breseq version 0.35.7 revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
read file | reads | bases | passed filters | average | longest | mapped | |
---|---|---|---|---|---|---|---|
errors | SRR2584534_1 | 1,720,420 | 173,762,420 | 100.0% | 101.0 bases | 101 bases | 84.8% |
errors | SRR2584534_2 | 1,720,414 | 173,761,814 | 100.0% | 101.0 bases | 101 bases | 84.2% |
total | 3,440,834 | 347,524,234 | 100.0% | 101.0 bases | 101 bases | 84.5% |
seq id | length | fit mean | fit dispersion | % mapped reads | description | ||
---|---|---|---|---|---|---|---|
coverage | distribution | 1 | 108,051 | 63.4 | 2.8 | 2.5% | na |
coverage | distribution | 2 | 103,027 | 63.4 | 2.8 | 2.1% | na |
coverage | distribution | 3 | 80,514 | 63.4 | 2.8 | 1.8% | na |
coverage | distribution | 4 | 78,067 | 63.4 | 2.8 | 1.6% | na |
coverage | distribution | 5 | 64,881 | 63.4 | 2.8 | 1.6% | na |
coverage | distribution | 6 | 60,364 | 63.4 | 2.8 | 1.3% | na |
coverage | distribution | 7 | 59,421 | 63.4 | 2.8 | 1.2% | na |
coverage | distribution | 8 | 56,436 | 63.4 | 2.8 | 1.1% | na |
coverage | distribution | 9 | 56,279 | 63.4 | 2.8 | 1.4% | na |
coverage | distribution | 10 | 54,363 | 63.4 | 2.8 | 1.3% | na |
coverage | distribution | 11 | 54,219 | 63.4 | 2.8 | 1.2% | na |
coverage | distribution | 12 | 53,253 | 63.4 | 2.8 | 1.2% | na |
coverage | distribution | 13 | 52,198 | 63.4 | 2.8 | 1.4% | na |
coverage | distribution | 14 | 52,173 | 63.4 | 2.8 | 1.4% | na |
coverage | distribution | 15 | 49,040 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 16 | 47,700 | 63.4 | 2.8 | 1.2% | na |
coverage | distribution | 17 | 46,866 | 63.4 | 2.8 | 1.1% | na |
coverage | distribution | 18 | 44,693 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 19 | 43,912 | 63.4 | 2.8 | 1.0% | na |
coverage | distribution | 20 | 43,865 | 63.4 | 2.8 | 1.0% | na |
coverage | distribution | 21 | 41,893 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 22 | 41,696 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 23 | 41,186 | 63.4 | 2.8 | 1.0% | na |
coverage | distribution | 24 | 40,740 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 25 | 39,931 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 26 | 39,746 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 27 | 39,041 | 63.4 | 2.8 | 1.0% | na |
coverage | distribution | 28 | 36,827 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 29 | 35,867 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 30 | 35,266 | 63.4 | 2.8 | 1.2% | na |
coverage | distribution | 31 | 34,016 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 32 | 33,900 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 33 | 33,871 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 34 | 33,761 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 35 | 33,599 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 36 | 33,227 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 37 | 32,985 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 38 | 32,819 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 39 | 32,802 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 40 | 32,569 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 41 | 32,291 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 42 | 32,020 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 43 | 31,196 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 44 | 31,078 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 45 | 30,869 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 46 | 30,710 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 47 | 30,112 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 48 | 29,957 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 49 | 29,908 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 50 | 29,744 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 51 | 29,294 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 52 | 29,257 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 53 | 29,077 | 63.4 | 2.8 | 0.7% | na |
coverage | distribution | 54 | 28,773 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 55 | 27,005 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 56 | 26,090 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 57 | 26,063 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 58 | 26,029 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 59 | 25,090 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 60 | 24,693 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 61 | 24,668 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 62 | 24,568 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 63 | 24,466 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 64 | 23,955 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 65 | 23,905 | 63.4 | 2.8 | 0.9% | na |
coverage | distribution | 66 | 23,726 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 67 | 23,717 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 68 | 23,344 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 69 | 23,343 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 70 | 22,849 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 71 | 22,716 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 72 | 22,438 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 73 | 22,246 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 74 | 22,019 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 75 | 21,857 | 63.4 | 2.8 | 0.6% | na |
coverage | distribution | 76 | 21,559 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 77 | 21,347 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 78 | 21,310 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 79 | 21,233 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 80 | 21,134 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 81 | 20,057 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 82 | 19,979 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 83 | 19,766 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 84 | 19,746 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 85 | 19,737 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 86 | 19,585 | 63.4 | 2.8 | 0.5% | na |
coverage | distribution | 87 | 19,524 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 88 | 19,252 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 89 | 18,552 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 90 | 18,370 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 91 | 18,160 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 92 | 17,887 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 93 | 17,731 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 94 | 17,606 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 95 | 17,232 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 96 | 17,144 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 97 | 17,078 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 98 | 17,037 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 99 | 16,584 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 100 | 16,396 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 101 | 16,326 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 102 | 16,281 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 103 | 16,246 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 104 | 16,231 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 105 | 15,857 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 106 | 15,781 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 107 | 15,491 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 108 | 15,407 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 109 | 15,277 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 110 | 15,236 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 