# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats. # The command line was: bcftools stats filtered_file.vcf # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 filtered_file.vcf # 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: 20285 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 20030 SN 0 number of MNPs: 0 SN 0 number of indels: 255 SN 0 number of others: 0 SN 0 number of multiallelic sites: 184 SN 0 number of multiallelic SNP sites: 183 # 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 13659 6554 2.08 13618 6412 2.12 # 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 17559 12046 5513 245 0 0 245 # 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 0.000000 17559 12046 5513 245 0 0 245 AF 0 0.990000 2654 1613 1041 11 0 0 11 # 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 30 59 41 18 1 QUAL 0 31 62 37 25 1 QUAL 0 32 61 37 24 1 QUAL 0 33 61 39 22 1 QUAL 0 34 53 35 18 2 QUAL 0 35 55 32 23 2 QUAL 0 36 42 35 7 1 QUAL 0 37 54 38 16 1 QUAL 0 38 56 35 21 0 QUAL 0 39 63 44 19 2 QUAL 0 40 46 27 19 0 QUAL 0 41 57 36 21 1 QUAL 0 42 62 39 23 0 QUAL 0 43 55 31 24 0 QUAL 0 44 58 41 17 0 QUAL 0 45 54 35 19 1 QUAL 0 46 59 36 23 1 QUAL 0 47 61 40 21 3 QUAL 0 48 61 39 22 1 QUAL 0 49 56 39 17 0 QUAL 0 50 27 21 6 0 QUAL 0 51 50 28 22 1 QUAL 0 52 65 49 16 0 QUAL 0 53 56 38 18 1 QUAL 0 54 44 31 13 1 QUAL 0 55 48 40 8 2 QUAL 0 56 45 31 14 2 QUAL 0 57 64 39 25 0 QUAL 0 58 54 35 19 0 QUAL 0 59 59 36 23 0 QUAL 0 60 65 43 22 1 QUAL 0 61 49 34 15 0 QUAL 0 62 58 39 19 0 QUAL 0 63 59 43 16 0 QUAL 0 64 58 42 16 1 QUAL 0 65 60 37 23 1 QUAL 0 66 53 36 17 0 QUAL 0 67 58 38 20 0 QUAL 0 68 46 33 13 1 QUAL 0 69 52 36 16 0 QUAL 0 70 76 56 20 2 QUAL 0 71 52 36 16 1 QUAL 0 72 71 41 30 1 QUAL 0 73 46 35 11 3 QUAL 0 74 52 30 22 2 QUAL 0 75 55 40 15 0 QUAL 0 76 49 33 16 2 QUAL 0 77 67 46 21 1 QUAL 0 78 54 41 13 2 QUAL 0 79 48 29 19 0 QUAL 0 80 57 38 19 0 QUAL 0 81 47 28 19 0 QUAL 0 82 43 29 14 1 QUAL 0 83 62 41 21 1 QUAL 0 84 62 37 25 0 QUAL 0 85 49 31 18 1 QUAL 0 86 44 31 13 1 QUAL 0 87 44 28 16 0 QUAL 0 88 38 28 10 1 QUAL 0 89 48 30 18 0 QUAL 0 90 54 32 22 1 QUAL 0 91 58 35 23 0 QUAL 0 92 53 39 14 0 QUAL 0 93 54 39 15 2 QUAL 0 94 44 24 20 2 QUAL 0 95 65 46 19 2 QUAL 0 96 44 35 9 0 QUAL 0 97 49 32 17 1 QUAL 0 98 51 33 18 1 QUAL 0 99 60 41 19 3 QUAL 0 100 44 35 9 0 QUAL 0 101 42 26 16 0 QUAL 0 102 55 28 27 2 QUAL 0 103 53 31 22 1 QUAL 0 104 59 39 20 0 QUAL 0 105 60 45 15 4 QUAL 0 106 42 30 12 1 QUAL 0 107 44 27 17 0 QUAL 0 108 37 19 18 0 QUAL 0 109 44 30 14 0 QUAL 0 110 60 39 21 1 QUAL 0 111 56 36 20 1 QUAL 0 112 47 35 12 0 QUAL 0 113 53 36 17 1 