# 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 chr3_filter.vcf # # Definition of sets: # ID [2]id [3]tab-separated file names ID 0 chr3_filter.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: 25741 SN 0 number of no-ALTs: 0 SN 0 number of SNPs: 25388 SN 0 number of MNPs: 0 SN 0 number of indels: 353 SN 0 number of others: 0 SN 0 number of multiallelic sites: 204 SN 0 number of multiallelic SNP sites: 204 # 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 17362 8230 2.11 17324 8064 2.15 # 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 22880 15732 7148 334 0 0 334 # 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 22880 15732 7148 334 0 0 334 AF 0 0.990000 2712 1630 1082 19 0 0 19 # 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 86 61 25 2 QUAL 0 31 82 48 34 4 QUAL 0 32 83 53 30 2 QUAL 0 33 67 37 30 1 QUAL 0 34 73 47 26 0 QUAL 0 35 73 51 22 3 QUAL 0 36 66 41 25 1 QUAL 0 37 84 47 37 0 QUAL 0 38 60 43 17 2 QUAL 0 39 71 43 28 0 QUAL 0 40 61 43 18 2 QUAL 0 41 64 40 24 5 QUAL 0 42 70 45 25 1 QUAL 0 43 60 41 19 0 QUAL 0 44 64 43 21 1 QUAL 0 45 62 45 17 0 QUAL 0 46 84 45 39 1 QUAL 0 47 66 44 22 3 QUAL 0 48 64 41 23 0 QUAL 0 49 84 57 27 1 QUAL 0 50 49 28 21 1 QUAL 0 51 79 54 25 1 QUAL 0 52 73 42 31 0 QUAL 0 53 77 55 22 1 QUAL 0 54 59 39 20 0 QUAL 0 55 71 47 24 1 QUAL 0 56 75 54 21 0 QUAL 0 57 70 50 20 2 QUAL 0 58 77 48 29 0 QUAL 0 59 62 42 20 0 QUAL 0 60 84 59 25 1 QUAL 0 61 72 51 21 3 QUAL 0 62 61 40 21 1 QUAL 0 63 67 43 24 0 QUAL 0 64 53 35 18 2 QUAL 0 65 63 41 22 1 QUAL 0 66 74 46 28 2 QUAL 0 67 64 40 24 3 QUAL 0 68 73 47 26 2 QUAL 0 69 67 49 18 2 QUAL 0 70 67 35 32 1 QUAL 0 71 61 45 16 2 QUAL 0 72 57 36 21 4 QUAL 0 73 77 47 30 1 QUAL 0 74 101 73 28 0 QUAL 0 75 64 46 18 0 QUAL 0 76 64 40 24 1 QUAL 0 77 71 48 23 0 QUAL 0 78 73 55 18 2 QUAL 0 79 87 58 29 3 QUAL 0 80 72 53 19 2 QUAL 0 81 61 44 17 0 QUAL 0 82 70 50 20 1 QUAL 0 83 57 38 19 1 QUAL 0 84 70 40 30 1 QUAL 0 85 66 42 24 2 QUAL 0 86 74 54 20 1 QUAL 0 87 70 49 21 0 QUAL 0 88 69 52 17 1 QUAL 0 89 75 46 29 0 QUAL 0 90 65 40 25 0 QUAL 0 91 62 34 28 2 QUAL 0 92 67 41 26 0 QUAL 0 93 70 46 24 2 QUAL 0 94 63 41 22 2 QUAL 0 95 58 41 17 2 QUAL 0 96 71 48 23 1 QUAL 0 97 70 44 26 0 QUAL 0 98 87 55 32 0 QUAL 0 99 59 40 19 0 QUAL 0 100 78 53 25 0 QUAL 0 101 72 46 26 1 QUAL 0 102 77 47 30 1 QUAL 0 103 83 54 29 0 QUAL 0 104 78 52 26 2 QUAL 0 105 62 41 21 2 QUAL 0 106 79 54 25 1 QUAL 0 107 97 66 31 4 QUAL 0 108 61 41 20 0 QUAL 0 109 73 44 29 1 QUAL 0 110 64 41 23 0 QUAL 0 111 62 40 22 1 QUAL 0 112 59 36 23 0 QUAL 0 113 60 42 18 1 QUAL 0 114 66 45 21 2 QUAL 0 115 