111 | 14,721 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 112 | 14,615 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 113 | 14,540 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 114 | 14,464 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 115 | 14,429 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 116 | 14,374 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 117 | 14,361 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 118 | 14,204 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 119 | 14,156 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 120 | 14,144 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 121 | 14,106 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 122 | 14,076 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 123 | 14,064 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 124 | 13,852 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 125 | 13,803 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 126 | 13,694 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 127 | 13,634 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 128 | 13,426 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 129 | 13,398 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 130 | 13,205 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 131 | 13,095 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 132 | 13,049 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 133 | 13,039 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 134 | 12,836 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 135 | 12,670 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 136 | 12,424 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 137 | 12,181 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 138 | 11,857 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 139 | 11,822 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 140 | 11,485 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 141 | 11,390 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 142 | 11,221 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 143 | 10,889 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 144 | 10,516 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 145 | 10,378 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 146 | 10,176 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 147 | 9,954 | 63.4 | 2.8 | 0.3% | na |
coverage | distribution | 148 | 9,904 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 149 | 9,895 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 150 | 9,892 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 151 | 9,732 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 152 | 9,680 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 153 | 9,642 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 154 | 9,582 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 155 | 9,554 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 156 | 9,528 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 157 | 9,373 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 158 | 9,359 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 159 | 8,925 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 160 | 8,899 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 161 | 8,872 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 162 | 8,767 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 163 | 8,564 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 164 | 8,502 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 165 | 8,501 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 166 | 8,398 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 167 | 8,289 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 168 | 8,158 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 169 | 7,848 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 170 | 7,767 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 171 | 7,707 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 172 | 7,705 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 173 | 7,637 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 174 | 7,466 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 175 | 7,365 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 176 | 7,365 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 177 | 7,332 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 178 | 7,327 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 179 | 7,204 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 180 | 7,195 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 181 | 6,978 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 182 | 6,967 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 183 | 6,872 | 63.4 | 2.8 | 0.8% | na |
coverage | distribution | 184 | 6,777 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 185 | 6,771 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 186 | 6,614 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 187 | 6,592 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 188 | 6,383 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 189 | 6,363 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 190 | 6,342 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 191 | 5,864 | 63.4 | 2.8 | 0.2% | na |
coverage | distribution | 192 | 5,790 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 193 | 5,681 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 194 | 5,424 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 195 | 5,423 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 196 | 5,276 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 197 | 5,170 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 198 | 5,050 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 199 | 4,737 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 200 | 4,567 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 201 | 4,520 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 202 | 4,399 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 203 | 4,306 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 204 | 4,218 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 205 | 4,123 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 206 | 4,098 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 207 | 3,729 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 208 | 3,676 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 209 | 3,401 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 210 | 2,923 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 211 | 2,719 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 212 | 2,487 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 213 | 2,456 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 214 | 2,433 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 215 | 2,341 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 216 | 2,311 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 217 | 2,224 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 218 | 1,999 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 219 | 1,818 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 220 | 1,766 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 221 | 1,707 | 63.4 | 2.8 | 0.1% | na |
coverage | distribution | 222 | 1,443 | 63.4 | 2.8 | 1.4% | na |
coverage | distribution | 223 | 698 | 63.4 | 2.8 | 0.4% | na |
coverage | distribution | 224 | 660 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 225 | 280 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 226 | 238 | 63.4 | 2.8 | 0.0% | na |
coverage | distribution | 227 | 188 | 63.4 | 2.8 | 0.0% | na |
total | 4,445,260 | 100.0% |
fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.
