD 0 30 3 0 .
IDD 0 31 5 0 .
IDD 0 32 3 0 .
IDD 0 33 1 0 .
IDD 0 34 2 0 .
IDD 0 39 2 0 .
IDD 0 42 3 0 .
IDD 0 47 1 0 .
IDD 0 48 1 0 .
IDD 0 49 2 0 .
IDD 0 50 1 0 .
IDD 0 51 2 0 .
IDD 0 53 4 0 .
IDD 0 54 2 0 .
IDD 0 56 1 0 .
IDD 0 58 3 0 .
IDD 0 59 2 0 .
IDD 0 60 60 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 241
ST 0 A>G 779
ST 0 A>T 312
ST 0 C>A 334
ST 0 C>G 275
ST 0 C>T 2551
ST 0 G>A 2555
ST 0 G>C 271
ST 0 G>T 358
ST 0 T>A 292
ST 0 T>C 751
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 11 0 0.000000 3 0.021989
DP 0 12 0 0.000000 2 0.014660
DP 0 13 0 0.000000 1 0.007330
DP 0 15 0 0.000000 6 0.043979
DP 0 16 0 0.000000 8 0.058638
DP 0 17 0 0.000000 4 0.029319
DP 0 18 0 0.000000 2 0.014660
DP 0 20 0 0.000000 2 0.014660
DP 0 21 0 0.000000 2 0.014660
DP 0 22 0 0.000000 3 0.021989
DP 0 23 0 0.000000 3 0.021989
DP 0 24 0 0.000000 1 0.007330
DP 0 25 0 0.000000 4 0.029319
DP 0 26 0 0.000000 1 0.007330
DP 0 27 0 0.000000 4 0.029319
DP 0 28 0 0.000000 2 0.014660
DP 0 29 0 0.000000 3 0.021989
DP 0 30 0 0.000000 8 0.058638
DP 0 31 0 0.000000 3 0.021989
DP 0 32 0 0.000000 3 0.021989
DP 0 33 0 0.000000 9 0.065968
DP 0 34 0 0.000000 1 0.007330
DP 0 35 0 0.000000 1 0.007330
DP 0 36 0 0.000000 1 0.007330
DP 0 37 0 0.000000 5 0.036649
DP 0 38 0 0.000000 5 0.036649
DP 0 39 0 0.000000 3 0.021989
DP 0 40 0 0.000000 1 0.007330
DP 0 41 0 0.000000 4 0.029319
DP 0 42 0 0.000000 2 0.014660
DP 0 44 0 0.000000 1 0.007330
DP 0 45 0 0.000000 1 0.007330
DP 0 46 0 0.000000 2 0.014660
DP 0 47 0 0.000000 1 0.007330
DP 0 48 0 0.000000 1 0.007330
DP 0 51 0 0.000000 4 0.029319
DP 0 52 0 0.000000 1 0.007330
DP 0 53 0 0.000000 1 0.007330
DP 0 54 0 0.000000 1 0.007330
DP 0 55 0 0.000000 2 0.014660
DP 0 58 0 0.000000 4 0.029319
DP 0 61 0 0.000000 1 0.007330
DP 0 62 0 0.000000 1 0.007330
DP 0 63 0 0.000000 1 0.007330
DP 0 65 0 0.000000 1 0.007330
DP 0 68 0 0.000000 1 0.007330
DP 0 69 0 0.000000 1 0.007330
DP 0 70 0 0.000000 1 0.007330
DP 0 71 0 0.000000 1 0.007330
DP 0 72 0 0.000000 1 0.007330
DP 0 82 0 0.000000 1 0.007330
DP 0 83 0 0.000000 1 0.007330
DP 0 84 0 0.000000 1 0.007330
DP 0 103 0 0.000000 1 0.007330
DP 0 105 0 0.000000 1 0.007330
DP 0 110 0 0.000000 1 0.007330
DP 0 116 0 0.000000 1 0.007330
DP 0 119 0 0.000000 1 0.007330
DP 0 122 0 0.000000 1 0.007330
DP 0 123 0 0.000000 2 0.014660
DP 0 124 0 0.000000 1 0.007330
DP 0 126 0 0.000000 1 0.007330
DP 0 127 0 0.000000 1 0.007330
DP 0 129 0 0.000000 3 0.021989
DP 0 134 0 0.000000 1 0.007330
DP 0 137 0 0.000000 1 0.007330
DP 0 138 0 0.000000 2 0.014660
DP 0 142 0 0.000000 1 0.007330
DP 0 144 0 0.000000 1 0.007330
DP 0 149 0 0.000000 1 0.007330
DP 0 151 0 0.000000 1 0.007330
DP 0 156 0 0.000000 1 0.007330