63 39 24 1 QUAL 0 116 68 46 22 1 QUAL 0 117 71 48 23 1 QUAL 0 118 67 47 20 3 QUAL 0 119 77 58 19 0 QUAL 0 120 84 55 29 0 QUAL 0 121 75 49 26 0 QUAL 0 122 73 43 30 3 QUAL 0 123 89 61 28 3 QUAL 0 124 64 45 19 2 QUAL 0 125 84 55 29 4 QUAL 0 126 78 61 17 1 QUAL 0 127 74 53 21 0 QUAL 0 128 84 60 24 0 QUAL 0 129 63 44 19 0 QUAL 0 130 67 46 21 0 QUAL 0 131 98 57 41 2 QUAL 0 132 73 44 29 2 QUAL 0 133 83 56 27 0 QUAL 0 134 61 47 14 1 QUAL 0 135 74 53 21 2 QUAL 0 136 88 59 29 1 QUAL 0 137 89 64 25 2 QUAL 0 138 64 38 26 1 QUAL 0 139 90 54 36 1 QUAL 0 140 85 58 27 1 QUAL 0 141 84 53 31 2 QUAL 0 142 87 52 35 4 QUAL 0 143 105 70 35 3 QUAL 0 144 78 45 33 2 QUAL 0 145 54 36 18 0 QUAL 0 146 73 48 25 1 QUAL 0 147 85 53 32 1 QUAL 0 148 76 50 26 0 QUAL 0 149 71 51 20 0 QUAL 0 150 79 56 23 2 QUAL 0 151 76 49 27 1 QUAL 0 152 75 52 23 0 QUAL 0 153 75 55 20 3 QUAL 0 154 73 59 14 2 QUAL 0 155 80 46 34 1 QUAL 0 156 70 53 17 0 QUAL 0 157 54 40 14 0 QUAL 0 158 65 43 22 1 QUAL 0 159 63 40 23 0 QUAL 0 160 55 33 22 1 QUAL 0 161 48 31 17 1 QUAL 0 162 72 52 20 0 QUAL 0 163 67 48 19 1 QUAL 0 164 60 34 26 1 QUAL 0 165 76 56 20 1 QUAL 0 166 68 45 23 0 QUAL 0 167 60 37 23 0 QUAL 0 168 68 39 29 0 QUAL 0 169 65 42 23 0 QUAL 0 170 54 37 17 1 QUAL 0 171 75 52 23 0 QUAL 0 172 68 52 16 1 QUAL 0 173 43 26 17 2 QUAL 0 174 57 40 17 0 QUAL 0 175 61 38 23 0 QUAL 0 176 82 63 19 0 QUAL 0 177 66 43 23 1 QUAL 0 178 53 37 16 1 QUAL 0 179 79 50 29 0 QUAL 0 180 60 44 16 1 QUAL 0 181 77 48 29 2 QUAL 0 182 59 39 20 1 QUAL 0 183 64 40 24 0 QUAL 0 184 68 43 25 0 QUAL 0 185 74 48 26 2 QUAL 0 186 64 44 20 0 QUAL 0 187 80 61 19 0 QUAL 0 188 62 46 16 0 QUAL 0 189 61 43 18 1 QUAL 0 190 58 32 26 1 QUAL 0 191 75 48 27 0 QUAL 0 192 69 48 21 2 QUAL 0 193 86 41 45 2 QUAL 0 194 100 46 54 1 QUAL 0 195 158 74 84 1 QUAL 0 196 77 51 26 0 QUAL 0 197 76 56 20 1 QUAL 0 198 76 41 35 0 QUAL 0 199 69 45 24 1 QUAL 0 200 66 37 29 0 QUAL 0 201 55 42 13 1 QUAL 0 202 65 43 22 0 QUAL 0 203 67 49 18 1 QUAL 0 204 60 44 16 0 QUAL 0 205 65 44 21 2 QUAL 0 206 61 38 23 1 QUAL 0 207 64 42 22 0 QUAL 0 208 67 48 19 0 QUAL 0 209 57 37 20 0 QUAL 0 210 51 35 16 0 QUAL 0 211 70 47 23 0 QUAL 0 212 63 41 22 3 QUAL 0 213 53 37 16 0 QUAL 0 214 65 44 21 0 QUAL 0 215 72 50 22 0 QUAL 0 216 68 53 15 0 QUAL 0 217 67 42 25 3 QUAL 0 218 71 49 22 0 QUAL 0 219 269 176 93 2 QUAL 0 220 797 549 248 7 QUAL 0 221 1474 1024 450 28 QUAL 0 222 7666 5589 2077 115 QUAL 0 223 13 5 8 0 QUAL 0 224 12 5 7 0 QUAL 0 225 605 433 172 0 QUAL 0 226 13 8 5 0 QUAL 0 227 7 4 3 0 QUAL 0 228 1183 717 466 8 # IDD, InDel distribution: # IDD [2]id [3]length (deletions