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_CH607-002R0004_good_1.fq | 4,263,449 | 636,038,093 | 100.0% | 149.2 bases | 150 bases | 96.9% |
| total | 4,263,449 | 636,038,093 | 100.0% | 149.2 bases | 150 bases | 96.9% |
| seq id | length | fit mean | fit relative_variance | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | Xen14_1 | 242,556 | 73.2 | 2.7 | 3.0% | na |
| coverage | distribution | Xen14_2 | 185,210 | 70.4 | 2.6 | 2.1% | na |
| coverage | distribution | Xen14_3 | 166,311 | 148.7 | 3.9 | 4.0% | na |
| coverage | distribution | Xen14_4 | 151,524 | 99.5 | 3.5 | 2.4% | na |
| coverage | distribution | Xen14_5 | 149,062 | 103.8 | 3.7 | 2.5% | na |
| coverage | distribution | Xen14_6 | 146,760 | 130.8 | 3.8 | 3.1% | na |
| coverage | distribution | Xen14_7 | 136,514 | 76.7 | 2.6 | 1.7% | na |
| coverage | distribution | Xen14_8 | 132,518 | 159.9 | 4.2 | 3.4% | na |
| coverage | distribution | Xen14_9 | 129,936 | 161.2 | 4.9 | 3.4% | na |
| coverage | distribution | Xen14_10 | 107,217 | 187.1 | 4.4 | 3.3% | na |
| coverage | distribution | Xen14_11 | 106,943 | 125.6 | 3.4 | 2.2% | na |
| coverage | distribution | Xen14_12 | 100,898 | 81.3 | 2.8 | 1.4% | na |
| coverage | distribution | Xen14_13 | 98,318 | 93.9 | 3.2 | 1.5% | na |
| coverage | distribution | Xen14_14 | 89,144 | 186.9 | 5.3 | 2.7% | na |
| coverage | distribution | Xen14_15 | 83,869 | 65.2 | 2.4 | 0.9% | na |
| coverage | distribution | Xen14_16 | 81,941 | 110.8 | 3.0 | 1.5% | na |
| coverage | distribution | Xen14_17 | 80,390 | 185.3 | 5.1 | 2.5% | na |
| coverage | distribution | Xen14_18 | 78,780 | 144.5 | 3.9 | 1.9% | na |
| coverage | distribution | Xen14_19 | 77,008 | 149.3 | 4.7 | 1.9% | na |
| coverage | distribution | Xen14_20 | 75,563 | 85.4 | 2.5 | 1.2% | na |
| coverage | distribution | Xen14_21 | 74,837 | 67.2 | 2.3 | 0.8% | na |
| coverage | distribution | Xen14_22 | 74,457 | 193.9 | 4.9 | 2.3% | na |
| coverage | distribution | Xen14_23 | 73,975 | 125.7 | 4.5 | 1.5% | na |
| coverage | distribution | Xen14_24 | 73,668 | 89.2 | 3.2 | 1.1% | na |
| coverage | distribution | Xen14_25 | 73,240 | 62.6 | 2.1 | 0.8% | na |
| coverage | distribution | Xen14_26 | 73,210 | 150.1 | 3.5 | 1.8% | na |
| coverage | distribution | Xen14_27 | 71,260 | 101.7 | 4.7 | 1.2% | na |
| coverage | distribution | Xen14_28 | 64,054 | 64.1 | 2.3 | 0.7% | na |
| coverage | distribution | Xen14_29 | 62,123 | 58.5 | 2.3 | 0.6% | na |
| coverage | distribution | Xen14_30 | 61,661 | 96.2 | 3.0 | 1.0% | na |
| coverage | distribution | Xen14_31 | 58,819 | 210.2 | 5.9 | 2.0% | na |
| coverage | distribution | Xen14_32 | 55,391 | 61.0 | 2.4 | 0.6% | na |
| coverage | distribution | Xen14_33 | 53,241 | 85.6 | 2.8 | 0.7% | na |
