mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 44,301 | (T)9→8 | intergenic (+132/‑359) | oprD_1 → / → czcR_2 | Porin D/Transcriptional activator protein CzcR |
| RA | 120,983 | (T)9→8 | intergenic (+280/+92) | polA → / ← engB | DNA polymerase I/putative GTP‑binding protein EngB |
| RA | 179,484 | T→C | C316R (TGC→CGC) | CJ019_00182 → | hypothetical protein |
| RA | 690,144 | A→G | intergenic (+21/‑2438) | bauC → / → PP_RS08750 | Putative 3‑oxopropanoate dehydrogenase/tRNA‑Val |
| JC | 2,191,046 | +CTGAAAATATCTCTTAT | intergenic (‑1/‑313) | PP_RS10045 ← / → purU_3 | LysR family transcriptional regulator/Formyltetrahydrofolate deformylase |
| JC | 4,257,335 | +GCGGCCGC | intergenic (‑281/+7) | CJ019_03991 ← / ← CJ019_03994 | putative ABC transporter ATP‑binding protein/hypothetical protein |
| RA | 4,759,606 | G→A | A28T (GCC→ACC) | ligM_KToptimized → | sequence generated by OPTIMIZER for KT2440 |
| RA | 5,386,500 | C→A | intergenic (‑509/+1142) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,503 | C→G | intergenic (‑512/+1139) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,506 | 1 bp→GT | intergenic (‑515/+1136) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,507 | +C | intergenic (‑516/+1135) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,510 | 2 bp→TA | intergenic (‑519/+1131) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,513 | +AA | intergenic (‑522/+1129) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,514 | T→C | intergenic (‑523/+1128) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,517 | G→C | intergenic (‑526/+1125) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,519 | G→A | intergenic (‑528/+1123) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| RA | 5,386,811 | C→T | intergenic (‑820/+831) | CJ019_05070 ← / ← nptII | hypothetical protein/neomycin phosphotransferase |
| JC | 5,391,707 | +54 bp | intergenic (+124/‑1253) | ligH → / → CJ019_05072 | 10‑formyltetrahydrofolate synthetase/hypothetical protein |
| RA | 5,760,598 | (A)6→5 | coding (781/834 nt) | CJ019_05400 → | hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | ACB143 | 87933 | 88060 | 128 | 21 [19] | [18] 21 | [CJ019_00094]–[CJ019_00095] | [CJ019_00094],[CJ019_00095] |
| * | * | ÷ | ACB143 | 277582 | 277681 | 100 | 21 [18] | [19] 20 | [betT2]–[tauD_2] | [betT2],[tauD_2] |
| * | * | ÷ | ACB143 | 517190 | 517314 | 125 | 28 [15] | [19] 20 | tyrS/birA | Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA |
| * | * | ÷ | ACB143 | 607303 | 607432 | 130 | 20 [19] | [19] 21 | [ispA] | [ispA] |
| * | * | ÷ | ACB143 | 674228 | 674418 | 191 | 24 [17] | [19] 20 | [nimR_1]–[mcpH_2] | [nimR_1],[mcpH_2] |
| * | * | ÷ | ACB143 | 1499936 | 1500088 | 153 | 23 [19] | [19] 23 | [sspA] | [sspA] |
| * | * | ÷ | ACB143 | 1608696 | 1608814 | 119 | 21 [18] | [19] 20 | [CJ019_01513]–[CJ019_01514] | [CJ019_01513],[CJ019_01514] |
| * | * | ÷ | ACB143 | 1697643 | 1697759 | 117 | 22 [17] | [19] 22 | [CJ019_01593]–[CJ019_01594] | [CJ019_01593],[CJ019_01594] |