DP 0 158 0 0.000000 1 0.007330
DP 0 165 0 0.000000 1 0.007330
DP 0 166 0 0.000000 1 0.007330
DP 0 167 0 0.000000 1 0.007330
DP 0 169 0 0.000000 1 0.007330
DP 0 174 0 0.000000 1 0.007330
DP 0 175 0 0.000000 2 0.014660
DP 0 177 0 0.000000 1 0.007330
DP 0 178 0 0.000000 1 0.007330
DP 0 182 0 0.000000 2 0.014660
DP 0 184 0 0.000000 1 0.007330
DP 0 185 0 0.000000 2 0.014660
DP 0 186 0 0.000000 1 0.007330
DP 0 193 0 0.000000 1 0.007330
DP 0 194 0 0.000000 1 0.007330
DP 0 198 0 0.000000 1 0.007330
DP 0 199 0 0.000000 1 0.007330
DP 0 201 0 0.000000 1 0.007330
DP 0 203 0 0.000000 2 0.014660
DP 0 206 0 0.000000 1 0.007330
DP 0 207 0 0.000000 1 0.007330
DP 0 209 0 0.000000 1 0.007330
DP 0 213 0 0.000000 3 0.021989
DP 0 216 0 0.000000 1 0.007330
DP 0 219 0 0.000000 1 0.007330
DP 0 220 0 0.000000 2 0.014660
DP 0 221 0 0.000000 1 0.007330
DP 0 222 0 0.000000 1 0.007330
DP 0 227 0 0.000000 1 0.007330
DP 0 228 0 0.000000 1 0.007330
DP 0 229 0 0.000000 2 0.014660
DP 0 232 0 0.000000 1 0.007330
DP 0 233 0 0.000000 1 0.007330
DP 0 234 0 0.000000 1 0.007330
DP 0 235 0 0.000000 3 0.021989
DP 0 236 0 0.000000 1 0.007330
DP 0 237 0 0.000000 1 0.007330
DP 0 238 0 0.000000 1 0.007330
DP 0 239 0 0.000000 3 0.021989
DP 0 240 0 0.000000 2 0.014660
DP 0 241 0 0.000000 2 0.014660
DP 0 245 0 0.000000 1 0.007330
DP 0 246 0 0.000000 1 0.007330
DP 0 248 0 0.000000 1 0.007330
DP 0 249 0 0.000000 1 0.007330
DP 0 250 0 0.000000 4 0.029319
DP 0 251 0 0.000000 2 0.014660
DP 0 252 0 0.000000 1 0.007330
DP 0 253 0 0.000000 3 0.021989
DP 0 256 0 0.000000 1 0.007330
DP 0 257 0 0.000000 1 0.007330
DP 0 259 0 0.000000 1 0.007330
DP 0 260 0 0.000000 3 0.021989
DP 0 261 0 0.000000 2 0.014660
DP 0 262 0 0.000000 1 0.007330
DP 0 263 0 0.000000 1 0.007330
DP 0 264 0 0.000000 2 0.014660
DP 0 265 0 0.000000 3 0.021989
DP 0 266 0 0.000000 1 0.007330
DP 0 269 0 0.000000 1 0.007330
DP 0 270 0 0.000000 1 0.007330
DP 0 271 0 0.000000 2 0.014660
DP 0 275 0 0.000000 2 0.014660
DP 0 277 0 0.000000 1 0.007330
DP 0 279 0 0.000000 1 0.007330
DP 0 280 0 0.000000 1 0.007330
DP 0 282 0 0.000000 1 0.007330
DP 0 283 0 0.000000 3 0.021989
DP 0 284 0 0.000000 2 0.014660
DP 0 285 0 0.000000 1 0.007330
DP 0 286 0 0.000000 1 0.007330
DP 0 287 0 0.000000 3 0.021989
DP 0 288 0 0.000000 2 0.014660
DP 0 290 0 0.000000 3 0.021989
DP 0 291 0 0.000000 4 0.029319
DP 0 292 0 0.000000 3 0.021989
DP 0 293 0 0.000000 1 0.007330
DP 0 294 0 0.000000 1 0.007330
DP 0 295 0 0.000000 1 0.007330
DP 0 300 0 0.000000 1 0.007330
DP 0 301 0 0.000000 1 0.007330
DP 0 302 0 0.000000 4 0.029319
DP 0 303 0 0.000000 3 0.021989
DP 0 304 0 0.000000 1 0.007330
DP 0 305 0 0.000000 2 0.014660
DP 0 306 0 0.000000 2 0.014660
DP 0 307 0 0.000000 2 0.014660