| coverage | distribution | Xen14_34 | 53,084 | 135.2 | 4.5 | 1.2% | na |
| coverage | distribution | Xen14_35 | 52,845 | 172.1 | 5.0 | 1.5% | na |
| coverage | distribution | Xen14_36 | 51,934 | 115.1 | 4.5 | 1.0% | na |
| coverage | distribution | Xen14_37 | 51,424 | 96.0 | 3.3 | 0.8% | na |
| coverage | distribution | Xen14_38 | 48,836 | 110.2 | 3.3 | 1.0% | na |
| coverage | distribution | Xen14_39 | 48,485 | 73.3 | 6.6 | 0.6% | na |
| coverage | distribution | Xen14_40 | 46,791 | 61.4 | 2.5 | 0.5% | na |
| coverage | distribution | Xen14_41 | 41,431 | 110.7 | 2.8 | 0.7% | na |
| coverage | distribution | Xen14_42 | 41,403 | 172.4 | 5.2 | 1.2% | na |
| coverage | distribution | Xen14_43 | 41,296 | 107.1 | 4.6 | 0.7% | na |
| coverage | distribution | Xen14_44 | 40,957 | 131.2 | 4.2 | 0.9% | na |
| coverage | distribution | Xen14_45 | 40,401 | 173.8 | 4.7 | 1.1% | na |
| coverage | distribution | Xen14_46 | 40,351 | 112.7 | 3.7 | 0.7% | na |
| coverage | distribution | Xen14_47 | 36,274 | 153.9 | 4.8 | 0.9% | na |
| coverage | distribution | Xen14_48 | 34,806 | 156.8 | 3.5 | 0.9% | na |
| coverage | distribution | Xen14_49 | 34,102 | 172.6 | 4.8 | 1.0% | na |
| coverage | distribution | Xen14_50 | 33,369 | 127.9 | 3.4 | 0.7% | na |
| coverage | distribution | Xen14_51 | 32,311 | 172.1 | 4.8 | 0.9% | na |
| coverage | distribution | Xen14_52 | 31,365 | 152.2 | 7.1 | 0.8% | na |
| coverage | distribution | Xen14_53 | 30,293 | 161.8 | 4.8 | 0.8% | na |
| coverage | distribution | Xen14_54 | 28,579 | 189.2 | 5.8 | 0.9% | na |
| coverage | distribution | Xen14_55 | 26,715 | 93.0 | 2.8 | 0.4% | na |
| coverage | distribution | Xen14_56 | 26,428 | 167.2 | 3.1 | 0.7% | na |
| coverage | distribution | Xen14_57 | 26,242 | 84.6 | 2.8 | 0.4% | na |
| coverage | distribution | Xen14_58 | 24,572 | 134.5 | 3.1 | 0.5% | na |
| coverage | distribution | Xen14_59 | 24,177 | 123.1 | 4.6 | 0.5% | na |
| coverage | distribution | Xen14_60 | 23,187 | 84.5 | 2.3 | 0.3% | na |
| coverage | distribution | Xen14_61 | 21,383 | 136.5 | 2.5 | 0.5% | na |
| coverage | distribution | Xen14_62 | 20,210 | 63.1 | 2.5 | 0.2% | na |
| coverage | distribution | Xen14_63 | 19,884 | 110.3 | 2.6 | 0.4% | na |
| coverage | distribution | Xen14_64 | 18,269 | 71.8 | 2.2 | 0.2% | na |
| coverage | distribution | Xen14_65 | 17,856 | 83.9 | 3.0 | 0.2% | na |
| coverage | distribution | Xen14_66 | 17,785 | 115.9 | 4.4 | 0.3% | na |
| coverage | distribution | Xen14_67 | 17,704 | 99.9 | 2.9 | 0.3% | na |
| coverage | distribution | Xen14_68 | 16,382 | 183.0 | 2.4 | 0.5% | na |
| coverage | distribution | Xen14_69 | 14,625 | 118.5 | 6.3 | 0.3% | na |
| coverage | distribution | Xen14_70 | 14,402 | 58.3 | 2.4 | 0.1% | na |
| coverage | distribution | Xen14_71 | 14,304 | 97.8 | 3.9 | 0.2% | na |
