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_CH607-002R0003_good_1.fq | 4,487,615 | 668,794,458 | 100.0% | 149.0 bases | 150 bases | 92.1% |
| total | 4,487,615 | 668,794,458 | 100.0% | 149.0 bases | 150 bases | 92.1% |
| seq id | length | fit mean | fit relative_variance | % mapped reads | description | ||
|---|---|---|---|---|---|---|---|
| coverage | distribution | Xen14_1 | 242,556 | 88.7 | 2.6 | 3.6% | na |
| coverage | distribution | Xen14_2 | 185,210 | 63.9 | 2.3 | 1.9% | na |
| coverage | distribution | Xen14_3 | 166,311 | 153.4 | 3.4 | 4.1% | na |
| coverage | distribution | Xen14_4 | 151,524 | 105.8 | 3.1 | 2.6% | na |
| coverage | distribution | Xen14_5 | 149,062 | 108.9 | 2.7 | 2.6% | na |
| coverage | distribution | Xen14_6 | 146,760 | 133.6 | 3.1 | 3.2% | na |
| coverage | distribution | Xen14_7 | 136,514 | 69.4 | 2.3 | 1.5% | na |
| coverage | distribution | Xen14_8 | 132,518 | 164.3 | 3.8 | 3.5% | na |
| coverage | distribution | Xen14_9 | 129,936 | 164.3 | 4.2 | 3.5% | na |
| coverage | distribution | Xen14_10 | 107,217 | 176.3 | 3.5 | 3.1% | na |
| coverage | distribution | Xen14_11 | 106,943 | 127.0 | 2.8 | 2.2% | na |
| coverage | distribution | Xen14_12 | 100,898 | 88.2 | 2.7 | 1.5% | na |
| coverage | distribution | Xen14_13 | 98,318 | 98.7 | 2.7 | 1.6% | na |
| coverage | distribution | Xen14_14 | 89,144 | 175.7 | 4.1 | 2.5% | na |
| coverage | distribution | Xen14_15 | 83,869 | 75.9 | 2.3 | 1.0% | na |
| coverage | distribution | Xen14_16 | 81,941 | 115.4 | 2.8 | 1.5% | na |
| coverage | distribution | Xen14_17 | 80,390 | 174.1 | 3.5 | 2.4% | na |
| coverage | distribution | Xen14_18 | 78,780 | 146.8 | 3.1 | 1.9% | na |
| coverage | distribution | Xen14_19 | 77,008 | 143.1 | 3.2 | 1.8% | na |
| coverage | distribution | Xen14_20 | 75,563 | 92.9 | 2.3 | 1.3% | na |
| coverage | distribution | Xen14_21 | 74,837 | 60.8 | 1.9 | 0.7% | na |
| coverage | distribution | Xen14_22 | 74,457 | 180.0 | 4.2 | 2.2% | na |
| coverage | distribution | Xen14_23 | 73,975 | 126.4 | 2.7 | 1.5% | na |
| coverage | distribution | Xen14_24 | 73,668 | 81.3 | 2.4 | 1.0% | na |
| coverage | distribution | Xen14_25 | 73,240 | 68.9 | 2.1 | 0.8% | na |
| coverage | distribution | Xen14_26 | 73,210 | 152.6 | 3.5 | 1.8% | na |
| coverage | distribution | Xen14_27 | 71,260 | 126.8 | 4.2 | 1.5% | na |
| coverage | distribution | Xen14_28 | 64,054 | 63.9 | 2.1 | 0.7% | na |
| coverage | distribution | Xen14_29 | 62,123 | 65.2 | 2.1 | 0.7% | na |
| coverage | distribution | Xen14_30 | 61,661 | 99.7 | 2.6 | 1.0% | na |
| coverage | distribution | Xen14_31 | 58,819 | 159.8 | 6.1 | 1.5% | na |
| coverage | distribution | Xen14_32 | 55,391 | 65.5 | 2.0 | 0.6% | na |
| coverage | distribution | Xen14_33 | 53,241 | 93.3 | 2.3 | 0.8% | na |