QUAL 0 114 46 33 13 0 QUAL 0 115 63 43 20 1 QUAL 0 116 59 41 18 0 QUAL 0 117 72 51 21 0 QUAL 0 118 55 33 22 0 QUAL 0 119 52 37 15 0 QUAL 0 120 39 27 12 0 QUAL 0 121 66 39 27 1 QUAL 0 122 72 49 23 0 QUAL 0 123 46 34 12 1 QUAL 0 124 61 40 21 0 QUAL 0 125 67 46 21 0 QUAL 0 126 58 33 25 4 QUAL 0 127 50 36 14 0 QUAL 0 128 46 32 14 2 QUAL 0 129 65 44 21 0 QUAL 0 130 42 28 14 0 QUAL 0 131 54 35 19 2 QUAL 0 132 59 39 20 2 QUAL 0 133 46 37 9 1 QUAL 0 134 50 35 15 0 QUAL 0 135 63 43 20 2 QUAL 0 136 58 38 20 0 QUAL 0 137 61 44 17 1 QUAL 0 138 75 50 25 0 QUAL 0 139 63 42 21 0 QUAL 0 140 59 44 15 0 QUAL 0 141 71 43 28 1 QUAL 0 142 50 31 19 0 QUAL 0 143 55 32 23 1 QUAL 0 144 68 45 23 2 QUAL 0 145 49 38 11 1 QUAL 0 146 65 41 24 1 QUAL 0 147 66 44 22 0 QUAL 0 148 80 55 25 0 QUAL 0 149 74 44 30 0 QUAL 0 150 60 47 13 0 QUAL 0 151 72 46 26 0 QUAL 0 152 68 49 19 0 QUAL 0 153 60 32 28 2 QUAL 0 154 42 28 14 1 QUAL 0 155 52 37 15 1 QUAL 0 156 60 38 22 0 QUAL 0 157 56 39 17 0 QUAL 0 158 47 38 9 0 QUAL 0 159 57 35 22 0 QUAL 0 160 46 32 14 0 QUAL 0 161 37 22 15 2 QUAL 0 162 42 24 18 0 QUAL 0 163 56 38 18 0 QUAL 0 164 59 45 14 1 QUAL 0 165 48 31 17 0 QUAL 0 166 43 29 14 0 QUAL 0 167 62 39 23 1 QUAL 0 168 43 28 15 1 QUAL 0 169 54 39 15 3 QUAL 0 170 48 33 15 0 QUAL 0 171 59 38 21 1 QUAL 0 172 50 37 13 0 QUAL 0 173 56 38 18 0 QUAL 0 174 41 30 11 2 QUAL 0 175 56 35 21 0 QUAL 0 176 58 43 15 1 QUAL 0 177 53 30 23 1 QUAL 0 178 58 39 19 0 QUAL 0 179 51 31 20 0 QUAL 0 180 74 58 16 0 QUAL 0 181 42 27 15 0 QUAL 0 182 52 31 21 0 QUAL 0 183 38 14 24 0 QUAL 0 184 52 30 22 0 QUAL 0 185 60 42 18 1 QUAL 0 186 40 29 11 0 QUAL 0 187 55 33 22 0 QUAL 0 188 46 31 15 0 QUAL 0 189 52 36 16 0 QUAL 0 190 56 40 16 1 QUAL 0 191 45 32 13 0 QUAL 0 192 50 35 15 0 QUAL 0 193 71 38 33 0 QUAL 0 194 89 37 52 0 QUAL 0 195 117 48 69 0 QUAL 0 196 57 39 18 0 QUAL 0 197 57 40 17 0 QUAL 0 198 46 37 9 2 QUAL 0 199 49 27 22 0 QUAL 0 200 43 31 12 1 QUAL 0 201 48 34 14 0 QUAL 0 202 45 23 22 2 QUAL 0 203 62 43 19 0 QUAL 0 204 41 26 15 0 QUAL 0 205 56 41 15 3 QUAL 0 206 48 29 19 1 QUAL 0 207 58 37 21 0 QUAL 0 208 61 42 19 0 QUAL 0 209 56 34 22 0 QUAL 0 210 64 40 24 0 QUAL 0 211 74 43 31 0 QUAL 0 212 62 46 16 1 QUAL 0 213 60 39 21 1 QUAL 0 214 48 34 14 2 QUAL 0 215 46 26 20 0 QUAL 0 216 53 28 25 1 QUAL 0 217 51 39 12 1 QUAL 0 218 57 37 20 3 QUAL 0 219 245 149 96 4 QUAL 0 220 530 333 197 5 QUAL 0 221 1237 881 356 18 QUAL 0 222 5975 4337 1638 92 QUAL 0 223 24 11 13 0 QUAL 0 224 14 10 4 0 QUAL 0 225 339 236 103 0 QUAL 0 226 7 3 4 0 QUAL 0 227 19 15 4 0 QUAL 0 228 1243 786 457 4 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]count