negative) [4]count IDD 0 -20 1 IDD 0 -12 4 IDD 0 -11 3 IDD 0 -10 3 IDD 0 -9 4 IDD 0 -8 2 IDD 0 -6 6 IDD 0 -5 12 IDD 0 -4 16 IDD 0 -3 15 IDD 0 -2 17 IDD 0 -1 45 IDD 0 1 94 IDD 0 2 37 IDD 0 3 53 IDD 0 4 22 IDD 0 5 4 IDD 0 6 4 IDD 0 7 3 IDD 0 8 5 IDD 0 9 1 IDD 0 14 1 IDD 0 15 1 # ST, Substitution types: # ST [2]id [3]type [4]count ST 0 A>C 1128 ST 0 A>G 4639 ST 0 A>T 859 ST 0 C>A 978 ST 0 C>G 1106 ST 0 C>T 3985 ST 0 G>A 4045 ST 0 G>C 1153 ST 0 G>T 1049 ST 0 T>A 879 ST 0 T>C 4693 ST 0 T>G 1078 # 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 325 1.262577 DP 0 52 0 0.000000 279 1.083874 DP 0 53 0 0.000000 293 1.138262 DP 0 54 0 0.000000 304 1.180995 DP 0 55 0 0.000000 293 1.138262 DP 0 56 0 0.000000 262 1.017831 DP 0 57 0 0.000000 275 1.068335 DP 0 58 0 0.000000 236 0.916825 DP 0 59 0 0.000000 252 0.978983 DP 0 60 0 0.000000 254 0.986753 DP 0 61 0 0.000000 230 0.893516 DP 0 62 0 0.000000 244 0.947904 DP 0 63 0 0.000000 243 0.944019 DP 0 64 0 0.000000 249 0.967328 DP 0 65 0 0.000000 234 0.909056 DP 0 66 0 0.000000 221 0.858553 DP 0 67 0 0.000000 203 0.788625 DP 0 68 0 0.000000 243 0.944019 DP 0 69 0 0.000000 227 0.881862 DP 0 70 0 0.000000 192 0.745892 DP 0 71 0 0.000000 254 0.986753 DP 0 72 0 0.000000 231 0.897401 DP 0 73 0 0.000000 266 1.033371 DP 0 74 0 0.000000 228 0.885746 DP 0 75 0 0.000000 221 0.858553 DP 0 76 0 0.000000 179 0.695389 DP 0 77 0 0.000000 191 0.742007 DP 0 78 0 0.000000 208 0.808049 DP 0 79 0 0.000000 201 0.780855 DP 0 80 0 0.000000 196 0.761431 DP 0 81 0 0.000000 184 0.714813 DP 0 82 0 0.000000 184 0.714813 DP 0 83 0 0.000000 189 0.734237 DP 0 84 0 0.000000 199 0.773086 DP 0 85 0 0.000000 171 0.664310 DP 0 86 0 0.000000 186 0.722583 DP 0 87 0 0.000000 166 0.644886 DP 0 88 0 0.000000 172 0.668195 DP 0 89 0 0.000000 142 0.551649 DP 0 90 0 0.000000 139 0.539995 DP 0 91 0 0.000000 172 0.668195 DP 0 92 0 0.000000 155 0.602152 DP 0 93 0 0.000000 152 0.590498 DP 0 94 0 0.000000 169 0.656540 DP 0 95 0 0.000000 173 0.672080 DP 0 96 0 0.000000 149 0.578843 DP 0 97 0 0.000000 142 0.551649 DP 0 98 0 0.000000 137 0.532225 DP 0 99 0 0.000000 151 0.586613 DP 0 100 0 0.000000 156 0.606037 DP 0 101 0 0.000000 136 0.528340 DP 0 102 0 0.000000 124 0.481722 DP 0 103 0 0.000000 154 0.598267 DP 0 104 0 0.000000 139 0.539995 DP 0 105 0 0.000000 150 0.582728 DP 0 106 0 0.000000 115 0.446758 DP 0 107 0 0.000000 122 0.473952 DP 0 108 0 0.000000 141 0.547764 DP 0 109 0 0.000000 124 0.481722 DP 0 110 0 0.000000 124 0.481722 DP 0 111 0 0.000000 109 0.423449 DP 0 112 0 0.000000 129 0.501146 DP 0 113 0 0.000000 126 0.489491 DP 0 114 0 0.000000 