| coverage | distribution | Xen14_72 | 13,687 | 132.6 | 3.3 | 0.3% | na |
| coverage | distribution | Xen14_73 | 13,160 | 157.8 | 4.3 | 0.3% | na |
| coverage | distribution | Xen14_74 | 13,069 | 193.9 | 5.4 | 0.4% | na |
| coverage | distribution | Xen14_75 | 13,052 | 124.9 | 2.5 | 0.3% | na |
| coverage | distribution | Xen14_76 | 12,931 | 106.2 | 3.6 | 0.2% | na |
| coverage | distribution | Xen14_77 | 12,669 | 101.3 | 2.7 | 0.2% | na |
| coverage | distribution | Xen14_78 | 12,559 | 205.4 | 4.4 | 0.4% | na |
| coverage | distribution | Xen14_79 | 12,553 | 146.6 | 2.6 | 0.3% | na |
| coverage | distribution | Xen14_80 | 12,035 | 139.1 | 5.8 | 0.3% | na |
| coverage | distribution | Xen14_81 | 12,020 | 91.7 | 3.1 | 0.2% | na |
| coverage | distribution | Xen14_82 | 11,983 | 123.6 | 2.9 | 0.2% | na |
| coverage | distribution | Xen14_83 | 11,356 | 125.4 | 5.7 | 0.2% | na |
| coverage | distribution | Xen14_84 | 11,356 | 90.7 | 7.1 | 0.2% | na |
| coverage | distribution | Xen14_85 | 11,197 | 136.4 | 2.5 | 0.3% | na |
| coverage | distribution | Xen14_86 | 10,953 | 89.8 | 3.4 | 0.2% | na |
| coverage | distribution | Xen14_87 | 10,348 | 241.3 | 5.4 | 0.4% | na |
| coverage | distribution | Xen14_88 | 10,259 | 69.1 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_89 | 10,105 | 168.9 | 3.9 | 0.3% | na |
| coverage | distribution | Xen14_90 | 9,218 | 132.8 | 3.8 | 0.2% | na |
| coverage | distribution | Xen14_91 | 8,913 | 110.2 | 3.2 | 0.2% | na |
| coverage | distribution | Xen14_92 | 8,232 | 69.8 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_93 | 7,777 | 72.2 | 3.5 | 0.1% | na |
| coverage | distribution | Xen14_94 | 7,584 | 74.6 | 2.3 | 0.1% | na |
| coverage | distribution | Xen14_95 | 7,342 | 68.8 | 2.1 | 0.1% | na |
| coverage | distribution | Xen14_96 | 6,916 | 165.3 | 8.4 | 0.1% | na |
| coverage | distribution | Xen14_97 | 6,746 | 187.0 | 5.6 | 0.2% | na |
| coverage | distribution | Xen14_98 | 6,594 | 162.6 | 6.0 | 0.2% | na |
| coverage | distribution | Xen14_99 | 6,045 | 76.2 | 2.1 | 0.1% | na |
| coverage | distribution | Xen14_100 | 5,846 | 145.8 | 3.3 | 0.1% | na |
| coverage | distribution | Xen14_101 | 5,615 | 1132.0 | 68.2 | 1.0% | na |
| coverage | distribution | Xen14_102 | 5,552 | 72.6 | 1.9 | 0.1% | na |
| coverage | distribution | Xen14_103 | 5,307 | 77.5 | 1.9 | 0.1% | na |
| coverage | distribution | Xen14_104 | 5,096 | 107.1 | 3.2 | 0.1% | na |
| coverage | distribution | Xen14_105 | 5,061 | 108.9 | 2.5 | 0.1% | na |
| coverage | distribution | Xen14_106 | 4,995 | 121.5 | 3.5 | 0.1% | na |
| coverage | distribution | Xen14_107 | 4,932 | 69.0 | 2.5 | 0.1% | na |
| coverage | distribution | Xen14_108 | 4,816 | 112.2 | 3.9 | 0.1% | na |