IDD 0 -16 1 IDD 0 -13 1 IDD 0 -9 2 IDD 0 -8 1 IDD 0 -7 2 IDD 0 -6 6 IDD 0 -5 5 IDD 0 -4 14 IDD 0 -3 21 IDD 0 -2 15 IDD 0 -1 24 IDD 0 1 52 IDD 0 2 24 IDD 0 3 33 IDD 0 4 29 IDD 0 5 9 IDD 0 6 4 IDD 0 7 7 IDD 0 8 4 IDD 0 9 1 IDD 0 18 1 # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 892 ST 0 A>G 3748 ST 0 A>T 791 ST 0 C>A 740 ST 0 C>G 842 ST 0 C>T 3210 ST 0 G>A 3108 ST 0 G>C 851 ST 0 G>T 775 ST 0 T>A 741 ST 0 T>C 3593 ST 0 T>G 922 # DP, Depth distribution # DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%) DP 0 51 0 0.000000 241 1.188070 DP 0 52 0 0.000000 206 1.015529 DP 0 53 0 0.000000 222 1.094405 DP 0 54 0 0.000000 219 1.079615 DP 0 55 0 0.000000 251 1.237368 DP 0 56 0 0.000000 219 1.079615 DP 0 57 0 0.000000 236 1.163421 DP 0 58 0 0.000000 217 1.069756 DP 0 59 0 0.000000 203 1.000739 DP 0 60 0 0.000000 225 1.109194 DP 0 61 0 0.000000 221 1.089475 DP 0 62 0 0.000000 195 0.961301 DP 0 63 0 0.000000 181 0.892285 DP 0 64 0 0.000000 203 1.000739 DP 0 65 0 0.000000 178 0.877496 DP 0 66 0 0.000000 196 0.966231 DP 0 67 0 0.000000 171 0.842987 DP 0 68 0 0.000000 170 0.838058 DP 0 69 0 0.000000 172 0.847917 DP 0 70 0 0.000000 189 0.931723 DP 0 71 0 0.000000 170 0.838058 DP 0 72 0 0.000000 160 0.788760 DP 0 73 0 0.000000 162 0.798620 DP 0 74 0 0.000000 156 0.769041 DP 0 75 0 0.000000 172 0.847917 DP 0 76 0 0.000000 156 0.769041 DP 0 77 0 0.000000 154 0.759182 DP 0 78 0 0.000000 157 0.773971 DP 0 79 0 0.000000 137 0.675376 DP 0 80 0 0.000000 141 0.695095 DP 0 81 0 0.000000 145 0.714814 DP 0 82 0 0.000000 150 0.739463 DP 0 83 0 0.000000 116 0.571851 DP 0 84 0 0.000000 108 0.532413 DP 0 85 0 0.000000 134 0.660587 DP 0 86 0 0.000000 133 0.655657 DP 0 87 0 0.000000 144 0.709884 DP 0 88 0 0.000000 125 0.616219 DP 0 89 0 0.000000 137 0.675376 DP 0 90 0 0.000000 127 0.626078 DP 0 91 0 0.000000 111 0.547202 DP 0 92 0 0.000000 134 0.660587 DP 0 93 0 0.000000 119 0.586640 DP 0 94 0 0.000000 126 0.621149 DP 0 95 0 0.000000 125 0.616219 DP 0 96 0 0.000000 119 0.586640 DP 0 97 0 0.000000 120 0.591570 DP 0 98 0 0.000000 130 0.640868 DP 0 99 0 0.000000 93 0.458467 DP 0 100 0 0.000000 129 0.635938 DP 0 101 0 0.000000 109 0.537343 DP 0 102 0 0.000000 108 0.532413 DP 0 103 0 0.000000 102 0.502835 DP 0 104 0 0.000000 91 0.448607 DP 0 105 0 0.000000 113 0.557062 DP 0 106 0 0.000000 89 0.438748 DP 0 107 0 0.000000 120 0.591570 DP 0 108 0 0.000000 115 0.566921 DP 0 109 0 0.000000 92 0.453537 DP 0 110 0 0.000000 100 0.492975 DP 0 111 0 0.000000 131 0.645797 DP 0 112 0 0.000000 91 0.448607 DP 0 113 0 0.000000 108 0.532413 DP 0 114 0 0.000000 94 0.463397 DP 0 115 0 