# 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 HCC1395_tumor_vs_HCC1395_BL.tnseq.filtered.vcf.gz # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 HCC1395_tumor_vs_HCC1395_BL.tnseq.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: 305 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 275 SN 0 number of MNPs: 6 SN 0 number of indels: 25 SN 0 number of others: 0 SN 0 number of multiallelic sites: 9 SN 0 number of multiallelic SNP sites: 0 # 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 0 213 62 3.44 213 62 3.44 # 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 1 275 213 62 48 0 0 48 # 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 275 213 62 48 0 0 48 # 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 . 275 213 62 25 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 1 0 . IDD 0 -24 1 0 . IDD 0 -9 1 0 . IDD 0 -8 1 0 . IDD 0 -6 2 0 . IDD 0 -4 3 0 . IDD 0 -3 8 0 . IDD 0 -2 8 0 . IDD 0 -1 6 0 . IDD 0 1 6 0 . IDD 0 2 7 0 . IDD 0 3 2 0 . IDD 0 4 1 0 . IDD 0 6 1 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 5 ST 0 A>G 48 ST 0 A>T 4 ST 0 C>A 9 ST 0 C>G 10 ST 0 C>T 55 ST 0 G>A 59 ST 0 G>C 18 ST 0 G>T 10 ST 0 T>A 1 ST 0 T>C 51 ST 0 T>G 5 # 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 6 0 0.000000 1 0.327869 DP 0 10 0 0.000000 1 0.327869 DP 0 124 0 0.000000 1 0.327869 DP 0 143 0 0.000000 1 0.327869 DP 0 196 0 0.000000 1 0.327869 DP 0 202 0 0.000000 1 0.327869 DP 0 210 0 0.000000 1 0.327869 DP 0 212 0 0.000000 1 0.327869 DP 0 240 0 0.000000 1 0.327869 DP 0 243 0 0.000000 1 0.327869 DP 0 244 0 0.000000 1 0.327869 DP 0 249 0 0.000000 1 0.327869 DP 0 263 0 0.000000 1 0.327869 DP 0 273 0 0.000000 1 0.327869 DP 0 275 0 0.000000 1 0.327869 DP 0 276 0 0.000000 1 0.327869 DP 0 277 0 0.000000 1 0.327869 DP 0 286 0 0.000000 1 0.327869 DP 0 288 0 0.000000 1 0.327869 DP 0 294 0 0.000000 2 0.655738 DP 0 295 0 0.000000 1 0.327869 DP 0 305 0 0.000000 1 0.327869 DP 0 317 0 0.000000 1 0.327869 DP 0 318 0 0.000000 1 0.327869 DP 0 319 0 0.000000 1 0.327869 DP 0 327 0 0.000000 1 0.327869 DP 0 331 0 0.000000 1 0.327869 DP 0 335 0 0.000000 1 0.327869 DP 0 350 0 0.000000 1 0.327869 DP 0 355 0 0.000000 1 0.327869 DP 0 356 0 0.000000 1 0.327869 DP 0 359 0 0.000000 1 0.327869 DP 0 360 0 0.000000 1 0.327869 DP 0 361 0 0.000000 1 0.327869 DP 0 363 0 0.000000 1 0.327869 DP 0 364 0 0.000000 1 0.327869 DP 0 372 0 0.000000 1 0.327869 DP 0 375 0 0.000000 1 0.327869 DP 0 377 0 0.000000 1 0.327869 DP 0 379 0 0.000000 1 0.327869 DP 0 380 0 0.000000 2 0.655738 DP 0 382 0 0.000000 1 0.327869 DP 0 384 0 0.000000 2 0.655738 DP 0 403 0 0.000000 1 0.327869 DP 0 405 0 0.000000 1 0.327869 DP 0 412 0 0.000000 2 0.655738 DP 0 420 0 0.000000 1 0.327869 DP 0 421 0 0.000000 1 0.327869 DP 0 422 0 0.000000 1 0.327869 DP 0 423 0 0.000000 1 0.327869 DP 0 424 0 0.000000 1 0.327869 DP 0 431 0 0.000000 1 0.327869 DP 0 433 0 0.000000 1 0.327869 DP 0 437 0 0.000000 1 0.327869 DP 0 438 0 0.000000 1 0.327869 DP 0 439 0 0.000000 2 0.655738 DP 0 440 0 0.000000 1 0.327869 DP 0 442 0 0.000000 1 0.327869 DP 0 443 0 0.000000 1 0.327869 DP 0 448 0 0.000000 1 0.327869 DP 0 453 0 0.000000 1 0.327869 DP 0 458 0 0.000000 1 0.327869 DP 0 459 0 0.000000 1 0.327869 DP 0 461 0 0.000000 1 0.327869 DP 0 462 0 0.000000 1 0.327869 DP 0 471 0 0.000000 1 0.327869 DP 0 472 0 0.000000 1 0.327869 DP 0 473 0 0.000000 2 0.655738 DP 0 475 0 0.000000 1 0.327869 DP 0 478 0 0.000000 2 0.655738 DP 0 479 0 0.000000 1 0.327869 DP 0 489 0 0.000000 1 0.327869 DP 0 494 0 0.000000 1 0.327869 DP 0 >500 0 0.000000 225 73.770492