# 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-07 --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-07.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-07.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: 3184844 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 2518546 SN 0 number of MNPs: 0 SN 0 number of indels: 666298 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 1673479 845067 1.98 1673479 845067 1.98 # ICS, Indel context summary: # ICS [2]id [3]repeat-consistent [4]repeat-inconsistent [5]not applicable [6]c/(c+i) ratio ICS 0 138315 19380 508603 0.8771 # 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 43980 3306 39170 4679 0.9124 ICL 0 3 8894 1541 5472 1943 0.8048 ICL 0 4 16170 2055 13312 2419 0.8682 ICL 0 5 4240 770 3052 754 0.8271 ICL 0 6 1272 395 752 423 0.7122 ICL 0 7 465 192 125 176 0.6159 ICL 0 8 549 167 154 177 0.6714 ICL 0 9 304 84 81 83 0.6975 ICL 0 10 264 101 59 115 0.5993 # 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 2518546 1673479 845067 666298 138315 19380 508603 # 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 2411 1052 1359 155 QUAL 0 6.0 4958 2168 2790 244 QUAL 0 7.0 1322 657 665 106 QUAL 0 8.0 2516 1101 1415 89 QUAL 0 9.0 1795 783 1012 110 QUAL 0 10.0 523 232 291 34 QUAL 0 11.0 1272 561 711 53 QUAL 0 12.0 2777 1642 1135 252 QUAL 0 13.0 559 272 287 53 QUAL 0 14.0 78 63 15 21 QUAL 0 15.0 327 202 125 42 QUAL 0 16.0 548 194 354 21 QUAL 0 17.0 134 74 60 22 QUAL 0 18.0 794 332 462 20 QUAL 0 19.0 524 264 260 13 QUAL 0 20.0 641 323 318 50 QUAL 0 21.0 223 95 128 4 QUAL 0 22.0 318 136 182 18 QUAL 0 23.0 86 56 30 11 QUAL 0 24.0 272 140 132 9 QUAL 0 25.0 696 357 339 67 QUAL 0 26.0 974 443 531 49 QUAL 0 27.0 6 2 4 2 QUAL 0 28.0 218 119 99 23 QUAL 0 29.0 548 299 249 40 QUAL 0 31.0 28 9 19 3 QUAL 0 32.0 606 273 333 35 QUAL 0 33.0 1944 922 1022 46 QUAL 0 34.0 156 88 68 4 QUAL 0 35.0 1334 856 478 219 QUAL 0 36.0 38 23 15 1 QUAL 0 37.0 503 253 250 15 QUAL 0 38.0 559 299 260 53 QUAL 0 42.0 50 35 15 19 QUAL 0 43.0 52 30 22 20 QUAL 0 45.0 840 357 483 23 QUAL 0 46.0 17 6 11 1 QUAL 0 47.0 604 259 345 16 QUAL 0 49.0 32 18 14 16 QUAL 0 50.0 343 213 130 40 QUAL 0 51.0 685 408 277 92 QUAL 0 53.0 457 294 163 47 QUAL 0 54.0 880 445 435 17 QUAL 0 56.0 31 19 12 5 QUAL 0 57.0 678 335 343 45 QUAL 0 58.0 363 146 217 16 QUAL 0 59.0 614 302 312 17 QUAL 0 60.0 2483212 1656322 826890 664040 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 4990 0 . IDD 0 -59 37 0 . IDD 0 -58 74 0 . IDD 0 -57 32 0 . IDD 0 -56 100 0 . IDD 0 -55 