0.000000 102 0.502835 DP 0 116 0 0.000000 102 0.502835 DP 0 117 0 0.000000 104 0.512694 DP 0 118 0 0.000000 87 0.428888 DP 0 119 0 0.000000 85 0.419029 DP 0 120 0 0.000000 91 0.448607 DP 0 121 0 0.000000 94 0.463397 DP 0 122 0 0.000000 91 0.448607 DP 0 123 0 0.000000 82 0.404240 DP 0 124 0 0.000000 93 0.458467 DP 0 125 0 0.000000 94 0.463397 DP 0 126 0 0.000000 86 0.423959 DP 0 127 0 0.000000 80 0.394380 DP 0 128 0 0.000000 100 0.492975 DP 0 129 0 0.000000 94 0.463397 DP 0 130 0 0.000000 83 0.409169 DP 0 131 0 0.000000 81 0.399310 DP 0 132 0 0.000000 87 0.428888 DP 0 133 0 0.000000 83 0.409169 DP 0 134 0 0.000000 68 0.335223 DP 0 135 0 0.000000 85 0.419029 DP 0 136 0 0.000000 59 0.290855 DP 0 137 0 0.000000 61 0.300715 DP 0 138 0 0.000000 90 0.443678 DP 0 139 0 0.000000 89 0.438748 DP 0 140 0 0.000000 81 0.399310 DP 0 141 0 0.000000 55 0.271136 DP 0 142 0 0.000000 80 0.394380 DP 0 143 0 0.000000 82 0.404240 DP 0 144 0 0.000000 63 0.310574 DP 0 145 0 0.000000 69 0.340153 DP 0 146 0 0.000000 80 0.394380 DP 0 147 0 0.000000 61 0.300715 DP 0 148 0 0.000000 69 0.340153 DP 0 149 0 0.000000 61 0.300715 DP 0 150 0 0.000000 68 0.335223 DP 0 151 0 0.000000 70 0.345083 DP 0 152 0 0.000000 65 0.320434 DP 0 153 0 0.000000 70 0.345083 DP 0 154 0 0.000000 51 0.251417 DP 0 155 0 0.000000 58 0.285926 DP 0 156 0 0.000000 70 0.345083 DP 0 157 0 0.000000 67 0.330293 DP 0 158 0 0.000000 61 0.300715 DP 0 159 0 0.000000 67 0.330293 DP 0 160 0 0.000000 59 0.290855 DP 0 161 0 0.000000 57 0.280996 DP 0 162 0 0.000000 55 0.271136 DP 0 163 0 0.000000 72 0.354942 DP 0 164 0 0.000000 62 0.305645 DP 0 165 0 0.000000 69 0.340153 DP 0 166 0 0.000000 55 0.271136 DP 0 167 0 0.000000 53 0.261277 DP 0 168 0 0.000000 51 0.251417 DP 0 169 0 0.000000 50 0.246488 DP 0 170 0 0.000000 64 0.315504 DP 0 171 0 0.000000 67 0.330293 DP 0 172 0 0.000000 46 0.226769 DP 0 173 0 0.000000 45 0.221839 DP 0 174 0 0.000000 54 0.266207 DP 0 175 0 0.000000 45 0.221839 DP 0 176 0 0.000000 72 0.354942 DP 0 177 0 0.000000 63 0.310574 DP 0 178 0 0.000000 58 0.285926 DP 0 179 0 0.000000 45 0.221839 DP 0 180 0 0.000000 56 0.276066 DP 0 181 0 0.000000 74 0.364802 DP 0 182 0 0.000000 48 0.236628 DP 0 183 0 0.000000 57 0.280996 DP 0 184 0 0.000000 59 0.290855 DP 0 185 0 0.000000 51 0.251417 DP 0 186 0 0.000000 49 0.241558 DP 0 187 0 0.000000 56 0.276066 DP 0 188 0 0.000000 45 0.221839 DP 0 189 0 0.000000 42 0.207050 DP 0 190 0 0.000000 49 0.241558 DP 0 191 0 0.000000 56 0.276066 DP 0 192 0 0.000000 49 0.241558 DP 0 193 0 0.000000 52 0.256347 DP 0 194 0 0.000000 41 0.202120 DP 0 195 0 0.000000 50 0.246488 DP 0 196 0 0.000000 