# 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.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-01.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: 3152115 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 2499910 SN 0 number of MNPs: 0 SN 0 number of indels: 652205 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 1659067 840843 1.97 1659067 840843 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 139483 19937 492785 0.8749 # 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 43502 3407 41482 5063 0.9094 ICL 0 3 8853 1444 5362 2028 0.8037 ICL 0 4 15968 1984 13005 2468 0.8668 ICL 0 5 4234 742 2992 772 0.8268 ICL 0 6 1285 413 738 409 0.7111 ICL 0 7 502 206 140 214 0.6045 ICL 0 8 556 168 155 183 0.6695 ICL 0 9 314 94 83 110 0.6606 ICL 0 10 254 117 58 115 0.5735 # 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 2499910 1659067 840843 652205 139483 19937 492785 # 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 5529 2485 3044 352 QUAL 0 6.0 3747 1771 1976 218 QUAL 0 7.0 1787 758 1029 125 QUAL 0 8.0 3181 1383 1798 197 QUAL 0 9.0 2425 1071 1354 85 QUAL 0 10.0 1814 842 972 81 QUAL 0 11.0 626 255 371 47 QUAL 0 12.0 738 362 376 42 QUAL 0 13.0 717 314 403 42 QUAL 0 14.0 409 174 235 17 QUAL 0 15.0 790 443 347 132 QUAL 0 16.0 1516 691 825 73 QUAL 0 17.0 269 130 139 24 QUAL 0 19.0 454 191 263 34 QUAL 0 20.0 211 134 77 37 QUAL 0 21.0 312 138 174 67 QUAL 0 22.0 96 43 53 1 QUAL 0 23.0 179 96 83 27 QUAL 0 24.0 689 420 269 105 QUAL 0 25.0 821 400 421 92 QUAL 0 26.0 39 31 8 17 QUAL 0 27.0 591 355 236 55 QUAL 0 28.0 276 128 148 51 QUAL 0 29.0 295 141 154 26 QUAL 0 30.0 321 128 193 12 QUAL 0 31.0 1297 784 513 132 QUAL 0 32.0 312 147 165 44 QUAL 0 33.0 908 409 499 50 QUAL 0 34.0 112 61 51 6 QUAL 0 35.0 536 274 262 18 QUAL 0 36.0 1035 498 537 50 QUAL 0 37.0 464 307 157 62 QUAL 0 38.0 200 127 73 26 QUAL 0 39.0 100 64 36 32 QUAL 0 40.0 31 17 14 19 QUAL 0 42.0 737 367 370 16 QUAL 0 43.0 296 138 158 44 QUAL 0 44.0 586 399 187 103 QUAL 0 46.0 67 50 17 33 QUAL 0 47.0 142 87 55 21 QUAL 0 48.0 8 4 4 3 QUAL 0 49.0 437 294 143 81 QUAL 0 51.0 89 59 30 17 QUAL 0 52.0 174 84 90 26 QUAL 0 53.0 273 139 134 47 QUAL 0 55.0 55 35 20 37 QUAL 0 56.0 417 205 212 18 QUAL 0 57.0 43 21 22 14 QUAL 0 58.0 84 38 46 12 QUAL 0 59.0 241 115 126 11 QUAL 0 60.0 2463434 1641460 821974 649324 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF IDD 0 -60 4979 0 . IDD 0 -59 29 0 . IDD 0 -58 66 0 . IDD 0 -57 45 0 . IDD 0 -56 89 0 . IDD 0 -55 53 0 . IDD 0 -54 