mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.38.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| read file | reads | bases | passed filters | average | longest | mapped | |
|---|---|---|---|---|---|---|---|
| errors | Unknown_CH607-002R0002_good_1.fq | 3,838,090 | 572,159,134 | 100.0% | 149.1 bases | 150 bases | 96.8% |
| total | 3,838,090 | 572,159,134 | 100.0% | 149.1 bases | 150 bases | 96.8% |
| seq id | length | fit mean | fit relative_variance | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | Xen14_1 | 242,556 | 67.4 | 2.5 | 3.1% | na |
| coverage | distribution | Xen14_2 | 185,210 | 63.7 | 2.3 | 2.1% | na |
| coverage | distribution | Xen14_3 | 166,311 | 133.8 | 3.0 | 4.0% | na |
| coverage | distribution | Xen14_4 | 151,524 | 90.4 | 2.7 | 2.5% | na |
| coverage | distribution | Xen14_5 | 149,062 | 95.5 | 2.9 | 2.6% | na |
| coverage | distribution | Xen14_6 | 146,760 | 117.0 | 3.4 | 3.1% | na |
| coverage | distribution | Xen14_7 | 136,514 | 71.5 | 2.6 | 1.8% | na |
| coverage | distribution | Xen14_8 | 132,518 | 147.3 | 3.7 | 3.5% | na |
| coverage | distribution | Xen14_9 | 129,936 | 148.6 | 3.7 | 3.5% | na |
| coverage | distribution | Xen14_10 | 107,217 | 160.3 | 3.2 | 3.2% | na |
| coverage | distribution | Xen14_11 | 106,943 | 113.2 | 2.7 | 2.2% | na |
| coverage | distribution | Xen14_12 | 100,898 | 75.6 | 2.6 | 1.4% | na |
| coverage | distribution | Xen14_13 | 98,318 | 86.4 | 2.5 | 1.5% | na |
| coverage | distribution | Xen14_14 | 89,144 | 165.2 | 3.5 | 2.7% | na |
| coverage | distribution | Xen14_15 | 83,869 | 58.7 | 2.5 | 0.9% | na |
| coverage | distribution | Xen14_16 | 81,941 | 100.9 | 3.0 | 1.5% | na |
| coverage | distribution | Xen14_17 | 80,390 | 159.2 | 4.0 | 2.4% | na |
| coverage | distribution | Xen14_18 | 78,780 | 131.8 | 3.5 | 1.9% | na |
| coverage | distribution | Xen14_19 | 77,008 | 137.6 | 3.5 | 1.9% | na |
| coverage | distribution | Xen14_20 | 75,563 | 79.9 | 2.4 | 1.2% | na |
| coverage | distribution | Xen14_21 | 74,837 | 60.6 | 2.2 | 0.8% | na |
| coverage | distribution | Xen14_22 | 74,457 | 164.4 | 3.7 | 2.2% | na |
| coverage | distribution | Xen14_23 | 73,975 | 110.4 | 2.9 | 1.5% | na |
| coverage | distribution | Xen14_24 | 73,668 | 84.3 | 2.5 | 1.1% | na |
| coverage | distribution | Xen14_25 | 73,240 | 56.7 | 2.7 | 0.8% | na |
| coverage | distribution | Xen14_26 | 73,210 | 136.7 | 3.1 | 1.8% | na |
| coverage | distribution | Xen14_27 | 71,260 | 84.7 | 3.3 | 1.2% | na |
| coverage | distribution | Xen14_28 | 64,054 | 58.6 | 2.1 | 0.7% | na |
| coverage | distribution | Xen14_29 | 62,123 | 54.8 | 2.3 | 0.6% | na |
| coverage | distribution | Xen14_30 | 61,661 | 87.2 | 2.4 | 1.0% | na |
| coverage | distribution | Xen14_31 | 58,819 | 176.4 | 4.3 | 1.9% | na |
| coverage | distribution | Xen14_32 | 55,391 | 56.8 | 2.3 | 0.6% | na |
| coverage | distribution | Xen14_33 | 53,241 | 78.7 | 2.4 | 0.8% | na |
| coverage | distribution | Xen14_34 | 53,084 | 125.5 | 3.4 | 1.2% | na |
| coverage | distribution | Xen14_35 | 52,845 | 154.3 | 4.0 | 1.5% | na |
| coverage | distribution | Xen14_36 | 51,934 | 107.0 | 2.8 | 1.0% | na |
