# 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.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-02.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: 3320043 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 2646867 SN 0 number of MNPs: 0 SN 0 number of indels: 673176 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 1756419 890448 1.97 1756419 890448 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 147701 20644 504831 0.8774 # 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 46087 3553 43412 5191 0.9110 ICL 0 3 9309 1545 5789 2034 0.8084 ICL 0 4 17050 2155 13887 2480 0.8697 ICL 0 5 4623 792 3303 799 0.8328 ICL 0 6 1304 416 773 432 0.7101 ICL 0 7 512 214 140 210 0.6059 ICL 0 8 589 191 163 194 0.6614 ICL 0 9 332 102 76 102 0.6667 ICL 0 10 284 123 68 111 0.6007 # 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 2646867 1756419 890448 673176 147701 20644 504831 # 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 6721 2880 3841 283 QUAL 0 6.0 2156 917 1239 109 QUAL 0 7.0 1368 614 754 84 QUAL 0 8.0 413 178 235 25 QUAL 0 9.0 1130 510 620 98 QUAL 0 10.0 2026 1066 960 153 QUAL 0 11.0 3442 1603 1839 153 QUAL 0 12.0 288 144 144 42 QUAL 0 13.0 2249 1128 1121 43 QUAL 0 15.0 441 204 237 16 QUAL 0 16.0 416 159 257 14 QUAL 0 17.0 309 136 173 34 QUAL 0 18.0 215 83 132 8 QUAL 0 19.0 8 3 5 0 QUAL 0 20.0 729 444 285 56 QUAL 0 21.0 11 7 4 2 QUAL 0 22.0 848 440 408 39 QUAL 0 23.0 418 226 192 27 QUAL 0 24.0 155 55 100 10 QUAL 0 25.0 515 238 277 42 QUAL 0 26.0 402 149 253 8 QUAL 0 28.0 16 6 10 4 QUAL 0 29.0 652 287 365 21 QUAL 0 30.0 1024 463 561 23 QUAL 0 31.0 49 19 30 5 QUAL 0 32.0 2048 1222 826 175 QUAL 0 33.0 722 372 350 63 QUAL 0 34.0 1183 695 488 158 QUAL 0 35.0 607 361 246 115 QUAL 0 36.0 94 36 58 2 QUAL 0 38.0 59 21 38 0 QUAL 0 39.0 216 119 97 26 QUAL 0 40.0 204 105 99 31 QUAL 0 41.0 728 353 375 50 QUAL 0 42.0 20 11 9 10 QUAL 0 43.0 508 201 307 27 QUAL 0 44.0 512 233 279 59 QUAL 0 45.0 440 191 249 23 QUAL 0 46.0 19 13 6 19 QUAL 0 48.0 225 104 121 59 QUAL 0 49.0 155 65 90 9 QUAL 0 50.0 216 114 102 17 QUAL 0 51.0 193 91 102 8 QUAL 0 52.0 309 190 119 23 QUAL 0 53.0 266 168 98 39 QUAL 0 54.0 22 8 14 0 QUAL 0 55.0 190 64 126 16 QUAL 0 56.0 51 28 23 15 QUAL 0 58.0 412 226 186 39 QUAL 0 59.0 388 156 232 14 QUAL 0 60.0 2611079 1739313 871766 670880 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 5018 0 . IDD 0 -59 45 0 . IDD 0 -58 80 0 . IDD 0 -57 39 0 . IDD 0 -56 112 0 . IDD 0 -55 56 0 . IDD 0 -54 98 0 . IDD 