90 0 . IDD 0 -53 52 0 . IDD 0 -52 125 0 . IDD 0 -51 66 0 . IDD 0 -50 117 0 . IDD 0 -49 102 0 . IDD 0 -48 141 0 . IDD 0 -47 76 0 . IDD 0 -46 112 0 . IDD 0 -45 80 0 . IDD 0 -44 134 0 . IDD 0 -43 77 0 . IDD 0 -42 165 0 . IDD 0 -41 96 0 . IDD 0 -40 254 0 . IDD 0 -39 114 0 . IDD 0 -38 197 0 . IDD 0 -37 133 0 . IDD 0 -36 300 0 . IDD 0 -35 138 0 . IDD 0 -34 255 0 . IDD 0 -33 191 0 . IDD 0 -32 398 0 . IDD 0 -31 213 0 . IDD 0 -30 468 0 . IDD 0 -29 237 0 . IDD 0 -28 613 0 . IDD 0 -27 273 0 . IDD 0 -26 540 0 . IDD 0 -25 373 0 . IDD 0 -24 930 0 . IDD 0 -23 343 0 . IDD 0 -22 723 0 . IDD 0 -21 456 0 . IDD 0 -20 1458 0 . IDD 0 -19 540 0 . IDD 0 -18 1267 0 . IDD 0 -17 717 0 . IDD 0 -16 2248 0 . IDD 0 -15 1345 0 . IDD 0 -14 2049 0 . IDD 0 -13 1262 0 . IDD 0 -12 4498 0 . IDD 0 -11 1581 0 . IDD 0 -10 4278 0 . IDD 0 -9 2442 0 . IDD 0 -8 7748 0 . IDD 0 -7 3240 0 . IDD 0 -6 9152 0 . IDD 0 -5 8516 0 . IDD 0 -4 28743 0 . IDD 0 -3 19258 0 . IDD 0 -2 52459 0 . IDD 0 -1 149079 0 . IDD 0 1 160997 0 . IDD 0 2 56068 0 . IDD 0 3 20765 0 . IDD 0 4 29367 0 . IDD 0 5 8447 0 . IDD 0 6 9179 0 . IDD 0 7 3209 0 . IDD 0 8 7829 0 . IDD 0 9 2542 0 . IDD 0 10 4261 0 . IDD 0 11 1603 0 . IDD 0 12 4385 0 . IDD 0 13 1230 0 . IDD 0 14 2118 0 . IDD 0 15 1283 0 . IDD 0 16 2204 0 . IDD 0 17 754 0 . IDD 0 18 1294 0 . IDD 0 19 549 0 . IDD 0 20 1444 0 . IDD 0 21 496 0 . IDD 0 22 784 0 . IDD 0 23 386 0 . IDD 0 24 965 0 . IDD 0 25 376 0 . IDD 0 26 541 0 . IDD 0 27 310 0 . IDD 0 28 613 0 . IDD 0 29 239 0 . IDD 0 30 477 0 . IDD 0 31 212 0 . IDD 0 32 418 0 . IDD 0 33 177 0 . IDD 0 34 284 0 . IDD 0 35 160 0 . IDD 0 36 317 0 . IDD 0 37 149 0 . IDD 0 38 180 0 . IDD 0 39 112 0 . IDD 0 40 263 0 . IDD 0 41 103 0 . IDD 0 42 162 0 . IDD 0 43 85 0 . IDD 0 44 144 0 . IDD 0 45 76 0 . IDD 0 46 125 0 . IDD 0 47 72 0 . IDD 0 48 167 0 . IDD 0 49 116 0 . IDD 0 50 123 0 . IDD 0 51 71 0 . IDD 0 52 122 0 . IDD 0 53 54 0 . IDD 0 54 106 0 . IDD 0 55 62 0 . IDD 0 56 113 0 . IDD 0 57 60 0 . IDD 0 58 89 0 . IDD 0 59 49 0 . IDD 0 60 7596 0 . # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 107423 ST 0 A>G 413376 ST 0 A>T 94320 ST 0 C>A 107547 ST 0 C>G 110097 ST 0 C>T 415698 ST 0 G>A 415191 ST 0 G>C 110187 ST 0 G>T 108505 ST 0 T>A 94584 ST 0 T>C 414802 ST 0 T>G 108180 # 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 2499910 0 1659067 840843 652205 0.0 3152115 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 336482 315723 # 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 3152115 0.000000 0.000000 0.000000