# 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-02 --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-02.hap1.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-02.hap1.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: 3329781 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 2652234 SN 0 number of MNPs: 0 SN 0 number of indels: 677547 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 1762702 889532 1.98 1762702 889532 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 149686 20689 507172 0.8786 # 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 46747 3529 44384 5131 0.9132 ICL 0 3 9448 1513 5873 2038 0.8118 ICL 0 4 17054 2213 14180 2549 0.8677 ICL 0 5 4447 771 3197 834 0.8265 ICL 0 6 1365 431 771 441 0.7101 ICL 0 7 534 213 150 218 0.6135 ICL 0 8 580 184 164 182 0.6703 ICL 0 9 351 113 90 109 0.6652 ICL 0 10 282 108 69 112 0.6147 # 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 2652234 1762702 889532 677547 149686 20689 507172 # 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 3786 1645 2141 170 QUAL 0 6.0 1327 531 796 69 QUAL 0 7.0 1677 752 925 86 QUAL 0 8.0 308 122 186 12 QUAL 0 9.0 363 170 193 49 QUAL 0 10.0 300 145 155 23 QUAL 0 11.0 1029 467 562 57 QUAL 0 12.0 1708 784 924 111 QUAL 0 13.0 359 144 215 26 QUAL 0 14.0 1543 851 692 96 QUAL 0 15.0 158 78 80 10 QUAL 0 16.0 248 143 105 84 QUAL 0 17.0 205 100 105 8 QUAL 0 18.0 259 105 154 11 QUAL 0 19.0 338 156 182 26 QUAL 0 20.0 592 236 356 22 QUAL 0 21.0 632 321 311 68 QUAL 0 22.0 57 26 31 5 QUAL 0 23.0 2 1 1 3 QUAL 0 24.0 105 65 40 31 QUAL 0 25.0 361 170 191 25 QUAL 0 26.0 12 7 5 2 QUAL 0 27.0 53 35 18 16 QUAL 0 28.0 171 119 52 59 QUAL 0 29.0 125 54 71 17 QUAL 0 30.0 84 51 33 10 QUAL 0 31.0 365 160 205 18 QUAL 0 32.0 470 211 259 24 QUAL 0 34.0 851 445 406 25 QUAL 0 35.0 374 147 227 11 QUAL 0 36.0 342 161 181 11 QUAL 0 37.0 147 97 50 13 QUAL 0 38.0 155 46 109 10 QUAL 0 40.0 1652 866 786 161 QUAL 0 42.0 10 4 6 0 QUAL 0 43.0 234 94 140 21 QUAL 0 45.0 122 58 64 11 QUAL 0 46.0 446 228 218 33 QUAL 0 47.0 703 426 277 77 QUAL 0 48.0 733 356 377 38 QUAL 0 49.0 363 171 192 4 QUAL 0 50.0 137 78 59 22 QUAL 0 52.0 226 140 86 44 QUAL 0 53.0 778 373 405 20 QUAL 0 54.0 122 64 58 26 QUAL 0 55.0 1 1 0 1 QUAL 0 57.0 509 303 206 36 QUAL 0 58.0 24 17 7 3 QUAL 0 59.0 767 396 371 78 QUAL 0 60.0 2626901 1750582 876319 675764 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 5064 0 . IDD 0 -59 31 0 . IDD 0 -58 69 0 . IDD 0 -57 42 0 . IDD 0 -56 100 0 . IDD 0 -55 54 0 . IDD 0 -54 91 0 . IDD 0 -53 57 0 . IDD 0 -52 123 0 . IDD 0 -51 69 0 . IDD 0 -50 121 0 . IDD 0 -49 107 0 . IDD 0 -48 158 0 . IDD 0 -47 72 0 . IDD 0 -46 125 0 . IDD 0 -45 83 0 . IDD 0 -44 148 0 . IDD 0 -43 79 0 . IDD 0 -42 180 0 . IDD 0 -41 108 0 . IDD 0 -40 271 0 . IDD 0 -39 138 0 . IDD 0 -38 207 0 . IDD 0 -37 139 0 . IDD 0 -36 321 0 . IDD 0 -35 160 0 . IDD 0 -34 278 0 . IDD 0 -33 190 0 . IDD 0 -32 407 0 . IDD 0 -31 223 0 . IDD 0 -30 498 0 . IDD 0 -29 249 0 . IDD 0 -28 647 0 . IDD 0 -27 317 0 . IDD 0 -26 594 0 . IDD 0 -25 401 0 . IDD 0 -24 974 0 . IDD 0 -23 362 0 . IDD 0 -22 795 0 . IDD 0 -21 449 0 . IDD 0 -20 1548 0 . IDD 0 -19 580 0 . IDD 0 -18 1404 0 . IDD 0 -17 721 0 . IDD 0 -16 2378 0 . IDD 0 -15 1437 0 . IDD 0 -14 2226 0 . IDD 0 -13 1344 0 . IDD 0 -12 4781 0 . IDD 0 -11 1642 0 . IDD 0 -10 4601 0 . IDD 0 -9 2671 0 . IDD 0 -8 8352 0 . IDD 0 -7 3432 0 . IDD 0 -6 9912 0 . IDD 0 -5 9131 0 . IDD 0 -4 31008 0 . IDD 0 -3 21269 0 . IDD 0 -2 57771 0 . IDD 0 -1 162866 0 . IDD 0 1 153817 0 . IDD 0 2 55843 0 . IDD 0 3 20608 0 . IDD 0 4 30655 0 . IDD 0 5 8822 0 . IDD 0 6 9724 0 . IDD 0 7 3289 0 . IDD 0 8 8259 0 . IDD 0 9 2659 0 . IDD 0 10 4483 0 . IDD 0 11 1678 0 . IDD 0 12 4689 0 . IDD 0 13 1261 0 . IDD 0 14 2203 0 . IDD 0 15 1368 0 . IDD 0 16 2383 0 . IDD 0 17 775 0 . IDD 0 18 1343 0 . IDD 0 19 612 0 . IDD 0 20 1519 0 . IDD 0 21 517 0 . IDD 0 22 797 0 . IDD 0 23 399 0 . IDD 0 24 1053 0 . IDD 0 25 419 0 . IDD 0 26 587 0 . IDD 0 27 353 0 . IDD 0 28 619 0 . IDD 0 29 233 0 . IDD 0 30 524 0 . IDD 0 31 216 0 . IDD 0 32 412 0 . IDD 0 33 185 0 . IDD 0 34 289 0 . IDD 0 35 177 0 . IDD 0 36 336 0 . IDD 0 37 153 0 . IDD 0 38 200 0 . IDD 0 39 119 0 . IDD 0 40 286 0 . IDD 0 41 113 0 . IDD 0 42 180 0 . IDD 0 43 77 0 . IDD 0 44 173 0 . IDD 0 45 81 0 . IDD 0 46 146 0 . IDD 0 47 78 0 . IDD 0 48 169 0 . IDD 0 49 126 0 . IDD 0 50 137 0 . IDD 0 51 79 0 . IDD 0 52 129 0 . IDD 0 53 61 0 . IDD 0 54 108 0 . IDD 0 55 51 0 . IDD 0 56 115 0 . IDD 0 57 63 0 . IDD 0 58 93 0 . IDD 0 59 55 0 . IDD 0 60 8074 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 113746 ST 0 A>G 439514 ST 0 A>T 99592 ST 0 C>A 113976 ST 0 C>G 116063 ST 0 C>T 441374 ST 0 G>A 441407 ST 0 G>C 116603 ST 0 G>T 114995 ST 0 T>A 99986 ST 0 T>C 440407 ST 0 T>G 114571 # 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-02 0 2652234 0 1762702 889532 677547 0.0 3329781 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-02 0 0 0 0.00 0 0 333972 343575 # 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 3329781 0.000000 0.000000 0.000000