| coverage | distribution | Xen14_37 | 51,424 | 88.1 | 2.7 | 0.8% | na |
| coverage | distribution | Xen14_38 | 48,836 | 98.0 | 3.3 | 1.0% | na |
| coverage | distribution | Xen14_39 | 48,485 | 69.6 | 4.3 | 0.6% | na |
| coverage | distribution | Xen14_40 | 46,791 | 54.7 | 2.4 | 0.5% | na |
| coverage | distribution | Xen14_41 | 41,431 | 100.4 | 3.1 | 0.7% | na |
| coverage | distribution | Xen14_42 | 41,403 | 152.3 | 4.0 | 1.2% | na |
| coverage | distribution | Xen14_43 | 41,296 | 89.1 | 3.4 | 0.7% | na |
| coverage | distribution | Xen14_44 | 40,957 | 120.0 | 3.1 | 0.9% | na |
| coverage | distribution | Xen14_45 | 40,401 | 155.8 | 3.2 | 1.1% | na |
| coverage | distribution | Xen14_46 | 40,351 | 101.7 | 2.4 | 0.7% | na |
| coverage | distribution | Xen14_47 | 36,274 | 141.5 | 3.2 | 0.9% | na |
| coverage | distribution | Xen14_48 | 34,806 | 139.1 | 3.2 | 0.9% | na |
| coverage | distribution | Xen14_49 | 34,102 | 151.7 | 2.9 | 0.9% | na |
| coverage | distribution | Xen14_50 | 33,369 | 113.7 | 2.5 | 0.7% | na |
| coverage | distribution | Xen14_51 | 32,311 | 159.6 | 3.9 | 0.9% | na |
| coverage | distribution | Xen14_52 | 31,365 | 136.7 | 4.0 | 0.8% | na |
| coverage | distribution | Xen14_53 | 30,293 | 145.2 | 3.1 | 0.8% | na |
| coverage | distribution | Xen14_54 | 28,579 | 163.1 | 5.1 | 0.8% | na |
| coverage | distribution | Xen14_55 | 26,715 | 87.3 | 2.8 | 0.4% | na |
| coverage | distribution | Xen14_56 | 26,428 | 144.5 | 2.9 | 0.7% | na |
| coverage | distribution | Xen14_57 | 26,242 | 81.1 | 2.7 | 0.4% | na |
| coverage | distribution | Xen14_58 | 24,572 | 130.6 | 3.3 | 0.6% | na |
| coverage | distribution | Xen14_59 | 24,177 | 105.6 | 3.2 | 0.5% | na |
| coverage | distribution | Xen14_60 | 23,187 | 78.3 | 2.2 | 0.3% | na |
| coverage | distribution | Xen14_61 | 21,383 | 117.8 | 3.0 | 0.5% | na |
| coverage | distribution | Xen14_62 | 20,210 | 59.7 | 1.9 | 0.2% | na |
| coverage | distribution | Xen14_63 | 19,884 | 100.6 | 2.4 | 0.4% | na |
| coverage | distribution | Xen14_64 | 18,269 | 62.2 | 2.5 | 0.2% | na |
| coverage | distribution | Xen14_65 | 17,856 | 80.1 | 2.3 | 0.3% | na |
| coverage | distribution | Xen14_66 | 17,785 | 107.5 | 2.9 | 0.3% | na |
| coverage | distribution | Xen14_67 | 17,704 | 91.6 | 2.3 | 0.3% | na |
| coverage | distribution | Xen14_68 | 16,382 | 162.2 | 3.2 | 0.5% | na |
| coverage | distribution | Xen14_69 | 14,625 | 97.8 | 4.5 | 0.3% | na |
| coverage | distribution | Xen14_70 | 14,402 | 54.3 | 1.8 | 0.1% | na |
| coverage | distribution | Xen14_71 | 14,304 | 84.6 | 4.8 | 0.2% | na |
| coverage | distribution | Xen14_72 | 13,687 | 116.8 | 3.6 | 0.3% | na |
| coverage | distribution | Xen14_73 | 13,160 | 131.7 | 4.2 | 0.3% | na |
| coverage | distribution | Xen14_74 | 13,069 | 171.4 | 3.9 | 0.4% | na |
| coverage | distribution | Xen14_75 | 13,052 | 94.0 | 2.6 | 0.2% | na |
| coverage | distribution | Xen14_76 | 12,931 | 98.9 | 2.1 | 0.2% | na |
| coverage | distribution | Xen14_77 | 12,669 | 88.2 | 3.0 | 0.2% | na |
| coverage | distribution | Xen14_78 | 12,559 | 175.3 | 3.5 | 0.4% | na |
| coverage | distribution | Xen14_79 | 12,553 | 134.7 | 2.4 | 0.3% | na |
