# This file was produced by bcftools stats (1.14+htslib-1.14) and can be plotted using plot-vcfstats. # The command line was: bcftools stats --threads 1 --samples AAP-01 --fasta-ref /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/human_GRCh38_no_alt_analysis_set.fasta /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/AAP-01.hap2.asm.GRCh38.paftools.vcf.gz # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 /mnt/miniwdl_task_container/work/_miniwdl_inputs/0/AAP-01.hap2.asm.GRCh38.paftools.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: 1 SN 0 number of records: 3071427 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 2440651 SN 0 number of MNPs: 0 SN 0 number of indels: 630776 SN 0 number of others: 0 SN 0 number of multiallelic sites: 0 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 1619842 820809 1.97 1619842 820809 1.97 # ICS, Indel context summary: # ICS [2]id [3]repeat-consistent [4]repeat-inconsistent [5]not applicable [6]c/(c+i) ratio ICS 0 135019 19238 476519 0.8753 # ICL, Indel context by length: # ICL [2]id [3]length of repeat element [4]repeat-consistent deletions) [5]repeat-inconsistent deletions [6]consistent insertions [7]inconsistent insertions [8]c/(c+i) ratio ICL 0 2 42636 3201 39880 4968 0.9099 ICL 0 3 8488 1400 5385 1911 0.8073 ICL 0 4 15094 2038 12535 2322 0.8637 ICL 0 5 4135 692 3013 750 0.8321 ICL 0 6 1209 376 699 418 0.7061 ICL 0 7 460 197 133 211 0.5924 ICL 0 8 531 178 129 178 0.6496 ICL 0 9 295 90 76 96 0.6661 ICL 0 10 265 100 56 112 0.6023 # 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 0 0 0 0 0 0 0 # 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 0.990000 2440651 1619842 820809 630776 135019 19238 476519 # 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 5.0 3935 1787 2148 186 QUAL 0 6.0 4562 2078 2484 244 QUAL 0 7.0 909 436 473 91 QUAL 0 8.0 1003 491 512 118 QUAL 0 9.0 1099 574 525 144 QUAL 0 10.0 1281 572 709 72 QUAL 0 11.0 1250 611 639 88 QUAL 0 12.0 444 233 211 61 QUAL 0 13.0 1211 556 655 52 QUAL 0 14.0 794 374 420 39 QUAL 0 15.0 556 299 257 75 QUAL 0 16.0 477 213 264 15 QUAL 0 17.0 110 76 34 18 QUAL 0 18.0 128 72 56 17 QUAL 0 19.0 529 340 189 41 QUAL 0 20.0 334 232 102 67 QUAL 0 21.0 1004 494 510 24 QUAL 0 22.0 164 84 80 6 QUAL 0 23.0 417 238 179 22 QUAL 0 24.0 146 109 37 45 QUAL 0 25.0 411 174 237 8 QUAL 0 26.0 15 10 5 6 QUAL 0 27.0 183 112 71 17 QUAL 0 28.0 929 402 527 17 QUAL 0 29.0 448 237 211 57 QUAL 0 30.0 48 27 21 2 QUAL 0 31.0 297 184 113 36 QUAL 0 32.0 483 308 175 88 QUAL 0 33.0 172 109 63 30 QUAL 0 34.0 112 44 68 4 QUAL 0 35.0 67 46 21 14 QUAL 0 36.0 555 258 297 30 QUAL 0 37.0 111 65 46 48 QUAL 0 38.0 67 39 28 8 QUAL 0 39.0 1552 811 741 119 QUAL 0 41.0 187 63 124 11 QUAL 0 43.0 442 265 177 40 QUAL 0 44.0 653 373 280 127 QUAL 0 46.0 754 349 405 69 QUAL 0 47.0 2313 1027 1286 91 QUAL 0 48.0 876 475 401 72 QUAL 0 49.0 297 164 133 25 QUAL 0 50.0 1331 685 646 86 QUAL 0 51.0 44 32 12 5 QUAL 0 52.0 538 249 289 22 QUAL 0 53.0 19 9 10 12 QUAL 0 54.0 4 1 3 0 QUAL 0 55.0 1 1 0 1 QUAL 0 56.0 421 253 168 45 QUAL 0 57.0 971 541 430 98 QUAL 0 58.0 275 155 120 6 QUAL 0 59.0 22 13 9 11 QUAL 0 60.0 2405700 1602492 803208 628146 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 4762 0 . IDD 