| coverage | distribution | Xen14_109 | 4,616 | 91.4 | 4.9 | 0.1% | na |
| coverage | distribution | Xen14_110 | 4,578 | 56.8 | 2.2 | 0.0% | na |
| coverage | distribution | Xen14_111 | 4,562 | 793.1 | 15.0 | 0.6% | na |
| coverage | distribution | Xen14_112 | 4,486 | 84.4 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_113 | 4,275 | 193.0 | 5.4 | 0.1% | na |
| coverage | distribution | Xen14_114 | 4,039 | 68.9 | 4.0 | 0.0% | na |
| coverage | distribution | Xen14_115 | 3,633 | 157.9 | 3.3 | 0.1% | na |
| coverage | distribution | Xen14_116 | 3,428 | 145.6 | 3.2 | 0.1% | na |
| coverage | distribution | Xen14_117 | 3,427 | 93.1 | 4.9 | 0.1% | na |
| coverage | distribution | Xen14_118 | 3,355 | 60.9 | 3.4 | 0.0% | na |
| coverage | distribution | Xen14_119 | 3,208 | 96.3 | 2.5 | 0.0% | na |
| coverage | distribution | Xen14_120 | 3,123 | 66.9 | 3.1 | 0.0% | na |
| coverage | distribution | Xen14_121 | 3,076 | 93.5 | 2.5 | 0.0% | na |
| coverage | distribution | Xen14_122 | 2,908 | 117.1 | 4.5 | 0.1% | na |
| coverage | distribution | Xen14_123 | 2,714 | 1219.0 | 10.8 | 0.5% | na |
| coverage | distribution | Xen14_124 | 2,576 | 136.9 | 3.0 | 0.1% | na |
| coverage | distribution | Xen14_125 | 2,519 | 152.2 | 3.6 | 0.1% | na |
| coverage | distribution | Xen14_126 | 2,515 | 141.2 | 1.8 | 0.1% | na |
| coverage | distribution | Xen14_127 | 2,166 | 1129.2 | 16.2 | 0.4% | na |
| coverage | distribution | Xen14_128 | 2,143 | 87.5 | 2.9 | 0.0% | na |
| coverage | distribution | Xen14_129 | 2,049 | 142.4 | 6.1 | 0.0% | na |
| coverage | distribution | Xen14_130 | 2,000 | 130.8 | 2.1 | 0.0% | na |
| coverage | distribution | Xen14_131 | 1,922 | 56.7 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_132 | 1,806 | 161.4 | 2.9 | 0.1% | na |
| coverage | distribution | Xen14_133 | 1,721 | 259.9 | 1.8 | 0.1% | na |
| coverage | distribution | Xen14_134 | 1,657 | 79.4 | 5.7 | 0.0% | na |
| coverage | distribution | Xen14_135 | 1,633 | 155.7 | 2.4 | 0.0% | na |
| coverage | distribution | Xen14_136 | 1,567 | 123.0 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_137 | 1,544 | 196.4 | 1.9 | 0.0% | na |
| coverage | distribution | Xen14_138 | 1,361 | 136.5 | 2.5 | 0.0% | na |
| coverage | distribution | Xen14_139 | 1,349 | 177.4 | 2.6 | 0.0% | na |
| coverage | distribution | Xen14_140 | 1,298 | 1181.8 | 3.5 | 0.2% | na |
| coverage | distribution | Xen14_141 | 1,292 | 2164.6 | 26.3 | 0.4% | na |
| coverage | distribution | Xen14_142 | 1,281 | 57.8 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_143 | 1,107 | 1278.3 | 7.4 | 0.1% | na |
| coverage | distribution | Xen14_144 | 1,091 | 792.4 | 17.5 | 0.1% | na |
| coverage | distribution | Xen14_145 | 1,062 | 823.4 | 2.8 | 0.1% | na |