| coverage | distribution | Xen14_80 | 12,035 | 129.0 | 4.2 | 0.3% | na |
| coverage | distribution | Xen14_81 | 12,020 | 81.2 | 3.2 | 0.2% | na |
| coverage | distribution | Xen14_82 | 11,983 | 100.3 | 2.6 | 0.2% | na |
| coverage | distribution | Xen14_83 | 11,356 | 96.9 | 4.2 | 0.2% | na |
| coverage | distribution | Xen14_84 | 11,356 | 71.6 | 3.9 | 0.2% | na |
| coverage | distribution | Xen14_85 | 11,197 | 125.2 | 2.7 | 0.3% | na |
| coverage | distribution | Xen14_86 | 10,953 | 83.3 | 2.5 | 0.2% | na |
| coverage | distribution | Xen14_87 | 10,348 | 227.5 | 4.0 | 0.4% | na |
| coverage | distribution | Xen14_88 | 10,259 | 67.8 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_89 | 10,105 | 136.3 | 3.4 | 0.3% | na |
| coverage | distribution | Xen14_90 | 9,218 | 113.8 | 2.2 | 0.2% | na |
| coverage | distribution | Xen14_91 | 8,913 | 91.4 | 3.9 | 0.1% | na |
| coverage | distribution | Xen14_92 | 8,232 | 63.2 | 2.3 | 0.1% | na |
| coverage | distribution | Xen14_93 | 7,777 | 64.8 | 2.2 | 0.1% | na |
| coverage | distribution | Xen14_94 | 7,584 | 62.1 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_95 | 7,342 | 60.5 | 2.2 | 0.1% | na |
| coverage | distribution | Xen14_96 | 6,916 | 71.1 | 2.4 | 0.1% | na |
| coverage | distribution | Xen14_97 | 6,746 | 158.6 | 4.1 | 0.2% | na |
| coverage | distribution | Xen14_98 | 6,594 | 143.1 | 2.3 | 0.2% | na |
| coverage | distribution | Xen14_99 | 6,045 | 67.1 | 1.7 | 0.1% | na |
| coverage | distribution | Xen14_100 | 5,846 | 129.3 | 3.0 | 0.1% | na |
| coverage | distribution | Xen14_101 | 5,615 | 910.1 | 38.0 | 0.9% | na |
| coverage | distribution | Xen14_102 | 5,552 | 59.3 | 3.4 | 0.1% | na |
| coverage | distribution | Xen14_103 | 5,307 | 75.8 | 2.6 | 0.1% | na |
| coverage | distribution | Xen14_104 | 5,096 | 104.4 | 3.3 | 0.1% | na |
| coverage | distribution | Xen14_105 | 5,061 | 93.1 | 1.0 | 0.1% | na |
| coverage | distribution | Xen14_106 | 4,995 | 97.1 | 2.1 | 0.1% | na |
| coverage | distribution | Xen14_107 | 4,932 | 65.7 | 1.5 | 0.1% | na |
| coverage | distribution | Xen14_108 | 4,816 | 93.0 | 2.5 | 0.1% | na |
| coverage | distribution | Xen14_109 | 4,616 | 89.7 | 3.6 | 0.1% | na |
| coverage | distribution | Xen14_110 | 4,578 | 49.5 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_111 | 4,562 | 729.4 | 19.4 | 0.6% | na |
| coverage | distribution | Xen14_112 | 4,486 | 81.0 | 3.7 | 0.1% | na |
| coverage | distribution | Xen14_113 | 4,275 | 160.5 | 4.0 | 0.1% | na |
| coverage | distribution | Xen14_114 | 4,039 | 61.6 | 3.9 | 0.0% | na |
| coverage | distribution | Xen14_115 | 3,633 | 128.8 | 3.3 | 0.1% | na |
| coverage | distribution | Xen14_116 | 3,428 | 131.9 | 2.6 | 0.1% | na |
| coverage | distribution | Xen14_117 | 3,427 | 79.8 | 2.6 | 0.0% | na |
| coverage | distribution | Xen14_118 | 3,355 | 59.8 | 2.7 | 0.0% | na |
| coverage | distribution | Xen14_119 | 3,208 | 90.6 | 2.9 | 0.0% | na |
| coverage | distribution | Xen14_120 | 3,123 | 54.0 | 3.2 | 0.0% | na |
| coverage | distribution | Xen14_121 | 3,076 | 86.3 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_122 | 2,908 | 106.8 | 4.2 | 0.1% | na |