0 -53 59 0 . IDD 0 -52 111 0 . IDD 0 -51 64 0 . IDD 0 -50 141 0 . IDD 0 -49 106 0 . IDD 0 -48 149 0 . IDD 0 -47 75 0 . IDD 0 -46 127 0 . IDD 0 -45 94 0 . IDD 0 -44 156 0 . IDD 0 -43 72 0 . IDD 0 -42 166 0 . IDD 0 -41 104 0 . IDD 0 -40 276 0 . IDD 0 -39 131 0 . IDD 0 -38 224 0 . IDD 0 -37 129 0 . IDD 0 -36 328 0 . IDD 0 -35 154 0 . IDD 0 -34 259 0 . IDD 0 -33 171 0 . IDD 0 -32 459 0 . IDD 0 -31 208 0 . IDD 0 -30 517 0 . IDD 0 -29 250 0 . IDD 0 -28 624 0 . IDD 0 -27 292 0 . IDD 0 -26 577 0 . IDD 0 -25 417 0 . IDD 0 -24 998 0 . IDD 0 -23 379 0 . IDD 0 -22 814 0 . IDD 0 -21 453 0 . IDD 0 -20 1539 0 . IDD 0 -19 580 0 . IDD 0 -18 1348 0 . IDD 0 -17 760 0 . IDD 0 -16 2370 0 . IDD 0 -15 1460 0 . IDD 0 -14 2147 0 . IDD 0 -13 1362 0 . IDD 0 -12 4694 0 . IDD 0 -11 1650 0 . IDD 0 -10 4672 0 . IDD 0 -9 2648 0 . IDD 0 -8 8366 0 . IDD 0 -7 3401 0 . IDD 0 -6 9862 0 . IDD 0 -5 9298 0 . IDD 0 -4 30867 0 . IDD 0 -3 21093 0 . IDD 0 -2 57312 0 . IDD 0 -1 161692 0 . IDD 0 1 153330 0 . IDD 0 2 54724 0 . IDD 0 3 20458 0 . IDD 0 4 30263 0 . IDD 0 5 8814 0 . IDD 0 6 9544 0 . IDD 0 7 3299 0 . IDD 0 8 8245 0 . IDD 0 9 2651 0 . IDD 0 10 4593 0 . IDD 0 11 1707 0 . IDD 0 12 4716 0 . IDD 0 13 1293 0 . IDD 0 14 2149 0 . IDD 0 15 1370 0 . IDD 0 16 2382 0 . IDD 0 17 795 0 . IDD 0 18 1315 0 . IDD 0 19 599 0 . IDD 0 20 1569 0 . IDD 0 21 514 0 . IDD 0 22 780 0 . IDD 0 23 413 0 . IDD 0 24 1024 0 . IDD 0 25 395 0 . IDD 0 26 587 0 . IDD 0 27 323 0 . IDD 0 28 601 0 . IDD 0 29 244 0 . IDD 0 30 536 0 . IDD 0 31 232 0 . IDD 0 32 424 0 . IDD 0 33 189 0 . IDD 0 34 305 0 . IDD 0 35 163 0 . IDD 0 36 334 0 . IDD 0 37 145 0 . IDD 0 38 196 0 . IDD 0 39 130 0 . IDD 0 40 282 0 . IDD 0 41 98 0 . IDD 0 42 169 0 . IDD 0 43 108 0 . IDD 0 44 175 0 . IDD 0 45 97 0 . IDD 0 46 133 0 . IDD 0 47 82 0 . IDD 0 48 170 0 . IDD 0 49 115 0 . IDD 0 50 124 0 . IDD 0 51 79 0 . IDD 0 52 128 0 . IDD 0 53 58 0 . IDD 0 54 107 0 . IDD 0 55 57 0 . IDD 0 56 114 0 . IDD 0 57 71 0 . IDD 0 58 85 0 . IDD 0 59 58 0 . IDD 0 60 7862 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 113801 ST 0 A>G 438163 ST 0 A>T 100273 ST 0 C>A 114310 ST 0 C>G 116431 ST 0 C>T 439763 ST 0 G>A 439025 ST 0 G>C 116496 ST 0 G>T 114765 ST 0 T>A 100124 ST 0 T>C 439468 ST 0 T>G 114248 # 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 2646867 0 1756419 890448 673176 0.0 3320043 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 331523 341653 # 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 3320043 0.000000 0.000000 0.000000