| coverage | distribution | Xen14_146 | 1,046 | 143.9 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_147 | 1,007 | 191.6 | 2.0 | 0.0% | na |
| coverage | distribution | Xen14_148 | 989 | 79.4 | 5.2 | 0.0% | na |
| coverage | distribution | Xen14_149 | 980 | 133.5 | 4.5 | 0.0% | na |
| coverage | distribution | Xen14_150 | 945 | 170.3 | 4.7 | 0.0% | na |
| coverage | distribution | Xen14_151 | 938 | 169.9 | 3.8 | 0.0% | na |
| coverage | distribution | Xen14_152 | 934 | 142.0 | 7.0 | 0.0% | na |
| coverage | distribution | Xen14_153 | 929 | 3044.5 | 147.2 | 0.4% | na |
| coverage | distribution | Xen14_154 | 920 | 210.6 | 5.9 | 0.0% | na |
| coverage | distribution | Xen14_155 | 900 | 78.0 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_156 | 862 | 220.2 | 2.5 | 0.0% | na |
| coverage | distribution | Xen14_157 | 857 | 264.4 | 6.8 | 0.0% | na |
| coverage | distribution | Xen14_158 | 799 | 123.4 | 2.3 | 0.0% | na |
| coverage | distribution | Xen14_159 | 798 | 169.9 | 6.5 | 0.0% | na |
| coverage | distribution | Xen14_160 | 780 | 199.2 | 7.3 | 0.0% | na |
| coverage | distribution | Xen14_161 | 770 | 146.8 | 3.4 | 0.0% | na |
| coverage | distribution | Xen14_162 | 765 | 185.5 | 1.8 | 0.0% | na |
| coverage | distribution | Xen14_163 | 753 | 272.0 | 3.6 | 0.0% | na |
| coverage | distribution | Xen14_164 | 746 | 83.2 | 1.6 | 0.0% | na |
| coverage | distribution | Xen14_165 | 691 | 176.4 | 4.0 | 0.0% | na |
| coverage | distribution | Xen14_166 | 685 | 2983.7 | 751.7 | 0.2% | na |
| coverage | distribution | Xen14_167 | 666 | 1020.5 | 27.9 | 0.1% | na |
| coverage | distribution | Xen14_168 | 629 | 4474.2 | 915.8 | 0.1% | na |
| coverage | distribution | Xen14_169 | 626 | 205.3 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_170 | 619 | 128.1 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_171 | 569 | 154.3 | 1.8 | 0.0% | na |
| coverage | distribution | Xen14_172 | 569 | 52.0 | 2.9 | 0.0% | na |
| coverage | distribution | Xen14_173 | 564 | 331.4 | 29.9 | 0.0% | na |
| coverage | distribution | Xen14_174 | 564 | 164.4 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_175 | 560 | 123.5 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_176 | 552 | 274.2 | 31.4 | 0.0% | na |
| coverage | distribution | Xen14_177 | 549 | 400.2 | 78.5 | 0.0% | na |
| coverage | distribution | Xen14_178 | 541 | 122.9 | 2.4 | 0.0% | na |
| coverage | distribution | Xen14_179 | 536 | 144.5 | 4.3 | 0.0% | na |
| coverage | distribution | Xen14_180 | 526 | 130.4 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_181 | 511 | 163.4 | 15.1 | 0.0% | na |
| coverage | distribution | Xen14_182 | 478 | 206.6 | 6.1 | 0.0% | na |
| coverage | distribution | Xen14_183 | 477 | 131.7 | 4.1 | 0.0% | na |