| coverage | distribution | Xen14_123 | 2,714 | 1019.8 | 7.3 | 0.5% | na |
| coverage | distribution | Xen14_124 | 2,576 | 127.1 | 4.9 | 0.1% | na |
| coverage | distribution | Xen14_125 | 2,519 | 129.1 | 2.1 | 0.1% | na |
| coverage | distribution | Xen14_126 | 2,515 | 125.7 | 3.1 | 0.1% | na |
| coverage | distribution | Xen14_127 | 2,166 | 1058.0 | 14.0 | 0.4% | na |
| coverage | distribution | Xen14_128 | 2,143 | 80.9 | 2.8 | 0.0% | na |
| coverage | distribution | Xen14_129 | 2,049 | 125.6 | 3.8 | 0.0% | na |
| coverage | distribution | Xen14_130 | 2,000 | 119.2 | 4.9 | 0.0% | na |
| coverage | distribution | Xen14_131 | 1,922 | 51.0 | 2.4 | 0.0% | na |
| coverage | distribution | Xen14_132 | 1,806 | 135.9 | 4.2 | 0.1% | na |
| coverage | distribution | Xen14_133 | 1,721 | 246.7 | 5.0 | 0.1% | na |
| coverage | distribution | Xen14_134 | 1,657 | 92.0 | 5.1 | 0.0% | na |
| coverage | distribution | Xen14_135 | 1,633 | 150.6 | 2.3 | 0.0% | na |
| coverage | distribution | Xen14_136 | 1,567 | 121.5 | 2.3 | 0.0% | na |
| coverage | distribution | Xen14_137 | 1,544 | 217.8 | 2.2 | 0.1% | na |
| coverage | distribution | Xen14_138 | 1,361 | 119.8 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_139 | 1,349 | 153.6 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_140 | 1,298 | 947.3 | 8.3 | 0.2% | na |
| coverage | distribution | Xen14_141 | 1,292 | 2027.6 | 46.7 | 0.4% | na |
| coverage | distribution | Xen14_142 | 1,281 | 57.0 | 2.8 | 0.0% | na |
| coverage | distribution | Xen14_143 | 1,107 | 1196.4 | 3.8 | 0.1% | na |
| coverage | distribution | Xen14_144 | 1,091 | 692.0 | 11.7 | 0.1% | na |
| coverage | distribution | Xen14_145 | 1,062 | 696.9 | 2.3 | 0.1% | na |
| coverage | distribution | Xen14_146 | 1,046 | 113.6 | 2.2 | 0.0% | na |
| coverage | distribution | Xen14_147 | 1,007 | 187.7 | 2.5 | 0.0% | na |
| coverage | distribution | Xen14_148 | 989 | 48.0 | 2.1 | 0.0% | na |
| coverage | distribution | Xen14_149 | 980 | 112.5 | 1.5 | 0.0% | na |
| coverage | distribution | Xen14_150 | 945 | 158.3 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_151 | 938 | 163.9 | 1.4 | 0.0% | na |
| coverage | distribution | Xen14_152 | 934 | 128.6 | 23.6 | 0.0% | na |
| coverage | distribution | Xen14_153 | 929 | 2756.3 | 134.8 | 0.4% | na |
| coverage | distribution | Xen14_154 | 920 | 218.5 | 1.1 | 0.0% | na |
| coverage | distribution | Xen14_155 | 900 | 73.3 | 11.0 | 0.0% | na |
| coverage | distribution | Xen14_156 | 862 | 194.8 | 4.5 | 0.0% | na |
| coverage | distribution | Xen14_157 | 857 | 209.1 | 7.7 | 0.0% | na |
| coverage | distribution | Xen14_158 | 799 | 109.5 | 8.7 | 0.0% | na |
| coverage | distribution | Xen14_159 | 798 | 137.8 | 6.9 | 0.0% | na |
| coverage | distribution | Xen14_160 | 780 | 196.5 | 24.4 | 0.0% | na |
| coverage | distribution | Xen14_161 | 770 | 119.8 | 1.1 | 0.0% | na |
| coverage | distribution | Xen14_162 | 765 | 181.6 | 2.8 | 0.0% | na |
| coverage | distribution | Xen14_163 | 753 | 263.1 | 2.4 | 0.0% | na |
| coverage | distribution | Xen14_164 | 746 | 85.0 | 5.6 | 0.0% | na |
| coverage | distribution | Xen14_165 | 691 | 150.8 | 5.1 | 0.0% | na |