option | limit | actual |
---|---|---|
Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 74515 |
Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 6 |
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 2138 |
Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.097 |
reference sequence | pr(no read start) |
---|---|
1 | 0.73330 |
2 | 0.75810 |
3 | 0.74584 |
4 | 0.76181 |
5 | 0.74036 |
6 | 0.74884 |
7 | 0.76948 |
8 | 0.76301 |
9 | 0.72594 |
10 | 0.73065 |
11 | 0.74848 |
12 | 0.73429 |
13 | 0.70725 |
14 | 0.69580 |
15 | 0.86710 |
16 | 0.72434 |
17 | 0.72814 |
18 | 0.75922 |
19 | 0.74650 |
20 | 0.73113 |
21 | 0.73937 |
22 | 0.75879 |
23 | 0.71522 |
24 | 0.80054 |
25 | 0.77367 |
26 | 0.73297 |
27 | 0.72370 |
28 | 0.73483 |
29 | 0.70651 |
30 | 0.63373 |
31 | 0.72603 |
32 | 0.72094 |
33 | 0.75680 |
34 | 0.71058 |
35 | 0.73688 |
36 | 0.72440 |
37 | 0.76558 |
38 | 0.75782 |
39 | 0.77492 |
40 | 0.74229 |
41 | 0.72734 |
42 | 0.70003 |
43 | 0.75442 |
44 | 0.72472 |
45 | 0.70236 |
46 | 0.76472 |
47 | 0.71757 |
48 | 0.75268 |
49 | 0.74360 |
50 | 0.71702 |
51 | 0.85811 |
52 | 0.75884 |
53 | 0.73078 |
54 | 0.75479 |
55 | 0.74151 |
56 | 0.76941 |
57 | 0.76399 |
58 | 0.72440 |
59 | 0.77770 |
60 | 0.76096 |
61 | 0.71727 |
62 | 0.71732 |
63 | 0.76183 |
64 | 0.74521 |
65 | 0.62945 |
66 | 0.76414 |
67 | 0.73705 |
68 | 0.75932 |
69 | 0.78647 |
70 | 0.74977 |
71 | 0.74342 |
72 | 0.75381 |
73 | 0.71772 |
74 | 0.76230 |
75 | 0.71128 |
76 | 0.75215 |
77 | 0.76732 |
78 | 0.72755 |
79 | 0.73098 |
80 | 0.77707 |
81 | 0.73997 |
82 | 0.87126 |
83 | 0.98621 |
84 | 0.75750 |
85 | 0.74054 |
86 | 0.73541 |
87 | 0.76478 |
88 | 0.74374 |
89 | 0.76299 |
90 | 0.75659 |
91 | 0.75146 |
92 | 0.98935 |
93 | 0.76310 |
94 | 0.73075 |
95 | 0.73369 |
96 | 0.77024 |
97 | 0.75146 |
98 | 0.74649 |
99 | 0.77713 |
100 | 0.76113 |
101 | 0.76305 |
102 | 0.76098 |
103 | 0.79170 |
104 | 0.75359 |
105 | 0.74532 |
106 | 0.77061 |
107 | 0.70218 |
108 | 0.70218 |
109 | 0.75741 |
110 | 0.72050 |
111 | 0.73382 |
112 | 0.74359 |
113 | 0.76974 |
114 | 0.70727 |
115 | 0.73501 |
116 | 0.72546 |
117 | 0.77686 |
118 | 0.73764 |
119 | 0.77098 |
120 | 0.70662 |
121 | 0.75872 |
122 | 0.76701 |
123 | 0.76280 |
124 | 0.74708 |
125 | 0.70003 |
126 | 0.73295 |
127 | 0.73225 |
128 | 0.72363 |
129 | 0.76015 |
130 | 0.99826 |
131 | 0.72073 |
132 | 0.73347 |
133 | 0.71731 |
134 | 0.73232 |
135 | 0.70367 |
136 | 0.76578 |
137 | 0.71361 |
138 | 0.72345 |
139 | 0.77491 |
140 | 0.75603 |
141 | 0.73464 |
142 | 0.76709 |
143 | 0.75875 |
144 | 0.76850 |
145 | 0.74860 |
146 | 0.74671 |
147 | 0.70449 |
148 | 0.73889 |
149 | 0.75836 |
150 | 0.75708 |
151 | 0.74255 |
152 | 0.74690 |
153 | 0.74761 |
154 | 0.74468 |
155 | 0.77292 |
156 | 0.76789 |
157 | 0.73056 |
158 | 0.72321 |
159 | 0.77350 |
160 | 0.77587 |
161 | 0.73259 |
162 | 0.75471 |
163 | 0.76045 |
164 | 0.99065 |
165 | 0.77150 |
166 | 0.72017 |
167 | 0.92309 |
168 | 0.75956 |
169 | 0.99694 |
170 | 0.75969 |
171 | 0.73427 |
172 | 0.74692 |
173 | 0.76823 |
174 | 0.77203 |
175 | 0.75580 |
176 | 0.75336 |
177 | 0.76637 |
178 | 0.81957 |
179 | 0.73105 |
180 | 0.76810 |
181 | 0.71303 |
182 | 0.74315 |
183 | 0.43997 |
184 | 0.72731 |
185 | 0.74310 |
186 | 0.69308 |
187 | 0.74393 |
188 | 0.79665 |
189 | 0.77424 |
190 | 0.75859 |
191 | 0.70891 |
192 | 0.75725 |
193 | 0.98733 |
194 | 0.74723 |
195 | 0.77264 |
196 | 0.79113 |
197 | 0.74458 |
198 | 0.74277 |
199 | 0.71332 |
200 | 0.80053 |
201 | 0.71084 |
202 | 0.75926 |
203 | 0.79587 |
204 | 0.72807 |
205 | 0.74169 |
206 | 0.70766 |
207 | 0.78426 |
208 | 0.99646 |
209 | 0.76345 |
210 | 0.77335 |
211 | 0.68408 |
212 | 0.74306 |
213 | 0.69951 |
214 | 0.99671 |
215 | 0.76036 |
216 | 0.70532 |
217 | 0.99505 |
218 | 0.77414 |
219 | 0.19939 |
220 | 0.74632 |
221 | 0.61306 |
222 | 0.06895 |
223 | 0.14685 |
224 | 0.80303 |
225 | 0.48036 |
226 | 0.78782 |
227 | 0.57979 |
pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.