| coverage | distribution | Xen14_34 | 53,084 | 138.5 | 3.1 | 1.2% | na |
| coverage | distribution | Xen14_35 | 52,845 | 168.2 | 3.4 | 1.4% | na |
| coverage | distribution | Xen14_36 | 51,934 | 121.0 | 2.8 | 1.0% | na |
| coverage | distribution | Xen14_37 | 51,424 | 101.7 | 2.8 | 0.8% | na |
| coverage | distribution | Xen14_38 | 48,836 | 111.6 | 3.5 | 1.0% | na |
| coverage | distribution | Xen14_39 | 48,485 | 68.4 | 3.4 | 0.5% | na |
| coverage | distribution | Xen14_40 | 46,791 | 69.4 | 2.1 | 0.6% | na |
| coverage | distribution | Xen14_41 | 41,431 | 111.3 | 4.0 | 0.7% | na |
| coverage | distribution | Xen14_42 | 41,403 | 168.7 | 4.5 | 1.1% | na |
| coverage | distribution | Xen14_43 | 41,296 | 124.4 | 4.0 | 0.8% | na |
| coverage | distribution | Xen14_44 | 40,957 | 134.8 | 2.7 | 0.9% | na |
| coverage | distribution | Xen14_45 | 40,401 | 168.1 | 3.8 | 1.1% | na |
| coverage | distribution | Xen14_46 | 40,351 | 116.4 | 2.7 | 0.8% | na |
| coverage | distribution | Xen14_47 | 36,274 | 159.0 | 3.6 | 0.9% | na |
| coverage | distribution | Xen14_48 | 34,806 | 153.8 | 3.5 | 0.9% | na |
| coverage | distribution | Xen14_49 | 34,102 | 168.9 | 4.4 | 0.9% | na |
| coverage | distribution | Xen14_50 | 33,369 | 129.5 | 3.1 | 0.7% | na |
| coverage | distribution | Xen14_51 | 32,311 | 172.9 | 3.8 | 0.9% | na |
| coverage | distribution | Xen14_52 | 31,365 | 150.5 | 4.8 | 0.7% | na |
| coverage | distribution | Xen14_53 | 30,293 | 163.4 | 3.8 | 0.8% | na |
| coverage | distribution | Xen14_54 | 28,579 | 175.7 | 3.3 | 0.8% | na |
| coverage | distribution | Xen14_55 | 26,715 | 99.3 | 2.7 | 0.4% | na |
| coverage | distribution | Xen14_56 | 26,428 | 160.3 | 2.8 | 0.7% | na |
| coverage | distribution | Xen14_57 | 26,242 | 80.7 | 2.2 | 0.3% | na |
| coverage | distribution | Xen14_58 | 24,572 | 141.6 | 3.0 | 0.6% | na |
| coverage | distribution | Xen14_59 | 24,177 | 124.6 | 2.7 | 0.5% | na |
| coverage | distribution | Xen14_60 | 23,187 | 76.4 | 2.3 | 0.3% | na |
| coverage | distribution | Xen14_61 | 21,383 | 124.4 | 2.6 | 0.4% | na |
| coverage | distribution | Xen14_62 | 20,210 | 75.3 | 2.2 | 0.2% | na |
| coverage | distribution | Xen14_63 | 19,884 | 113.2 | 2.2 | 0.4% | na |
| coverage | distribution | Xen14_64 | 18,269 | 84.2 | 1.7 | 0.3% | na |
| coverage | distribution | Xen14_65 | 17,856 | 76.9 | 2.1 | 0.2% | na |
| coverage | distribution | Xen14_66 | 17,785 | 122.7 | 3.3 | 0.3% | na |
| coverage | distribution | Xen14_67 | 17,704 | 102.6 | 2.9 | 0.3% | na |
| coverage | distribution | Xen14_68 | 16,382 | 175.5 | 3.2 | 0.5% | na |
| coverage | distribution | Xen14_69 | 14,625 | 137.1 | 4.3 | 0.3% | na |
| coverage | distribution | Xen14_70 | 14,402 | 70.2 | 2.1 | 0.2% | na |