| coverage | distribution | Xen14_166 | 685 | 11009.8 | 7409.3 | 0.2% | na |
| coverage | distribution | Xen14_167 | 666 | 886.1 | 32.8 | 0.1% | na |
| coverage | distribution | Xen14_168 | 629 | 2900.8 | 395.3 | 0.1% | na |
| coverage | distribution | Xen14_169 | 626 | 197.9 | 2.0 | 0.0% | na |
| coverage | distribution | Xen14_170 | 619 | 100.6 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_171 | 569 | 133.6 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_172 | 569 | 40.1 | 1.3 | 0.0% | na |
| coverage | distribution | Xen14_173 | 564 | 200.3 | 8.4 | 0.0% | na |
| coverage | distribution | Xen14_174 | 564 | 130.6 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_175 | 560 | 99.3 | 1.3 | 0.0% | na |
| coverage | distribution | Xen14_176 | 552 | [163.7] | [28.7] | 0.0% | na |
| coverage | distribution | Xen14_177 | 549 | 173.6 | 11.9 | 0.0% | na |
| coverage | distribution | Xen14_178 | 541 | 123.7 | 9.3 | 0.0% | na |
| coverage | distribution | Xen14_179 | 536 | 146.4 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_180 | 526 | 99.1 | 2.2 | 0.0% | na |
| coverage | distribution | Xen14_181 | 511 | [140.8] | [23.1] | 0.0% | na |
| coverage | distribution | Xen14_182 | 478 | 167.6 | 12.4 | 0.0% | na |
| coverage | distribution | Xen14_183 | 477 | 136.7 | 3.6 | 0.0% | na |
| coverage | distribution | Xen14_184 | 473 | 1351.0 | 56.6 | 0.1% | na |
| coverage | distribution | Xen14_185 | 471 | [366.7] | [50.9] | 0.0% | na |
| coverage | distribution | Xen14_186 | 465 | 132.5 | 18.3 | 0.0% | na |
| coverage | distribution | Xen14_187 | 464 | 372.8 | 18.4 | 0.0% | na |
| coverage | distribution | Xen14_188 | 458 | [235.6] | [25.8] | 0.0% | na |
| coverage | distribution | Xen14_189 | 453 | 194.1 | 8.5 | 0.0% | na |
| coverage | distribution | Xen14_190 | 448 | 70.0 | 13.3 | 0.0% | na |
| coverage | distribution | Xen14_191 | 447 | [322.6] | [159.4] | 0.0% | na |
| coverage | distribution | Xen14_192 | 445 | 128.2 | 1.9 | 0.0% | na |
| coverage | distribution | Xen14_193 | 444 | 343.1 | 11.9 | 0.0% | na |
| coverage | distribution | Xen14_194 | 442 | 81.8 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_195 | 441 | 73.6 | 2.1 | 0.0% | na |
| coverage | distribution | Xen14_196 | 436 | 137.7 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_197 | 433 | 101.0 | 2.3 | 0.0% | na |
| coverage | distribution | Xen14_198 | 431 | 96.3 | 1.4 | 0.0% | na |
| coverage | distribution | Xen14_199 | 428 | 156.1 | 2.8 | 0.0% | na |
| coverage | distribution | Xen14_200 | 423 | 1099.0 | 29.5 | 0.1% | na |
| coverage | distribution | Xen14_201 | 421 | 436.0 | 137.7 | 0.0% | na |
| coverage | distribution | Xen14_202 | 421 | 1597.4 | 434.6 | 0.0% | na |
| coverage | distribution | Xen14_203 | 416 | 106.9 | 8.5 | 0.0% | na |
| coverage | distribution | Xen14_204 | 415 | [103.4] | [22.8] | 0.0% | na |
| coverage | distribution | Xen14_205 | 404 | 1004.2 | 35.7 | 0.0% | na |
| coverage | distribution | Xen14_206 | 403 | [945.6] | [106.5] | 0.1% | na |
| total | 4,963,538 | 100.0% |
fit relative_variance 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.