| coverage | distribution | Xen14_184 | 473 | 1302.0 | 3.3 | 0.1% | na |
| coverage | distribution | Xen14_185 | 471 | 515.1 | 2.2 | 0.0% | na |
| coverage | distribution | Xen14_186 | 465 | 122.4 | 4.9 | 0.0% | na |
| coverage | distribution | Xen14_187 | 464 | 349.1 | 2.4 | 0.0% | na |
| coverage | distribution | Xen14_188 | 458 | 641.7 | 69.8 | 0.0% | na |
| coverage | distribution | Xen14_189 | 453 | 210.6 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_190 | 448 | [85.5] | [19.3] | 0.0% | na |
| coverage | distribution | Xen14_191 | 447 | [423.1] | [219.7] | 0.0% | na |
| coverage | distribution | Xen14_192 | 445 | 125.5 | 1.1 | 0.0% | na |
| coverage | distribution | Xen14_193 | 444 | 330.1 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_194 | 442 | 119.8 | 15.3 | 0.0% | na |
| coverage | distribution | Xen14_195 | 441 | 82.0 | 13.1 | 0.0% | na |
| coverage | distribution | Xen14_196 | 436 | 154.2 | 13.6 | 0.0% | na |
| coverage | distribution | Xen14_197 | 433 | 112.5 | 1.1 | 0.0% | na |
| coverage | distribution | Xen14_198 | 431 | 115.7 | 1.3 | 0.0% | na |
| coverage | distribution | Xen14_199 | 428 | 162.4 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_200 | 423 | 1893.3 | 132.9 | 0.1% | na |
| coverage | distribution | Xen14_201 | 421 | [84.6] | [16.5] | 0.0% | na |
| coverage | distribution | Xen14_202 | 421 | 1270.3 | 147.1 | 0.0% | na |
| coverage | distribution | Xen14_203 | 416 | [81.2] | [18.1] | 0.0% | na |
| coverage | distribution | Xen14_204 | 415 | [120.1] | [28.3] | 0.0% | na |
| coverage | distribution | Xen14_205 | 404 | 1179.1 | 7.9 | 0.1% | na |
| coverage | distribution | Xen14_206 | 403 | 1324.7 | 13.7 | 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 | 84324 |
| 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 | 460 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.026 |
| reference sequence | pr(no read start) |
|---|---|
| Xen14_1 | 0.82279 |
| Xen14_2 | 0.82954 |
| Xen14_3 | 0.68674 |
| Xen14_4 | 0.77225 |
| Xen14_5 | 0.76341 |
| Xen14_6 | 0.71529 |
| Xen14_7 | 0.81697 |
| Xen14_8 | 0.67011 |
| Xen14_9 | 0.66823 |
| Xen14_10 | 0.63189 |
| Xen14_11 | 0.72521 |
| Xen14_12 | 0.80671 |
| Xen14_13 | 0.78401 |
| Xen14_14 | 0.63069 |
| Xen14_15 | 0.84110 |
| Xen14_16 | 0.75003 |
| Xen14_17 | 0.63109 |
| Xen14_18 | 0.69318 |
| Xen14_19 | 0.68679 |
| Xen14_20 | 0.79618 |
| Xen14_21 | 0.83514 |
| Xen14_22 | 0.62216 |
| Xen14_23 | 0.72638 |
| Xen14_24 | 0.79197 |
| Xen14_25 | 0.84597 |
| Xen14_26 | 0.68351 |
| Xen14_27 | 0.76372 |
| Xen14_28 | 0.84174 |
| Xen14_29 | 0.85584 |
| Xen14_30 | 0.77833 |
| Xen14_31 | 0.60600 |
| Xen14_32 | 0.84724 |
| Xen14_33 | 0.79935 |
| Xen14_34 | 0.71093 |
| Xen14_35 | 0.65254 |
| Xen14_36 | 0.74118 |
| Xen14_37 | 0.78030 |
| Xen14_38 | 0.74905 |