| coverage | distribution | Xen14_71 | 14,304 | 122.6 | 5.0 | 0.3% | na |
| coverage | distribution | Xen14_72 | 13,687 | 132.2 | 2.2 | 0.3% | na |
| coverage | distribution | Xen14_73 | 13,160 | 134.3 | 4.0 | 0.3% | na |
| coverage | distribution | Xen14_74 | 13,069 | 181.6 | 2.2 | 0.4% | na |
| coverage | distribution | Xen14_75 | 13,052 | 103.5 | 3.7 | 0.2% | na |
| coverage | distribution | Xen14_76 | 12,931 | 115.8 | 3.8 | 0.2% | na |
| coverage | distribution | Xen14_77 | 12,669 | 100.8 | 3.7 | 0.2% | na |
| coverage | distribution | Xen14_78 | 12,559 | 188.6 | 4.0 | 0.4% | na |
| coverage | distribution | Xen14_79 | 12,553 | 150.1 | 2.4 | 0.3% | na |
| coverage | distribution | Xen14_80 | 12,035 | 138.9 | 4.3 | 0.3% | na |
| coverage | distribution | Xen14_81 | 12,020 | 72.2 | 3.6 | 0.1% | na |
| coverage | distribution | Xen14_82 | 11,983 | 120.7 | 3.9 | 0.2% | na |
| coverage | distribution | Xen14_83 | 11,356 | 133.2 | 3.1 | 0.2% | na |
| coverage | distribution | Xen14_84 | 11,356 | 122.3 | 2.4 | 0.2% | na |
| coverage | distribution | Xen14_85 | 11,197 | 137.2 | 2.3 | 0.3% | na |
| coverage | distribution | Xen14_86 | 10,953 | 75.0 | 2.3 | 0.2% | na |
| coverage | distribution | Xen14_87 | 10,348 | 244.1 | 6.0 | 0.4% | na |
| coverage | distribution | Xen14_88 | 10,259 | 66.1 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_89 | 10,105 | 134.8 | 6.3 | 0.2% | na |
| coverage | distribution | Xen14_90 | 9,218 | 126.7 | 3.3 | 0.2% | na |
| coverage | distribution | Xen14_91 | 8,913 | 138.3 | 4.9 | 0.2% | na |
| coverage | distribution | Xen14_92 | 8,232 | 64.6 | 2.1 | 0.1% | na |
| coverage | distribution | Xen14_93 | 7,777 | 75.7 | 2.3 | 0.1% | na |
| coverage | distribution | Xen14_94 | 7,584 | 70.3 | 4.3 | 0.1% | na |
| coverage | distribution | Xen14_95 | 7,342 | 64.2 | 1.6 | 0.1% | na |
| coverage | distribution | Xen14_96 | 6,916 | 79.5 | 6.0 | 0.1% | na |
| coverage | distribution | Xen14_97 | 6,746 | 166.6 | 5.1 | 0.2% | na |
| coverage | distribution | Xen14_98 | 6,594 | 154.7 | 3.6 | 0.2% | na |
| coverage | distribution | Xen14_99 | 6,045 | 76.5 | 1.6 | 0.1% | na |
| coverage | distribution | Xen14_100 | 5,846 | 146.8 | 3.4 | 0.1% | na |
| coverage | distribution | Xen14_101 | 5,615 | 865.0 | 30.2 | 0.8% | na |
| coverage | distribution | Xen14_102 | 5,552 | 64.9 | 2.6 | 0.1% | na |
| coverage | distribution | Xen14_103 | 5,307 | 73.5 | 2.1 | 0.1% | na |
| coverage | distribution | Xen14_104 | 5,096 | 97.5 | 2.2 | 0.1% | na |
| coverage | distribution | Xen14_105 | 5,061 | 112.9 | 1.6 | 0.1% | na |
| coverage | distribution | Xen14_106 | 4,995 | 130.3 | 4.4 | 0.1% | na |
| coverage | distribution | Xen14_107 | 4,932 | 85.7 | 2.7 | 0.1% | na |
| coverage | distribution | Xen14_108 | 4,816 | 128.2 | 3.0 | 0.1% | na |