Fit failed Negative binomial fit failed for this reference sequence. It may have an unusual coverage depth distribution. JC and MC predictions may be less accurate.
| option | limit | actual |
|---|---|---|
| Number of alignment pairs examined for constructing junction candidates | ≤ 100000 | 76784 |
| Coverage evenness (position-hash) score of junction candidates | ≥ 2 | ≥ 2 |
| Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold | 100 ≤ n ≤ 5000 | 418 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.024 |
| reference sequence | pr(no read start) |
|---|---|
| Xen14_1 | 0.84506 |
| Xen14_2 | 0.85381 |
| Xen14_3 | 0.72748 |
| Xen14_4 | 0.80065 |
| Xen14_5 | 0.79186 |
| Xen14_6 | 0.75465 |
| Xen14_7 | 0.83775 |
| Xen14_8 | 0.70884 |
| Xen14_9 | 0.70581 |
| Xen14_10 | 0.68437 |
| Xen14_11 | 0.76254 |
| Xen14_12 | 0.82849 |
| Xen14_13 | 0.80917 |
| Xen14_14 | 0.68168 |
| Xen14_15 | 0.86365 |
| Xen14_16 | 0.78360 |
| Xen14_17 | 0.68570 |
| Xen14_18 | 0.72897 |
| Xen14_19 | 0.72437 |
| Xen14_20 | 0.82038 |
| Xen14_21 | 0.86050 |
| Xen14_22 | 0.68134 |
| Xen14_23 | 0.76644 |
| Xen14_24 | 0.81378 |
| Xen14_25 | 0.86917 |
| Xen14_26 | 0.72113 |
| Xen14_27 | 0.80708 |
| Xen14_28 | 0.86216 |
| Xen14_29 | 0.87292 |
| Xen14_30 | 0.80879 |
| Xen14_31 | 0.66912 |
| Xen14_32 | 0.86714 |
| Xen14_33 | 0.82435 |
| Xen14_34 | 0.74312 |
| Xen14_35 | 0.69656 |
| Xen14_36 | 0.77526 |
| Xen14_37 | 0.80677 |
| Xen14_38 | 0.78478 |
| Xen14_39 | 0.84079 |
| Xen14_40 | 0.87248 |
| Xen14_41 | 0.78718 |
| Xen14_42 | 0.69460 |
| Xen14_43 | 0.80585 |
| Xen14_44 | 0.75082 |
| Xen14_45 | 0.69393 |
| Xen14_46 | 0.78043 |
| Xen14_47 | 0.71897 |
| Xen14_48 | 0.71814 |
| Xen14_49 | 0.69745 |
| Xen14_50 | 0.75969 |
| Xen14_51 | 0.69226 |
| Xen14_52 | 0.72705 |
| Xen14_53 | 0.70544 |
| Xen14_54 | 0.68647 |
| Xen14_55 | 0.80502 |
| Xen14_56 | 0.71184 |
| Xen14_57 | 0.81832 |
| Xen14_58 | 0.73028 |
| Xen14_59 | 0.77106 |
| Xen14_60 | 0.82211 |
| Xen14_61 | 0.75642 |
| Xen14_62 | 0.85997 |
| Xen14_63 | 0.78108 |
| Xen14_64 | 0.85108 |
| Xen14_65 | 0.82185 |
| Xen14_66 | 0.77231 |
| Xen14_67 | 0.80437 |
| Xen14_68 | 0.68044 |
| Xen14_69 | 0.79135 |
| Xen14_70 | 0.87340 |
| Xen14_71 | 0.81708 |
| Xen14_72 | 0.75597 |
| Xen14_73 | 0.73970 |
| Xen14_74 | 0.67652 |
| Xen14_75 | 0.79842 |
| Xen14_76 | 0.78629 |
| Xen14_77 | 0.80488 |
| Xen14_78 | 0.66462 |