DP 0 308 0 0.000000 3 0.021989
DP 0 311 0 0.000000 2 0.014660
DP 0 312 0 0.000000 2 0.014660
DP 0 313 0 0.000000 1 0.007330
DP 0 315 0 0.000000 3 0.021989
DP 0 316 0 0.000000 1 0.007330
DP 0 317 0 0.000000 4 0.029319
DP 0 319 0 0.000000 1 0.007330
DP 0 320 0 0.000000 2 0.014660
DP 0 322 0 0.000000 3 0.021989
DP 0 323 0 0.000000 2 0.014660
DP 0 324 0 0.000000 2 0.014660
DP 0 325 0 0.000000 3 0.021989
DP 0 326 0 0.000000 1 0.007330
DP 0 328 0 0.000000 5 0.036649
DP 0 330 0 0.000000 2 0.014660
DP 0 331 0 0.000000 1 0.007330
DP 0 332 0 0.000000 2 0.014660
DP 0 333 0 0.000000 1 0.007330
DP 0 334 0 0.000000 1 0.007330
DP 0 335 0 0.000000 2 0.014660
DP 0 336 0 0.000000 1 0.007330
DP 0 337 0 0.000000 1 0.007330
DP 0 338 0 0.000000 1 0.007330
DP 0 339 0 0.000000 2 0.014660
DP 0 340 0 0.000000 2 0.014660
DP 0 341 0 0.000000 1 0.007330
DP 0 342 0 0.000000 2 0.014660
DP 0 343 0 0.000000 3 0.021989
DP 0 344 0 0.000000 2 0.014660
DP 0 345 0 0.000000 1 0.007330
DP 0 346 0 0.000000 1 0.007330
DP 0 347 0 0.000000 2 0.014660
DP 0 348 0 0.000000 4 0.029319
DP 0 349 0 0.000000 2 0.014660
DP 0 350 0 0.000000 1 0.007330
DP 0 351 0 0.000000 2 0.014660
DP 0 353 0 0.000000 2 0.014660
DP 0 354 0 0.000000 3 0.021989
DP 0 356 0 0.000000 1 0.007330
DP 0 357 0 0.000000 2 0.014660
DP 0 360 0 0.000000 1 0.007330
DP 0 361 0 0.000000 2 0.014660
DP 0 362 0 0.000000 2 0.014660
DP 0 363 0 0.000000 2 0.014660
DP 0 364 0 0.000000 1 0.007330
DP 0 365 0 0.000000 3 0.021989
DP 0 366 0 0.000000 1 0.007330
DP 0 367 0 0.000000 1 0.007330
DP 0 368 0 0.000000 1 0.007330
DP 0 369 0 0.000000 1 0.007330
DP 0 371 0 0.000000 1 0.007330
DP 0 372 0 0.000000 2 0.014660
DP 0 373 0 0.000000 5 0.036649
DP 0 374 0 0.000000 3 0.021989
DP 0 376 0 0.000000 1 0.007330
DP 0 377 0 0.000000 3 0.021989
DP 0 378 0 0.000000 2 0.014660
DP 0 379 0 0.000000 1 0.007330
DP 0 380 0 0.000000 2 0.014660
DP 0 381 0 0.000000 3 0.021989
DP 0 382 0 0.000000 1 0.007330
DP 0 383 0 0.000000 1 0.007330
DP 0 384 0 0.000000 1 0.007330
DP 0 385 0 0.000000 4 0.029319
DP 0 386 0 0.000000 1 0.007330
DP 0 387 0 0.000000 2 0.014660
DP 0 388 0 0.000000 2 0.014660
DP 0 389 0 0.000000 3 0.021989
DP 0 390 0 0.000000 2 0.014660
DP 0 391 0 0.000000 1 0.007330
DP 0 392 0 0.000000 2 0.014660
DP 0 393 0 0.000000 2 0.014660
DP 0 394 0 0.000000 3 0.021989
DP 0 395 0 0.000000 2 0.014660
DP 0 396 0 0.000000 2 0.014660
DP 0 397 0 0.000000 3 0.021989
DP 0 398 0 0.000000 3 0.021989
DP 0 399 0 0.000000 3 0.021989
DP 0 400 0 0.000000 3 0.021989
DP 0 402 0 0.000000 3 0.021989
DP 0 403 0 0.000000 3 0.021989
DP 0 404 0 0.000000 4 0.029319
DP 0 405 0 0.000000 2 0.014660
DP 0 406 0 0.000000 4 0.029319
DP 0 407 0 0.000000 3 0.021989