| coverage | distribution | Xen14_109 | 4,616 | 99.3 | 2.8 | 0.1% | na |
| coverage | distribution | Xen14_110 | 4,578 | 59.9 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_111 | 4,562 | 695.5 | 22.4 | 0.5% | na |
| coverage | distribution | Xen14_112 | 4,486 | 77.2 | 1.8 | 0.1% | na |
| coverage | distribution | Xen14_113 | 4,275 | 189.2 | 2.7 | 0.1% | na |
| coverage | distribution | Xen14_114 | 4,039 | 75.8 | 2.2 | 0.0% | na |
| coverage | distribution | Xen14_115 | 3,633 | 131.6 | 4.1 | 0.1% | na |
| coverage | distribution | Xen14_116 | 3,428 | 145.1 | 1.6 | 0.1% | na |
| coverage | distribution | Xen14_117 | 3,427 | 71.4 | 1.8 | 0.0% | na |
| coverage | distribution | Xen14_118 | 3,355 | 77.0 | 4.6 | 0.0% | na |
| coverage | distribution | Xen14_119 | 3,208 | 101.7 | 3.7 | 0.1% | na |
| coverage | distribution | Xen14_120 | 3,123 | 67.9 | 2.6 | 0.0% | na |
| coverage | distribution | Xen14_121 | 3,076 | 100.9 | 2.1 | 0.0% | na |
| coverage | distribution | Xen14_122 | 2,908 | 124.2 | 1.3 | 0.1% | na |
| coverage | distribution | Xen14_123 | 2,714 | 1116.8 | 4.3 | 0.5% | na |
| coverage | distribution | Xen14_124 | 2,576 | 126.0 | 2.5 | 0.1% | na |
| coverage | distribution | Xen14_125 | 2,519 | 124.0 | 2.9 | 0.0% | na |
| coverage | distribution | Xen14_126 | 2,515 | 130.1 | 1.4 | 0.1% | na |
| coverage | distribution | Xen14_127 | 2,166 | 692.6 | 19.9 | 0.2% | na |
| coverage | distribution | Xen14_128 | 2,143 | 89.8 | 3.0 | 0.0% | na |
| coverage | distribution | Xen14_129 | 2,049 | 135.3 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_130 | 2,000 | 136.6 | 2.1 | 0.0% | na |
| coverage | distribution | Xen14_131 | 1,922 | 59.9 | 2.7 | 0.0% | na |
| coverage | distribution | Xen14_132 | 1,806 | 166.9 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_133 | 1,721 | 296.0 | 2.3 | 0.1% | na |
| coverage | distribution | Xen14_134 | 1,657 | 73.2 | 5.9 | 0.0% | na |
| coverage | distribution | Xen14_135 | 1,633 | 145.0 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_136 | 1,567 | 125.8 | 2.0 | 0.0% | na |
| coverage | distribution | Xen14_137 | 1,544 | 240.6 | 4.2 | 0.1% | na |
| coverage | distribution | Xen14_138 | 1,361 | 138.5 | 3.6 | 0.0% | na |
| coverage | distribution | Xen14_139 | 1,349 | 143.6 | 1.6 | 0.0% | na |
| coverage | distribution | Xen14_140 | 1,298 | 1042.4 | 3.2 | 0.2% | na |
| coverage | distribution | Xen14_141 | 1,292 | 2411.0 | 79.0 | 0.4% | na |
| coverage | distribution | Xen14_142 | 1,281 | 59.7 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_143 | 1,107 | 1408.3 | 10.9 | 0.1% | na |
| coverage | distribution | Xen14_144 | 1,091 | 754.7 | 21.2 | 0.1% | na |
| coverage | distribution | Xen14_145 | 1,062 | 802.3 | 4.5 | 0.1% | na |