| Xen14_79 | 0.72763 |
| Xen14_80 | 0.73639 |
| Xen14_81 | 0.82899 |
| Xen14_82 | 0.78503 |
| Xen14_83 | 0.79372 |
| Xen14_84 | 0.83471 |
| Xen14_85 | 0.73230 |
| Xen14_86 | 0.80510 |
| Xen14_87 | 0.60084 |
| Xen14_88 | 0.83439 |
| Xen14_89 | 0.72241 |
| Xen14_90 | 0.76508 |
| Xen14_91 | 0.80809 |
| Xen14_92 | 0.85836 |
| Xen14_93 | 0.85631 |
| Xen14_94 | 0.85951 |
| Xen14_95 | 0.86414 |
| Xen14_96 | 0.77345 |
| Xen14_97 | 0.68255 |
| Xen14_98 | 0.70890 |
| Xen14_99 | 0.85054 |
| Xen14_100 | 0.74359 |
| Xen14_101 | 0.23393 |
| Xen14_102 | 0.86635 |
| Xen14_103 | 0.82900 |
| Xen14_104 | 0.79003 |
| Xen14_105 | 0.75598 |
| Xen14_106 | 0.79920 |
| Xen14_107 | 0.85148 |
| Xen14_108 | 0.79662 |
| Xen14_109 | 0.81161 |
| Xen14_110 | 0.88041 |
| Xen14_111 | 0.30173 |
| Xen14_112 | 0.81621 |
| Xen14_113 | 0.69626 |
| Xen14_114 | 0.85999 |
| Xen14_115 | 0.75062 |
| Xen14_116 | 0.74460 |
| Xen14_117 | 0.83149 |
| Xen14_118 | 0.86587 |
| Xen14_119 | 0.81016 |
| Xen14_120 | 0.87096 |
| Xen14_121 | 0.82152 |
| Xen14_122 | 0.77957 |
| Xen14_123 | 0.22476 |
| Xen14_124 | 0.75699 |
| Xen14_125 | 0.74931 |
| Xen14_126 | 0.70636 |
| Xen14_127 | 0.22922 |
| Xen14_128 | 0.83179 |
| Xen14_129 | 0.75939 |
| Xen14_130 | 0.77025 |
| Xen14_131 | 0.86157 |
| Xen14_132 | 0.68810 |
| Xen14_133 | 0.60895 |
| Xen14_134 | 0.80396 |
| Xen14_135 | 0.70667 |
| Xen14_136 | 0.77186 |
| Xen14_137 | 0.63245 |
| Xen14_138 | 0.77443 |
| Xen14_139 | 0.72313 |
| Xen14_140 | 0.28005 |
| Xen14_141 | 0.16602 |
| Xen14_142 | 0.86127 |
| Xen14_143 | 0.50469 |
| Xen14_144 | 0.37672 |
| Xen14_145 | 0.34934 |
| Xen14_146 | 0.78824 |
| Xen14_147 | 0.64548 |
| Xen14_148 | 0.88423 |
| Xen14_149 | 0.80000 |
| Xen14_150 | 0.74392 |
| Xen14_151 | 0.72388 |
| Xen14_152 | 0.81317 |
| Xen14_153 | 0.18030 |
| Xen14_154 | 0.68587 |
| Xen14_155 | 0.89111 |
| Xen14_156 | 0.70584 |
| Xen14_157 | 0.67678 |
| Xen14_158 | 0.81164 |
| Xen14_159 | 0.77130 |
| Xen14_160 | 0.75128 |
| Xen14_161 | 0.78442 |
| Xen14_162 | 0.73856 |
| Xen14_163 | 0.64011 |
| Xen14_164 | 0.84853 |
| Xen14_165 | 0.74891 |
| Xen14_166 | 0.41826 |
| Xen14_167 | 0.37162 |
| Xen14_168 | 0.29491 |
| Xen14_169 | 0.61994 |
| Xen14_170 | 0.81664 |
| Xen14_171 | 0.78032 |
| Xen14_172 | 0.91564 |
| Xen14_173 | 0.70922 |
| Xen14_174 | 0.78191 |
| Xen14_175 | 0.83393 |
| Xen14_176 | NA |
| Xen14_177 | 0.75137 |
| Xen14_178 | 0.80314 |