124 0.481722 DP 0 115 0 0.000000 134 0.520570 DP 0 116 0 0.000000 124 0.481722 DP 0 117 0 0.000000 125 0.485607 DP 0 118 0 0.000000 127 0.493376 DP 0 119 0 0.000000 105 0.407910 DP 0 120 0 0.000000 104 0.404025 DP 0 121 0 0.000000 119 0.462298 DP 0 122 0 0.000000 101 0.392370 DP 0 123 0 0.000000 108 0.419564 DP 0 124 0 0.000000 103 0.400140 DP 0 125 0 0.000000 110 0.427334 DP 0 126 0 0.000000 99 0.384600 DP 0 127 0 0.000000 106 0.411794 DP 0 128 0 0.000000 93 0.361291 DP 0 129 0 0.000000 92 0.357406 DP 0 130 0 0.000000 94 0.365176 DP 0 131 0 0.000000 99 0.384600 DP 0 132 0 0.000000 106 0.411794 DP 0 133 0 0.000000 94 0.365176 DP 0 134 0 0.000000 97 0.376831 DP 0 135 0 0.000000 101 0.392370 DP 0 136 0 0.000000 87 0.337982 DP 0 137 0 0.000000 84 0.326328 DP 0 138 0 0.000000 94 0.365176 DP 0 139 0 0.000000 77 0.299134 DP 0 140 0 0.000000 79 0.306903 DP 0 141 0 0.000000 97 0.376831 DP 0 142 0 0.000000 82 0.318558 DP 0 143 0 0.000000 94 0.365176 DP 0 144 0 0.000000 96 0.372946 DP 0 145 0 0.000000 92 0.357406 DP 0 146 0 0.000000 73 0.283594 DP 0 147 0 0.000000 79 0.306903 DP 0 148 0 0.000000 82 0.318558 DP 0 149 0 0.000000 87 0.337982 DP 0 150 0 0.000000 77 0.299134 DP 0 151 0 0.000000 72 0.279709 DP 0 152 0 0.000000 92 0.357406 DP 0 153 0 0.000000 83 0.322443 DP 0 154 0 0.000000 78 0.303019 DP 0 155 0 0.000000 77 0.299134 DP 0 156 0 0.000000 88 0.341867 DP 0 157 0 0.000000 91 0.353522 DP 0 158 0 0.000000 77 0.299134 DP 0 159 0 0.000000 72 0.279709 DP 0 160 0 0.000000 80 0.310788 DP 0 161 0 0.000000 78 0.303019 DP 0 162 0 0.000000 72 0.279709 DP 0 163 0 0.000000 99 0.384600 DP 0 164 0 0.000000 76 0.295249 DP 0 165 0 0.000000 75 0.291364 DP 0 166 0 0.000000 81 0.314673 DP 0 167 0 0.000000 82 0.318558 DP 0 168 0 0.000000 86 0.334097 DP 0 169 0 0.000000 85 0.330213 DP 0 170 0 0.000000 74 0.287479 DP 0 171 0 0.000000 66 0.256400 DP 0 172 0 0.000000 80 0.310788 DP 0 173 0 0.000000 74 0.287479 DP 0 174 0 0.000000 86 0.334097 DP 0 175 0 0.000000 65 0.252515 DP 0 176 0 0.000000 80 0.310788 DP 0 177 0 0.000000 72 0.279709 DP 0 178 0 0.000000 69 0.268055 DP 0 179 0 0.000000 65 0.252515 DP 0 180 0 0.000000 73 0.283594 DP 0 181 0 0.000000 72 0.279709 DP 0 182 0 0.000000 67 0.260285 DP 0 183 0 0.000000 64 0.248631 DP 0 184 0 0.000000 67 0.260285 DP 0 185 0 0.000000 66 0.256400 DP 0 186 0 0.000000 81 0.314673 DP 0 187 0 0.000000 64 0.248631 DP 0 188 0 0.000000 66 0.256400 DP 0 189 0 0.000000 68 0.264170 DP 0 190 0 0.000000 61 0.236976 DP 0 191 0 0.000000 46 0.178703 DP 0 192 0 0.000000 63 0.244746 DP 0 193 0 0.000000 67 0.260285 DP 0 194 0 0.000000 