| Xen14_39 | 0.82498 |
| Xen14_40 | 0.84974 |
| Xen14_41 | 0.75506 |
| Xen14_42 | 0.65128 |
| Xen14_43 | 0.76176 |
| Xen14_44 | 0.71894 |
| Xen14_45 | 0.65203 |
| Xen14_46 | 0.74987 |
| Xen14_47 | 0.68227 |
| Xen14_48 | 0.67500 |
| Xen14_49 | 0.65218 |
| Xen14_50 | 0.72458 |
| Xen14_51 | 0.65012 |
| Xen14_52 | 0.68937 |
| Xen14_53 | 0.66397 |
| Xen14_54 | 0.63380 |
| Xen14_55 | 0.78441 |
| Xen14_56 | 0.66068 |
| Xen14_57 | 0.80025 |
| Xen14_58 | 0.70853 |
| Xen14_59 | 0.73316 |
| Xen14_60 | 0.80088 |
| Xen14_61 | 0.70862 |
| Xen14_62 | 0.84359 |
| Xen14_63 | 0.75101 |
| Xen14_64 | 0.82504 |
| Xen14_65 | 0.80101 |
| Xen14_66 | 0.74487 |
| Xen14_67 | 0.77590 |
| Xen14_68 | 0.63881 |
| Xen14_69 | 0.73831 |
| Xen14_70 | 0.85205 |
| Xen14_71 | 0.77202 |
| Xen14_72 | 0.71696 |
| Xen14_73 | 0.68438 |
| Xen14_74 | 0.62744 |
| Xen14_75 | 0.73413 |
| Xen14_76 | 0.75679 |
| Xen14_77 | 0.77449 |
| Xen14_78 | 0.60658 |
| Xen14_79 | 0.68892 |
| Xen14_80 | 0.70843 |
| Xen14_81 | 0.79359 |
| Xen14_82 | 0.72774 |
| Xen14_83 | 0.73234 |
| Xen14_84 | 0.79933 |
| Xen14_85 | 0.69106 |
| Xen14_86 | 0.78133 |
| Xen14_87 | 0.57335 |
| Xen14_88 | 0.81681 |
| Xen14_89 | 0.66259 |
| Xen14_90 | 0.72169 |
| Xen14_91 | 0.76080 |
| Xen14_92 | 0.83157 |
| Xen14_93 | 0.83188 |
| Xen14_94 | 0.82641 |
| Xen14_95 | 0.83642 |
| Xen14_96 | 0.74971 |
| Xen14_97 | 0.63897 |
| Xen14_98 | 0.66822 |
| Xen14_99 | 0.82060 |
| Xen14_100 | 0.69911 |
| Xen14_101 | 0.18415 |
| Xen14_102 | 0.83177 |
| Xen14_103 | 0.80535 |
| Xen14_104 | 0.76442 |
| Xen14_105 | 0.71784 |
| Xen14_106 | 0.74615 |
| Xen14_107 | 0.83394 |
| Xen14_108 | 0.75311 |
| Xen14_109 | 0.79455 |
| Xen14_110 | 0.85671 |
| Xen14_111 | 0.26600 |
| Xen14_112 | 0.79665 |
| Xen14_113 | 0.63953 |
| Xen14_114 | 0.83276 |
| Xen14_115 | 0.68869 |
| Xen14_116 | 0.69822 |
| Xen14_117 | 0.79268 |
| Xen14_118 | 0.84978 |
| Xen14_119 | 0.78647 |
| Xen14_120 | 0.84662 |
| Xen14_121 | 0.79096 |
| Xen14_122 | 0.74209 |
| Xen14_123 | 0.16949 |
| Xen14_124 | 0.72069 |
| Xen14_125 | 0.70013 |
| Xen14_126 | 0.66620 |
| Xen14_127 | 0.20776 |
| Xen14_128 | 0.81616 |
| Xen14_129 | 0.71645 |
| Xen14_130 | 0.72675 |
| Xen14_131 | 0.84002 |
| Xen14_132 | 0.64780 |
| Xen14_133 | 0.57379 |
| Xen14_134 | 0.78365 |
| Xen14_135 | 0.66622 |
| Xen14_136 | 0.74697 |
| Xen14_137 | 0.62565 |
| Xen14_138 | 0.73292 |
| Xen14_139 | 0.68087 |
| Xen14_140 | 0.21225 |
| Xen14_141 | 0.15441 |
| Xen14_142 | 0.83949 |
| Xen14_143 | 0.46102 |
| Xen14_144 | 0.32493 |
| Xen14_145 | 0.29614 |
| Xen14_146 | 0.74857 |
| Xen14_147 | 0.64052 |
| Xen14_148 | 0.83771 |
| Xen14_149 | 0.74388 |
| Xen14_150 | 0.69312 |
| Xen14_151 | 0.69883 |
| Xen14_152 | 0.74197 |
| Xen14_153 | 0.16416 |
| Xen14_154 | 0.65054 |
| Xen14_155 | 0.83944 |