| coverage | distribution | Xen14_146 | 1,046 | 126.4 | 1.8 | 0.0% | na |
| coverage | distribution | Xen14_147 | 1,007 | 204.2 | 3.4 | 0.0% | na |
| coverage | distribution | Xen14_148 | 989 | 76.7 | 3.8 | 0.0% | na |
| coverage | distribution | Xen14_149 | 980 | 139.7 | 3.4 | 0.0% | na |
| coverage | distribution | Xen14_150 | 945 | 161.8 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_151 | 938 | 198.4 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_152 | 934 | 143.5 | 3.6 | 0.0% | na |
| coverage | distribution | Xen14_153 | 929 | 2848.4 | 85.2 | 0.4% | na |
| coverage | distribution | Xen14_154 | 920 | 570.6 | 116.5 | 0.0% | na |
| coverage | distribution | Xen14_155 | 900 | 61.0 | 1.8 | 0.0% | na |
| coverage | distribution | Xen14_156 | 862 | 239.4 | 2.1 | 0.0% | na |
| coverage | distribution | Xen14_157 | 857 | 362.7 | 33.3 | 0.0% | na |
| coverage | distribution | Xen14_158 | 799 | 153.7 | 6.1 | 0.0% | na |
| coverage | distribution | Xen14_159 | 798 | 139.8 | 2.0 | 0.0% | na |
| coverage | distribution | Xen14_160 | 780 | 177.2 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_161 | 770 | 139.7 | 7.0 | 0.0% | na |
| coverage | distribution | Xen14_162 | 765 | 161.2 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_163 | 753 | 297.2 | 8.7 | 0.0% | na |
| coverage | distribution | Xen14_164 | 746 | 78.4 | 2.4 | 0.0% | na |
| coverage | distribution | Xen14_165 | 691 | 161.6 | 8.8 | 0.0% | na |
| coverage | distribution | Xen14_166 | 685 | 2463.5 | 335.0 | 0.2% | na |
| coverage | distribution | Xen14_167 | 666 | 1083.8 | 18.1 | 0.1% | na |
| coverage | distribution | Xen14_168 | 629 | 3509.7 | 557.4 | 0.1% | na |
| coverage | distribution | Xen14_169 | 626 | 243.3 | 1.4 | 0.0% | na |
| coverage | distribution | Xen14_170 | 619 | 160.7 | 5.7 | 0.0% | na |
| coverage | distribution | Xen14_171 | 569 | 160.0 | 1.8 | 0.0% | na |
| coverage | distribution | Xen14_172 | 569 | 61.9 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_173 | 564 | [235.8] | [36.4] | 0.0% | na |
| coverage | distribution | Xen14_174 | 564 | 159.3 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_175 | 560 | 151.3 | 5.9 | 0.0% | na |
| coverage | distribution | Xen14_176 | 552 | 248.4 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_177 | 549 | 162.6 | 6.8 | 0.0% | na |
| coverage | distribution | Xen14_178 | 541 | 129.7 | 5.6 | 0.0% | na |
| coverage | distribution | Xen14_179 | 536 | 141.6 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_180 | 526 | 165.7 | 1.3 | 0.0% | na |
| coverage | distribution | Xen14_181 | 511 | 196.2 | 26.9 | 0.0% | na |
| coverage | distribution | Xen14_182 | 478 | 210.2 | 10.7 | 0.0% | na |
| coverage | distribution | Xen14_183 | 477 | 132.8 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_184 | 473 | 1214.1 | 2.0 | 0.1% | na |