| Xen14_179 | 0.77892 |
| Xen14_180 | 0.83650 |
| Xen14_181 | NA |
| Xen14_182 | 0.76829 |
| Xen14_183 | 0.73009 |
| Xen14_184 | 0.39958 |
| Xen14_185 | NA |
| Xen14_186 | 0.83656 |
| Xen14_187 | 0.65409 |
| Xen14_188 | NA |
| Xen14_189 | 0.74172 |
| Xen14_190 | 0.87946 |
| Xen14_191 | NA |
| Xen14_192 | 0.81798 |
| Xen14_193 | 0.66216 |
| Xen14_194 | 0.86312 |
| Xen14_195 | 0.88869 |
| Xen14_196 | 0.85570 |
| Xen14_197 | 0.77835 |
| Xen14_198 | 0.84687 |
| Xen14_199 | 0.82092 |
| Xen14_200 | 0.20364 |
| Xen14_201 | 0.85273 |
| Xen14_202 | 0.55107 |
| Xen14_203 | 0.85457 |
| Xen14_204 | NA |
| Xen14_205 | 0.42946 |
| Xen14_206 | NA |
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 | s.2023.01/rocky8/x86_64/amd/zen3/software/Bowtie2/2.4.5-GCC-11.3.0/bin/bowtie2-align-s |
| R | 4.2.1 |
| step | start | end | elapsed |
|---|---|---|---|
| Read and reference sequence file input | 21:16:59 30 Oct 2024 | 21:18:59 30 Oct 2024 | 2 minutes 0 seconds |
| Read alignment to reference genome | 21:19:01 30 Oct 2024 | 21:20:54 30 Oct 2024 | 1 minute 53 seconds |
| Preprocessing alignments for candidate junction identification | 21:20:54 30 Oct 2024 | 21:21:37 30 Oct 2024 | 43 seconds |
| Preliminary analysis of coverage distribution | 21:21:38 30 Oct 2024 | 21:32:30 30 Oct 2024 | 10 minutes 52 seconds |
| Identifying junction candidates | 21:32:30 30 Oct 2024 | 21:33:16 30 Oct 2024 | 46 seconds |
| Re-alignment to junction candidates | 21:33:17 30 Oct 2024 | 21:33:52 30 Oct 2024 | 35 seconds |
| Resolving best read alignments | 21:33:52 30 Oct 2024 | 21:35:13 30 Oct 2024 | 1 minute 21 seconds |
| Creating BAM files | 21:35:13 30 Oct 2024 | 21:36:07 30 Oct 2024 | 54 seconds |
| Tabulating error counts | 21:36:07 30 Oct 2024 | 21:38:17 30 Oct 2024 | 2 minutes 10 seconds |
| Re-calibrating base error rates | 21:38:17 30 Oct 2024 | 21:43:08 30 Oct 2024 | 4 minutes 51 seconds |
| Examining read alignment evidence | 21:43:08 30 Oct 2024 | 21:51:14 30 Oct 2024 | 8 minutes 6 seconds |
| Polymorphism statistics | 21:51:14 30 Oct 2024 | 21:51:17 30 Oct 2024 | 3 seconds |
| Output | 21:51:18 30 Oct 2024 | 21:51:45 30 Oct 2024 | 27 seconds |
| Output :: Mutation Prediction | 21:51:18 30 Oct 2024 | 21:51:20 30 Oct 2024 | 2 seconds |
| Output :: Mutation Annotation | 21:51:20 30 Oct 2024 | 21:51:20 30 Oct 2024 | 0 seconds |
| Total | 34 minutes 43 seconds | ||