| Xen14_156 | 0.68175 |
| Xen14_157 | 0.61669 |
| Xen14_158 | 0.76846 |
| Xen14_159 | 0.73120 |
| Xen14_160 | 0.69423 |
| Xen14_161 | 0.74610 |
| Xen14_162 | 0.70980 |
| Xen14_163 | 0.60093 |
| Xen14_164 | 0.84048 |
| Xen14_165 | 0.71274 |
| Xen14_166 | 0.38745 |
| Xen14_167 | 0.31532 |
| Xen14_168 | 0.26630 |
| Xen14_169 | 0.71694 |
| Xen14_170 | 0.77948 |
| Xen14_171 | 0.75659 |
| Xen14_172 | 0.89895 |
| Xen14_173 | 0.65869 |
| Xen14_174 | 0.74557 |
| Xen14_175 | 0.79018 |
| Xen14_176 | 0.71014 |
| Xen14_177 | 0.71038 |
| Xen14_178 | 0.78373 |
| Xen14_179 | 0.76679 |
| Xen14_180 | 0.73265 |
| Xen14_181 | 0.74238 |
| Xen14_182 | 0.68933 |
| Xen14_183 | 0.71829 |
| Xen14_184 | 0.35941 |
| Xen14_185 | 0.52548 |
| Xen14_186 | 0.79677 |
| Xen14_187 | 0.60884 |
| Xen14_188 | 0.62664 |
| Xen14_189 | 0.73400 |
| Xen14_190 | NA |
| Xen14_191 | NA |
| Xen14_192 | 0.79663 |
| Xen14_193 | 0.65878 |
| Xen14_194 | 0.85294 |
| Xen14_195 | 0.85689 |
| Xen14_196 | 0.76032 |
| Xen14_197 | 0.83141 |
| Xen14_198 | 0.81671 |
| Xen14_199 | 0.79433 |
| Xen14_200 | 0.15172 |
| Xen14_201 | NA |
| Xen14_202 | 0.52138 |
| Xen14_203 | NA |
| Xen14_204 | NA |
| Xen14_205 | 0.43193 |
| Xen14_206 | 0.40695 |
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 | 22:24:01 30 Oct 2024 | 22:25:36 30 Oct 2024 | 1 minute 35 seconds |
| Read alignment to reference genome | 22:25:37 30 Oct 2024 | 22:27:15 30 Oct 2024 | 1 minute 38 seconds |
| Preprocessing alignments for candidate junction identification | 22:27:15 30 Oct 2024 | 22:28:01 30 Oct 2024 | 46 seconds |
| Preliminary analysis of coverage distribution | 22:28:01 30 Oct 2024 | 22:34:44 30 Oct 2024 | 6 minutes 43 seconds |
| Identifying junction candidates | 22:34:44 30 Oct 2024 | 22:35:40 30 Oct 2024 | 56 seconds |
| Re-alignment to junction candidates | 22:35:40 30 Oct 2024 | 22:36:11 30 Oct 2024 | 31 seconds |
| Resolving best read alignments | 22:36:11 30 Oct 2024 | 22:37:25 30 Oct 2024 | 1 minute 14 seconds |
| Creating BAM files | 22:37:26 30 Oct 2024 | 22:38:28 30 Oct 2024 | 1 minute 2 seconds |
| Tabulating error counts | 22:38:28 30 Oct 2024 | 22:39:46 30 Oct 2024 | 1 minute 18 seconds |
| Re-calibrating base error rates | 22:39:46 30 Oct 2024 | 22:43:58 30 Oct 2024 | 4 minutes 12 seconds |
| Examining read alignment evidence | 22:43:58 30 Oct 2024 | 22:52:12 30 Oct 2024 | 8 minutes 14 seconds |
| Polymorphism statistics | 22:52:12 30 Oct 2024 | 22:52:14 30 Oct 2024 | 2 seconds |
| Output | 22:52:15 30 Oct 2024 | 22:52:51 30 Oct 2024 | 36 seconds |
| Output :: Mutation Prediction | 22:52:15 30 Oct 2024 | 22:52:17 30 Oct 2024 | 2 seconds |
| Output :: Mutation Annotation | 22:52:17 30 Oct 2024 | 22:52:17 30 Oct 2024 | 0 seconds |
| Total | 28 minutes 49 seconds | ||