DP 0 408 0 0.000000 5 0.036649
DP 0 409 0 0.000000 3 0.021989
DP 0 410 0 0.000000 1 0.007330
DP 0 411 0 0.000000 2 0.014660
DP 0 413 0 0.000000 3 0.021989
DP 0 414 0 0.000000 2 0.014660
DP 0 416 0 0.000000 2 0.014660
DP 0 417 0 0.000000 1 0.007330
DP 0 418 0 0.000000 1 0.007330
DP 0 420 0 0.000000 1 0.007330
DP 0 421 0 0.000000 3 0.021989
DP 0 422 0 0.000000 1 0.007330
DP 0 423 0 0.000000 5 0.036649
DP 0 425 0 0.000000 2 0.014660
DP 0 426 0 0.000000 2 0.014660
DP 0 427 0 0.000000 1 0.007330
DP 0 428 0 0.000000 2 0.014660
DP 0 429 0 0.000000 2 0.014660
DP 0 430 0 0.000000 2 0.014660
DP 0 431 0 0.000000 3 0.021989
DP 0 432 0 0.000000 2 0.014660
DP 0 433 0 0.000000 1 0.007330
DP 0 434 0 0.000000 3 0.021989
DP 0 435 0 0.000000 3 0.021989
DP 0 436 0 0.000000 1 0.007330
DP 0 437 0 0.000000 3 0.021989
DP 0 438 0 0.000000 2 0.014660
DP 0 439 0 0.000000 5 0.036649
DP 0 440 0 0.000000 5 0.036649
DP 0 442 0 0.000000 2 0.014660
DP 0 443 0 0.000000 3 0.021989
DP 0 444 0 0.000000 1 0.007330
DP 0 445 0 0.000000 1 0.007330
DP 0 446 0 0.000000 2 0.014660
DP 0 447 0 0.000000 2 0.014660
DP 0 448 0 0.000000 1 0.007330
DP 0 449 0 0.000000 3 0.021989
DP 0 450 0 0.000000 4 0.029319
DP 0 451 0 0.000000 4 0.029319
DP 0 452 0 0.000000 4 0.029319
DP 0 453 0 0.000000 2 0.014660
DP 0 454 0 0.000000 1 0.007330
DP 0 455 0 0.000000 6 0.043979
DP 0 456 0 0.000000 3 0.021989
DP 0 457 0 0.000000 3 0.021989
DP 0 458 0 0.000000 2 0.014660
DP 0 459 0 0.000000 4 0.029319
DP 0 460 0 0.000000 4 0.029319
DP 0 461 0 0.000000 4 0.029319
DP 0 462 0 0.000000 4 0.029319
DP 0 463 0 0.000000 4 0.029319
DP 0 464 0 0.000000 3 0.021989
DP 0 465 0 0.000000 4 0.029319
DP 0 466 0 0.000000 3 0.021989
DP 0 467 0 0.000000 4 0.029319
DP 0 468 0 0.000000 1 0.007330
DP 0 469 0 0.000000 5 0.036649
DP 0 470 0 0.000000 6 0.043979
DP 0 471 0 0.000000 2 0.014660
DP 0 472 0 0.000000 4 0.029319
DP 0 473 0 0.000000 2 0.014660
DP 0 474 0 0.000000 1 0.007330
DP 0 475 0 0.000000 6 0.043979
DP 0 476 0 0.000000 6 0.043979
DP 0 477 0 0.000000 8 0.058638
DP 0 478 0 0.000000 6 0.043979
DP 0 479 0 0.000000 2 0.014660
DP 0 480 0 0.000000 2 0.014660
DP 0 481 0 0.000000 4 0.029319
DP 0 482 0 0.000000 3 0.021989
DP 0 484 0 0.000000 5 0.036649
DP 0 485 0 0.000000 6 0.043979
DP 0 486 0 0.000000 4 0.029319
DP 0 487 0 0.000000 2 0.014660
DP 0 488 0 0.000000 4 0.029319
DP 0 489 0 0.000000 4 0.029319
DP 0 490 0 0.000000 5 0.036649
DP 0 491 0 0.000000 3 0.021989
DP 0 492 0 0.000000 3 0.021989
DP 0 493 0 0.000000 3 0.021989
DP 0 494 0 0.000000 4 0.029319
DP 0 496 0 0.000000 2 0.014660
DP 0 497 0 0.000000 3 0.021989
DP 0 498 0 0.000000 3 0.021989
DP 0 499 0 0.000000 3 0.021989
DP 0 500 0 0.000000 5 0.036649
DP 0 >500 0 0.000000 12914 94.656600