68 0.335223 DP 0 197 0 0.000000 54 0.266207 DP 0 198 0 0.000000 51 0.251417 DP 0 199 0 0.000000 39 0.192260 DP 0 200 0 0.000000 56 0.276066 DP 0 201 0 0.000000 59 0.290855 DP 0 202 0 0.000000 57 0.280996 DP 0 203 0 0.000000 43 0.211979 DP 0 204 0 0.000000 61 0.300715 DP 0 205 0 0.000000 60 0.295785 DP 0 206 0 0.000000 65 0.320434 DP 0 207 0 0.000000 40 0.197190 DP 0 208 0 0.000000 57 0.280996 DP 0 209 0 0.000000 56 0.276066 DP 0 210 0 0.000000 52 0.256347 DP 0 211 0 0.000000 46 0.226769 DP 0 212 0 0.000000 54 0.266207 DP 0 213 0 0.000000 57 0.280996 DP 0 214 0 0.000000 58 0.285926 DP 0 215 0 0.000000 47 0.231698 DP 0 216 0 0.000000 62 0.305645 DP 0 217 0 0.000000 59 0.290855 DP 0 218 0 0.000000 50 0.246488 DP 0 219 0 0.000000 58 0.285926 DP 0 220 0 0.000000 56 0.276066 DP 0 221 0 0.000000 61 0.300715 DP 0 222 0 0.000000 56 0.276066 DP 0 223 0 0.000000 40 0.197190 DP 0 224 0 0.000000 74 0.364802 DP 0 225 0 0.000000 65 0.320434 DP 0 226 0 0.000000 70 0.345083 DP 0 227 0 0.000000 75 0.369731 DP 0 228 0 0.000000 72 0.354942 DP 0 229 0 0.000000 70 0.345083 DP 0 230 0 0.000000 70 0.345083 DP 0 231 0 0.000000 53 0.261277 DP 0 232 0 0.000000 80 0.394380 DP 0 233 0 0.000000 87 0.428888 DP 0 234 0 0.000000 77 0.379591 DP 0 235 0 0.000000 77 0.379591 DP 0 236 0 0.000000 84 0.414099 DP 0 237 0 0.000000 99 0.488045 DP 0 238 0 0.000000 98 0.483116 DP 0 239 0 0.000000 86 0.423959 DP 0 240 0 0.000000 97 0.478186 DP 0 241 0 0.000000 107 0.527483 DP 0 242 0 0.000000 132 0.650727 DP 0 243 0 0.000000 127 0.626078 DP 0 244 0 0.000000 156 0.769041 DP 0 245 0 0.000000 223 1.099334 DP 0 246 0 0.000000 205 1.010599 DP 0 247 0 0.000000 218 1.074686 DP 0 248 0 0.000000 232 1.143702 DP 0 249 0 0.000000 256 1.262016 DP 0 250 0 0.000000 166 0.818339 DP 0 251 0 0.000000 72 0.354942 DP 0 252 0 0.000000 49 0.241558 DP 0 253 0 0.000000 47 0.231698 DP 0 254 0 0.000000 55 0.271136 DP 0 255 0 0.000000 34 0.167612 DP 0 256 0 0.000000 28 0.138033 DP 0 257 0 0.000000 25 0.123244 DP 0 258 0 0.000000 22 0.108455 DP 0 259 0 0.000000 15 0.073946 DP 0 260 0 0.000000 25 0.123244 DP 0 261 0 0.000000 10 0.049298 DP 0 262 0 0.000000 9 0.044368 DP 0 263 0 0.000000 7 0.034508 DP 0 264 0 0.000000 6 0.029579 DP 0 265 0 0.000000 5 0.024649 DP 0 266 0 0.000000 10 0.049298 DP 0 267 0 0.000000 1 0.004930 DP 0 268 0 0.000000 9 0.044368 DP 0 269 0 0.000000 2 0.009860 DP 0 270 0 0.000000 2 0.009860 DP 0 271 0 0.000000 4 0.019719 DP 0 272 0 0.000000 1 0.004930 DP 0 275 0 0.000000 1 0.004930 DP 0 277 0 0.000000 1 0.004930 DP 0 278 0 0.000000 2 0.009860 DP 0 280 0 0.000000 1 0.004930 DP 0 281 0 0.000000 1 0.004930