| coverage | distribution | Xen14_185 | 471 | [427.6] | [67.1] | 0.0% | na |
| coverage | distribution | Xen14_186 | 465 | 153.3 | 34.3 | 0.0% | na |
| coverage | distribution | Xen14_187 | 464 | [270.1] | [26.9] | 0.0% | na |
| coverage | distribution | Xen14_188 | 458 | 565.6 | 67.3 | 0.0% | na |
| coverage | distribution | Xen14_189 | 453 | 278.3 | 43.6 | 0.0% | na |
| coverage | distribution | Xen14_190 | 448 | 72.8 | 5.1 | 0.0% | na |
| coverage | distribution | Xen14_191 | 447 | [428.3] | [247.4] | 0.0% | na |
| coverage | distribution | Xen14_192 | 445 | [99.7] | [19.5] | 0.0% | na |
| coverage | distribution | Xen14_193 | 444 | 379.3 | 4.9 | 0.0% | na |
| coverage | distribution | Xen14_194 | 442 | 23.0 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_195 | 441 | [46.9] | [14.9] | 0.0% | na |
| coverage | distribution | Xen14_196 | 436 | 218.5 | 21.6 | 0.0% | na |
| coverage | distribution | Xen14_197 | 433 | 134.6 | 1.2 | 0.0% | na |
| coverage | distribution | Xen14_198 | 431 | [73.3] | [15.4] | 0.0% | na |
| coverage | distribution | Xen14_199 | 428 | 205.3 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_200 | 423 | [1023.0] | [122.2] | 0.1% | na |
| coverage | distribution | Xen14_201 | 421 | 141.6 | 1.0 | 0.0% | na |
| coverage | distribution | Xen14_202 | 421 | 1399.8 | 176.1 | 0.0% | na |
| coverage | distribution | Xen14_203 | 416 | [113.7] | [21.1] | 0.0% | na |
| coverage | distribution | Xen14_204 | 415 | 166.7 | 1.7 | 0.0% | na |
| coverage | distribution | Xen14_205 | 404 | [856.0] | [83.6] | 0.0% | na |
| coverage | distribution | Xen14_206 | 403 | 1393.2 | 4.4 | 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 | 100000 |
| 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 | 532 |
| Total length of all junction candidates (factor times the reference genome length) | ≤ 0.1 | 0.030 |
| reference sequence | pr(no read start) |
|---|---|
| Xen14_1 | 0.79116 |
| Xen14_2 | 0.84258 |
| Xen14_3 | 0.67839 |
| Xen14_4 | 0.75841 |
| Xen14_5 | 0.75192 |
| Xen14_6 | 0.70762 |
| Xen14_7 | 0.82979 |
| Xen14_8 | 0.66137 |
| Xen14_9 | 0.66105 |
| Xen14_10 | 0.64311 |
| Xen14_11 | 0.71971 |
| Xen14_12 | 0.79252 |
| Xen14_13 | 0.77088 |
| Xen14_14 | 0.64686 |
| Xen14_15 | 0.81469 |
| Xen14_16 | 0.73897 |
| Xen14_17 | 0.64292 |
| Xen14_18 | 0.68789 |
| Xen14_19 | 0.69623 |
| Xen14_20 | 0.78145 |
| Xen14_21 | 0.84816 |
| Xen14_22 | 0.63669 |
| Xen14_23 | 0.72149 |
| Xen14_24 | 0.80643 |
| Xen14_25 | 0.83009 |
| Xen14_26 | 0.67735 |
| Xen14_27 | 0.71835 |
| Xen14_28 | 0.84091 |
| Xen14_29 | 0.83825 |
| Xen14_30 | 0.77143 |
| Xen14_31 | 0.67421 |
| Xen14_32 | 0.83804 |
| Xen14_33 | 0.78359 |
| Xen14_34 | 0.70132 |
| Xen14_35 | 0.65694 |
| Xen14_36 | 0.73204 |