option | value |
---|---|
Coverage evenness (position-hash) score of predicted junctions must be | ≥ 3 |
Minimum probablilty assigned that no mapped read will start at a given position and strand for junction prediction | 0.1 |
Junction allow suboptimal matches | FALSE |
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be | ≤ 3 |
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction | ≥ 1 |
option | value |
---|---|
Mode | Consensus/Mixed Base |
Ploidy | 1 (haploid) |
Consensus mutation E-value cutoff | 10 |
Consensus frequency cutoff | 0.8 |
Consensus minimum variant coverage each strand | OFF |
Consensus minimum total coverage each strand | OFF |
Consensus minimum variant coverage | OFF |
Consensus minimum total coverage | OFF |
Polymorphism E-value cutoff | 10 |
Polymorphism frequency cutoff | 0.2 |
Polymorphism minimum variant coverage each strand | OFF |
Polymorphism minimum total coverage each strand | OFF |
Polymorphism minimum variant coverage | OFF |
Polymorphism minimum total coverage | OFF |
Polymorphism bias cutoff | OFF |
Predict indel polymorphisms | YES |
Skip indel polymorphisms in homopolymers runs of | OFF |
Skip base substitutions when they create a homopolymer flanked on each side by | OFF |
program | version |
---|---|
bowtie2 | 2.3.4.1 |
R | 4.0.0 |
step | start | end | elapsed |
---|---|---|---|
Read and reference sequence file input | 10:34:00 20 Jul 2021 | 10:35:56 20 Jul 2021 | 1 minute 56 seconds |
Read alignment to reference genome | 10:35:56 20 Jul 2021 | 10:38:26 20 Jul 2021 | 2 minutes 30 seconds |
Preprocessing alignments for candidate junction identification | 10:38:26 20 Jul 2021 | 10:39:54 20 Jul 2021 | 1 minute 28 seconds |
Preliminary analysis of coverage distribution | 10:39:54 20 Jul 2021 | 10:41:07 20 Jul 2021 | 1 minute 13 seconds |
Identifying junction candidates | 10:41:07 20 Jul 2021 | 10:49:38 20 Jul 2021 | 8 minutes 31 seconds |
Re-alignment to junction candidates | 10:49:38 20 Jul 2021 | 10:50:03 20 Jul 2021 | 25 seconds |
Resolving best read alignments | 10:50:03 20 Jul 2021 | 10:51:55 20 Jul 2021 | 1 minute 52 seconds |
Creating BAM files | 10:51:55 20 Jul 2021 | 10:52:49 20 Jul 2021 | 54 seconds |
Tabulating error counts | 10:52:49 20 Jul 2021 | 10:53:14 20 Jul 2021 | 25 seconds |
Re-calibrating base error rates | 10:53:14 20 Jul 2021 | 10:53:15 20 Jul 2021 | 1 second |
Examining read alignment evidence | 10:53:15 20 Jul 2021 | 10:56:04 20 Jul 2021 | 2 minutes 49 seconds |
Polymorphism statistics | 10:56:04 20 Jul 2021 | 10:56:06 20 Jul 2021 | 2 seconds |
Output | 10:56:06 20 Jul 2021 | 10:57:49 20 Jul 2021 | 1 minute 43 seconds |
Output :: Mutation Prediction | 10:56:06 20 Jul 2021 | 10:56:13 20 Jul 2021 | 7 seconds |
Output :: Mutation Annotation | 10:56:13 20 Jul 2021 | 10:56:13 20 Jul 2021 | 0 seconds |
Total | 23 minutes 56 seconds |