0 -59 41 0 . IDD 0 -58 60 0 . IDD 0 -57 40 0 . IDD 0 -56 94 0 . IDD 0 -55 55 0 . IDD 0 -54 97 0 . IDD 0 -53 55 0 . IDD 0 -52 111 0 . IDD 0 -51 50 0 . IDD 0 -50 125 0 . IDD 0 -49 90 0 . IDD 0 -48 149 0 . IDD 0 -47 66 0 . IDD 0 -46 122 0 . IDD 0 -45 81 0 . IDD 0 -44 145 0 . IDD 0 -43 78 0 . IDD 0 -42 156 0 . IDD 0 -41 89 0 . IDD 0 -40 252 0 . IDD 0 -39 131 0 . IDD 0 -38 193 0 . IDD 0 -37 123 0 . IDD 0 -36 283 0 . IDD 0 -35 156 0 . IDD 0 -34 253 0 . IDD 0 -33 153 0 . IDD 0 -32 387 0 . IDD 0 -31 183 0 . IDD 0 -30 469 0 . IDD 0 -29 209 0 . IDD 0 -28 571 0 . IDD 0 -27 269 0 . IDD 0 -26 510 0 . IDD 0 -25 359 0 . IDD 0 -24 888 0 . IDD 0 -23 337 0 . IDD 0 -22 759 0 . IDD 0 -21 391 0 . IDD 0 -20 1374 0 . IDD 0 -19 534 0 . IDD 0 -18 1251 0 . IDD 0 -17 651 0 . IDD 0 -16 2127 0 . IDD 0 -15 1263 0 . IDD 0 -14 1983 0 . IDD 0 -13 1210 0 . IDD 0 -12 4270 0 . IDD 0 -11 1489 0 . IDD 0 -10 4258 0 . IDD 0 -9 2403 0 . IDD 0 -8 7595 0 . IDD 0 -7 3035 0 . IDD 0 -6 8892 0 . IDD 0 -5 8194 0 . IDD 0 -4 27592 0 . IDD 0 -3 18726 0 . IDD 0 -2 51137 0 . IDD 0 -1 144196 0 . IDD 0 1 155565 0 . IDD 0 2 53733 0 . IDD 0 3 20460 0 . IDD 0 4 28323 0 . IDD 0 5 8416 0 . IDD 0 6 8934 0 . IDD 0 7 3144 0 . IDD 0 8 7571 0 . IDD 0 9 2477 0 . IDD 0 10 4187 0 . IDD 0 11 1591 0 . IDD 0 12 4149 0 . IDD 0 13 1209 0 . IDD 0 14 1990 0 . IDD 0 15 1324 0 . IDD 0 16 2194 0 . IDD 0 17 703 0 . IDD 0 18 1209 0 . IDD 0 19 560 0 . IDD 0 20 1422 0 . IDD 0 21 465 0 . IDD 0 22 696 0 . IDD 0 23 357 0 . IDD 0 24 964 0 . IDD 0 25 377 0 . IDD 0 26 529 0 . IDD 0 27 316 0 . IDD 0 28 537 0 . IDD 0 29 235 0 . IDD 0 30 458 0 . IDD 0 31 193 0 . IDD 0 32 382 0 . IDD 0 33 173 0 . IDD 0 34 236 0 . IDD 0 35 171 0 . IDD 0 36 281 0 . IDD 0 37 121 0 . IDD 0 38 203 0 . IDD 0 39 115 0 . IDD 0 40 244 0 . IDD 0 41 94 0 . IDD 0 42 177 0 . IDD 0 43 79 0 . IDD 0 44 155 0 . IDD 0 45 89 0 . IDD 0 46 137 0 . IDD 0 47 75 0 . IDD 0 48 152 0 . IDD 0 49 102 0 . IDD 0 50 111 0 . IDD 0 51 71 0 . IDD 0 52 121 0 . IDD 0 53 60 0 . IDD 0 54 84 0 . IDD 0 55 53 0 . IDD 0 56 88 0 . IDD 0 57 57 0 . IDD 0 58 81 0 . IDD 0 59 57 0 . IDD 0 60 7197 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 105052 ST 0 A>G 403844 ST 0 A>T 92401 ST 0 C>A 105187 ST 0 C>G 106904 ST 0 C>T 405641 ST 0 G>A 405691 ST 0 G>C 107518 ST 0 G>T 106074 ST 0 T>A 92141 ST 0 T>C 404666 ST 0 T>G 105532 # DP, Depth distribution # DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%) # PSC, Per-sample counts. Note that the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and indels. # PSC [2]id [3]sample [4]nRefHom [5]nNonRefHom [6]nHets [7]nTransitions [8]nTransversions [9]nIndels [10]average depth [11]nSingletons [12]nHapRef [13]nHapAlt [14]nMissing PSC 0 AAP-01 0 2440651 0 1619842 820809 630776 0.0 3071427 0 0 0 # PSI, Per-Sample Indels. Note that alt-het genotypes with both ins and del allele are counted twice, in both nInsHets and nDelHets. # PSI [2]id [3]sample [4]in-frame [5]out-frame [6]not applicable [7]out/(in+out) ratio [8]nInsHets [9]nDelHets [10]nInsAltHoms [11]nDelAltHoms PSI 0 AAP-01 0 0 0 0.00 0 0 325254 305522 # HWE # HWE [2]id [3]1st ALT allele frequency [4]Number of observations [5]25th percentile [6]median [7]75th percentile HWE 0 0.990000 3071427 0.000000 0.000000 0.000000