| Xen14_37 | 0.76802 |
| Xen14_38 | 0.74270 |
| Xen14_39 | 0.83468 |
| Xen14_40 | 0.83074 |
| Xen14_41 | 0.75118 |
| Xen14_42 | 0.65151 |
| Xen14_43 | 0.72569 |
| Xen14_44 | 0.70979 |
| Xen14_45 | 0.65512 |
| Xen14_46 | 0.73900 |
| Xen14_47 | 0.67164 |
| Xen14_48 | 0.67713 |
| Xen14_49 | 0.65294 |
| Xen14_50 | 0.71710 |
| Xen14_51 | 0.65201 |
| Xen14_52 | 0.69005 |
| Xen14_53 | 0.65933 |
| Xen14_54 | 0.65172 |
| Xen14_55 | 0.76946 |
| Xen14_56 | 0.66708 |
| Xen14_57 | 0.80512 |
| Xen14_58 | 0.69435 |
| Xen14_59 | 0.72761 |
| Xen14_60 | 0.81432 |
| Xen14_61 | 0.72682 |
| Xen14_62 | 0.81608 |
| Xen14_63 | 0.74407 |
| Xen14_64 | 0.79890 |
| Xen14_65 | 0.81575 |
| Xen14_66 | 0.73092 |
| Xen14_67 | 0.76528 |
| Xen14_68 | 0.64553 |
| Xen14_69 | 0.70714 |
| Xen14_70 | 0.83014 |
| Xen14_71 | 0.73147 |
| Xen14_72 | 0.71064 |
| Xen14_73 | 0.72033 |
| Xen14_74 | 0.64511 |
| Xen14_75 | 0.76061 |
| Xen14_76 | 0.74000 |
| Xen14_77 | 0.77149 |
| Xen14_78 | 0.62704 |
| Xen14_79 | 0.68275 |
| Xen14_80 | 0.70274 |
| Xen14_81 | 0.83648 |
| Xen14_82 | 0.73454 |
| Xen14_83 | 0.71786 |
| Xen14_84 | 0.74949 |
| Xen14_85 | 0.68786 |
| Xen14_86 | 0.80171 |
| Xen14_87 | 0.55861 |
| Xen14_88 | 0.82521 |
| Xen14_89 | 0.72014 |
| Xen14_90 | 0.72559 |
| Xen14_91 | 0.70885 |
| Xen14_92 | 0.84603 |
| Xen14_93 | 0.81953 |
| Xen14_94 | 0.83742 |
| Xen14_95 | 0.84241 |
| Xen14_96 | 0.73936 |
| Xen14_97 | 0.67099 |
| Xen14_98 | 0.67497 |
| Xen14_99 | 0.82035 |
| Xen14_100 | 0.68645 |
| Xen14_101 | 0.21380 |
| Xen14_102 | 0.84609 |
| Xen14_103 | 0.81807 |
| Xen14_104 | 0.77698 |
| Xen14_105 | 0.70846 |
| Xen14_106 | 0.72703 |
| Xen14_107 | 0.80647 |
| Xen14_108 | 0.71782 |
| Xen14_109 | 0.78189 |
| Xen14_110 | 0.84851 |
| Xen14_111 | 0.29614 |
| Xen14_112 | 0.80915 |
| Xen14_113 | 0.64877 |
| Xen14_114 | 0.82310 |
| Xen14_115 | 0.72695 |
| Xen14_116 | 0.70405 |
| Xen14_117 | 0.83309 |
| Xen14_118 | 0.82876 |
| Xen14_119 | 0.76683 |
| Xen14_120 | 0.83333 |
| Xen14_121 | 0.77259 |
| Xen14_122 | 0.73986 |
| Xen14_123 | 0.17668 |
| Xen14_124 | 0.73447 |
| Xen14_125 | 0.74137 |
| Xen14_126 | 0.67674 |
| Xen14_127 | 0.29963 |
| Xen14_128 | 0.80339 |
| Xen14_129 | 0.71547 |
| Xen14_130 | 0.71425 |
| Xen14_131 | 0.81556 |
| Xen14_132 | 0.62138 |
| Xen14_133 | 0.53312 |
| Xen14_134 | 0.78600 |
| Xen14_135 | 0.67425 |
| Xen14_136 | 0.74505 |
| Xen14_137 | 0.58290 |
| Xen14_138 | 0.69583 |
| Xen14_139 | 0.71868 |
| Xen14_140 | 0.22612 |
| Xen14_141 | 0.14745 |
| Xen14_142 | 0.82365 |
| Xen14_143 | 0.41328 |
| Xen14_144 | 0.31072 |
| Xen14_145 | 0.31733 |
| Xen14_146 | 0.76769 |
| Xen14_147 | 0.62399 |
| Xen14_148 | 0.83670 |
| Xen14_149 | 0.73827 |
| Xen14_150 | 0.73016 |
| Xen14_151 | 0.67005 |
| Xen14_152 | 0.72270 |
| Xen14_153 | 0.15985 |
| Xen14_154 | 0.63424 |