51 0 . IDD 0 -54 96 0 . IDD 0 -53 56 0 . IDD 0 -52 107 0 . IDD 0 -51 51 0 . IDD 0 -50 118 0 . IDD 0 -49 103 0 . IDD 0 -48 155 0 . IDD 0 -47 73 0 . IDD 0 -46 116 0 . IDD 0 -45 74 0 . IDD 0 -44 156 0 . IDD 0 -43 80 0 . IDD 0 -42 166 0 . IDD 0 -41 102 0 . IDD 0 -40 260 0 . IDD 0 -39 111 0 . IDD 0 -38 199 0 . IDD 0 -37 115 0 . IDD 0 -36 300 0 . IDD 0 -35 128 0 . IDD 0 -34 265 0 . IDD 0 -33 173 0 . IDD 0 -32 403 0 . IDD 0 -31 188 0 . IDD 0 -30 464 0 . IDD 0 -29 238 0 . IDD 0 -28 606 0 . IDD 0 -27 268 0 . IDD 0 -26 559 0 . IDD 0 -25 379 0 . IDD 0 -24 927 0 . IDD 0 -23 349 0 . IDD 0 -22 733 0 . IDD 0 -21 437 0 . IDD 0 -20 1436 0 . IDD 0 -19 579 0 . IDD 0 -18 1289 0 . IDD 0 -17 664 0 . IDD 0 -16 2236 0 . IDD 0 -15 1351 0 . IDD 0 -14 2090 0 . IDD 0 -13 1335 0 . IDD 0 -12 4477 0 . IDD 0 -11 1636 0 . IDD 0 -10 4505 0 . IDD 0 -9 2539 0 . IDD 0 -8 7942 0 . IDD 0 -7 3221 0 . IDD 0 -6 9517 0 . IDD 0 -5 8876 0 . IDD 0 -4 29637 0 . IDD 0 -3 21107 0 . IDD 0 -2 57488 0 . IDD 0 -1 173915 0 . IDD 0 1 148978 0 . IDD 0 2 52037 0 . IDD 0 3 19777 0 . IDD 0 4 28700 0 . IDD 0 5 8325 0 . IDD 0 6 8952 0 . IDD 0 7 3140 0 . IDD 0 8 7633 0 . IDD 0 9 2512 0 . IDD 0 10 4193 0 . IDD 0 11 1560 0 . IDD 0 12 4350 0 . IDD 0 13 1282 0 . IDD 0 14 1938 0 . IDD 0 15 1321 0 . IDD 0 16 2105 0 . IDD 0 17 722 0 . IDD 0 18 1158 0 . IDD 0 19 562 0 . IDD 0 20 1340 0 . IDD 0 21 524 0 . IDD 0 22 675 0 . IDD 0 23 385 0 . IDD 0 24 935 0 . IDD 0 25 373 0 . IDD 0 26 478 0 . IDD 0 27 308 0 . IDD 0 28 522 0 . IDD 0 29 212 0 . IDD 0 30 455 0 . IDD 0 31 201 0 . IDD 0 32 349 0 . IDD 0 33 165 0 . IDD 0 34 242 0 . IDD 0 35 147 0 . IDD 0 36 286 0 . IDD 0 37 132 0 . IDD 0 38 161 0 . IDD 0 39 111 0 . IDD 0 40 229 0 . IDD 0 41 94 0 . IDD 0 42 144 0 . IDD 0 43 73 0 . IDD 0 44 130 0 . IDD 0 45 75 0 . IDD 0 46 133 0 . IDD 0 47 61 0 . IDD 0 48 147 0 . IDD 0 49 109 0 . IDD 0 50 110 0 . IDD 0 51 66 0 . IDD 0 52 121 0 . IDD 0 53 54 0 . IDD 0 54 79 0 . IDD 0 55 44 0 . IDD 0 56 94 0 . IDD 0 57 61 0 . IDD 0 58 85 0 . IDD 0 59 46 0 . IDD 0 60 7418 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 108047 ST 0 A>G 417947 ST 0 A>T 94113 ST 0 C>A 108502 ST 0 C>G 110828 ST 0 C>T 418731 ST 0 G>A 418342 ST 0 G>C 111065 ST 0 G>T 109291 ST 0 T>A 94212 ST 0 T>C 418459 ST 0 T>G 109009 # 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-07 0 2518546 0 1673479 845067 666298 0.0 3184844 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-07 0 0 0 0.00 0 0 316619 349679 # 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 3184844 0.000000 0.000000 0.000000