51 0.198128 DP 0 195 0 0.000000 52 0.202012 DP 0 196 0 0.000000 57 0.221437 DP 0 197 0 0.000000 59 0.229206 DP 0 198 0 0.000000 64 0.248631 DP 0 199 0 0.000000 58 0.225321 DP 0 200 0 0.000000 52 0.202012 DP 0 201 0 0.000000 56 0.217552 DP 0 202 0 0.000000 57 0.221437 DP 0 203 0 0.000000 64 0.248631 DP 0 204 0 0.000000 72 0.279709 DP 0 205 0 0.000000 73 0.283594 DP 0 206 0 0.000000 81 0.314673 DP 0 207 0 0.000000 71 0.275825 DP 0 208 0 0.000000 78 0.303019 DP 0 209 0 0.000000 72 0.279709 DP 0 210 0 0.000000 73 0.283594 DP 0 211 0 0.000000 66 0.256400 DP 0 212 0 0.000000 56 0.217552 DP 0 213 0 0.000000 79 0.306903 DP 0 214 0 0.000000 68 0.264170 DP 0 215 0 0.000000 64 0.248631 DP 0 216 0 0.000000 66 0.256400 DP 0 217 0 0.000000 87 0.337982 DP 0 218 0 0.000000 58 0.225321 DP 0 219 0 0.000000 85 0.330213 DP 0 220 0 0.000000 77 0.299134 DP 0 221 0 0.000000 63 0.244746 DP 0 222 0 0.000000 84 0.326328 DP 0 223 0 0.000000 85 0.330213 DP 0 224 0 0.000000 83 0.322443 DP 0 225 0 0.000000 84 0.326328 DP 0 226 0 0.000000 73 0.283594 DP 0 227 0 0.000000 97 0.376831 DP 0 228 0 0.000000 111 0.431219 DP 0 229 0 0.000000 80 0.310788 DP 0 230 0 0.000000 86 0.334097 DP 0 231 0 0.000000 118 0.458413 DP 0 232 0 0.000000 102 0.396255 DP 0 233 0 0.000000 83 0.322443 DP 0 234 0 0.000000 109 0.423449 DP 0 235 0 0.000000 92 0.357406 DP 0 236 0 0.000000 116 0.450643 DP 0 237 0 0.000000 124 0.481722 DP 0 238 0 0.000000 130 0.505031 DP 0 239 0 0.000000 123 0.477837 DP 0 240 0 0.000000 148 0.574958 DP 0 241 0 0.000000 155 0.602152 DP 0 242 0 0.000000 195 0.757546 DP 0 243 0 0.000000 226 0.877977 DP 0 244 0 0.000000 241 0.936250 DP 0 245 0 0.000000 242 0.940134 DP 0 246 0 0.000000 261 1.013947 DP 0 247 0 0.000000 312 1.212074 DP 0 248 0 0.000000 318 1.235383 DP 0 249 0 0.000000 329 1.278117 DP 0 250 0 0.000000 204 0.792510 DP 0 251 0 0.000000 84 0.326328 DP 0 252 0 0.000000 61 0.236976 DP 0 253 0 0.000000 53 0.205897 DP 0 254 0 0.000000 40 0.155394 DP 0 255 0 0.000000 24 0.093236 DP 0 256 0 0.000000 26 0.101006 DP 0 257 0 0.000000 29 0.112661 DP 0 258 0 0.000000 13 0.050503 DP 0 259 0 0.000000 21 0.081582 DP 0 260 0 0.000000 12 0.046618 DP 0 261 0 0.000000 11 0.042733 DP 0 262 0 0.000000 15 0.058273 DP 0 263 0 0.000000 7 0.027194 DP 0 264 0 0.000000 1 0.003885 DP 0 265 0 0.000000 4 0.015539 DP 0 267 0 0.000000 2 0.007770 DP 0 268 0 0.000000 1 0.003885 DP 0 269 0 0.000000 1 0.003885 DP 0 270 0 0.000000 1 0.003885 DP 0 271 0 0.000000 1 0.003885 DP 0 272 0 0.000000 1 0.003885 DP 0 275 0 0.000000 1 0.003885 DP 0 280 0 0.000000 1 0.003885 DP 0 286 0 0.000000 1 0.003885