| Xen14_155 | 0.86389 |
| Xen14_156 | 0.68047 |
| Xen14_157 | 0.58985 |
| Xen14_158 | 0.73529 |
| Xen14_159 | 0.76504 |
| Xen14_160 | 0.71154 |
| Xen14_161 | 0.76558 |
| Xen14_162 | 0.71503 |
| Xen14_163 | 0.59429 |
| Xen14_164 | 0.84406 |
| Xen14_165 | 0.73227 |
| Xen14_166 | 0.39557 |
| Xen14_167 | 0.31907 |
| Xen14_168 | 0.27027 |
| Xen14_169 | 0.70573 |
| Xen14_170 | 0.73667 |
| Xen14_171 | 0.73989 |
| Xen14_172 | 0.88840 |
| Xen14_173 | NA |
| Xen14_174 | 0.73138 |
| Xen14_175 | 0.75446 |
| Xen14_176 | 0.64855 |
| Xen14_177 | 0.74681 |
| Xen14_178 | 0.77542 |
| Xen14_179 | 0.76866 |
| Xen14_180 | 0.74905 |
| Xen14_181 | 0.71918 |
| Xen14_182 | 0.67573 |
| Xen14_183 | 0.69174 |
| Xen14_184 | 0.36469 |
| Xen14_185 | NA |
| Xen14_186 | 0.80323 |
| Xen14_187 | NA |
| Xen14_188 | 0.60153 |
| Xen14_189 | 0.71854 |
| Xen14_190 | 0.86942 |
| Xen14_191 | NA |
| Xen14_192 | NA |
| Xen14_193 | 0.59685 |
| Xen14_194 | 0.87783 |
| Xen14_195 | NA |
| Xen14_196 | 0.75573 |
| Xen14_197 | 0.69759 |
| Xen14_198 | NA |
| Xen14_199 | 0.79433 |
| Xen14_200 | NA |
| Xen14_201 | 0.79572 |
| Xen14_202 | 0.51306 |
| Xen14_203 | NA |
| Xen14_204 | 0.75301 |
| Xen14_205 | NA |
| Xen14_206 | 0.40074 |
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 | 21:51:46 30 Oct 2024 | 21:53:09 30 Oct 2024 | 1 minute 23 seconds |
| Read alignment to reference genome | 21:53:10 30 Oct 2024 | 21:55:22 30 Oct 2024 | 2 minutes 12 seconds |
| Preprocessing alignments for candidate junction identification | 21:55:22 30 Oct 2024 | 21:56:09 30 Oct 2024 | 47 seconds |
| Preliminary analysis of coverage distribution | 21:56:09 30 Oct 2024 | 22:03:27 30 Oct 2024 | 7 minutes 18 seconds |
| Identifying junction candidates | 22:03:27 30 Oct 2024 | 22:04:37 30 Oct 2024 | 1 minute 10 seconds |
| Re-alignment to junction candidates | 22:04:37 30 Oct 2024 | 22:05:23 30 Oct 2024 | 46 seconds |
| Resolving best read alignments | 22:05:23 30 Oct 2024 | 22:06:42 30 Oct 2024 | 1 minute 19 seconds |
| Creating BAM files | 22:06:42 30 Oct 2024 | 22:07:43 30 Oct 2024 | 1 minute 1 second |
| Tabulating error counts | 22:07:43 30 Oct 2024 | 22:09:33 30 Oct 2024 | 1 minute 50 seconds |
| Re-calibrating base error rates | 22:09:33 30 Oct 2024 | 22:13:56 30 Oct 2024 | 4 minutes 23 seconds |
| Examining read alignment evidence | 22:13:56 30 Oct 2024 | 22:23:21 30 Oct 2024 | 9 minutes 25 seconds |
| Polymorphism statistics | 22:23:21 30 Oct 2024 | 22:23:26 30 Oct 2024 | 5 seconds |
| Output | 22:23:26 30 Oct 2024 | 22:23:59 30 Oct 2024 | 33 seconds |
| Output :: Mutation Prediction | 22:23:26 30 Oct 2024 | 22:23:31 30 Oct 2024 | 5 seconds |
| Output :: Mutation Annotation | 22:23:31 30 Oct 2024 | 22:23:31 30 Oct 2024 | 0 seconds |
| Total | 32 minutes 17 seconds | ||