| * | * | ÷ | ACB143 | 1914554 | 1914659 | 106 | 21 [19] | [19] 20 | [ppsC_1]–[CJ019_01830] | [ppsC_1],[CJ019_01830] |
| * | * | ÷ | ACB143 | 1940799 | 1940925 | 127 | 21 [14] | [18] 20 | CJ019_01857/gshAB | hypothetical protein/Glutathione biosynthesis bifunctional proteinGshAB |
| * | * | ÷ | ACB143 | 2288809 | 2288922 | 114 | 20 [18] | [19] 21 | CJ019_02171/CJ019_02172 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 2467190 | 2467208 | 19 | 26 [1] | [14] 36 | CJ019_02325/tal | hypothetical protein/Transaldolase |
| * | * | ÷ | ACB143 | 2657037 | 2657151 | 115 | 20 [19] | [19] 20 | prpC/acnM | 2‑methylcitrate synthase/Aconitate hydratase A |
| * | * | ÷ | ACB143 | 2716442 | 2716446 | 5 | 38 [0] | [0] 45 | rhaR_3 | HTH‑type transcriptional activator RhaR |
| * | * | ÷ | ACB143 | 3046179 | 3046300 | 122 | 20 [19] | [19] 23 | [rcsC_5]–[degU_2] | [rcsC_5],[degU_2] |
| * | * | ÷ | ACB143 | 3769361 | 3769492 | 132 | 21 [19] | [18] 20 | CJ019_03581/CJ019_03582 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 4331603 | 4331778 | 176 | 20 [19] | [19] 20 | [ribBA_2] | [ribBA_2] |
| * | * | ÷ | ACB143 | 4521548 | 4521686 | 139 | 22 [19] | [18] 21 | [CJ019_04289] | [CJ019_04289] |
| * | * | ÷ | ACB143 | 4732379 | 4732484 | 106 | 20 [19] | [19] 20 | [CJ019_04468] | [CJ019_04468] |
| * | * | ÷ | ACB143 | 4944211 | 4944340 | 130 | 20 [19] | [18] 20 | [CJ019_04642] | [CJ019_04642] |
| * | * | ÷ | ACB143 | 5250107 | 5250228 | 122 | 20 [19] | [16] 21 | [CJ019_04947]–[CJ019_04948] | [CJ019_04947],[CJ019_04948] |
| * | * | ÷ | ACB143 | 5503642 | 5503834 | 193 | 20 [19] | [19] 20 | [CJ019_05176] | [CJ019_05176] |
| * | * | ÷ | ACB143 | 5678536 | 5678659 | 124 | 20 [19] | [19] 20 | CJ019_05328/CJ019_05329 | hypothetical protein/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | ACB143 | 1837190 = | 0 (0.000) | 54 (0.940) | 32/252 | 0.4 | 34.8% | coding (660/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | = 2172433 | 202 (3.500) | intergenic (+175/+93) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein | |||||
| * | ? | ACB143 | = 1837193 | 0 (0.000) | 33 (0.570) | 24/254 | 0.9 | 35.3% | coding (657/2754 nt) | barA | Signal transduction histidine‑protein kinaseBarA |
| ? | ACB143 | 2170759 = | 121 (2.080) | intergenic (‑774/‑63) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 | |||||
| * | ? | ACB143 | 2155685 = | 49 (0.820) | 139 (2.320) | 53/262 | 0.0 | 73.4% | coding (301/369 nt) | tmk_1 | Thymidylate kinase |
| ? | ACB143 | = 2220562 | 52 (0.870) | coding (36/369 nt) | tmk_2 | Thymidylate kinase | |||||
| * | ? | ACB143 | 2170755 = | 130 (2.170) | 43 (0.740) | 30/254 | 0.5 | 40.6% | intergenic (‑770/‑67) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | 2716447 = | 0 (0.000) | coding (185/846 nt) | rhaR_3 | HTH‑type transcriptional activator RhaR | |||||
| * | ? | ACB143 | 2170758 = | 122 (2.030) | 33 (0.550) | 24/260 | 1.0 | 34.9% | intergenic (‑773/‑64) | arsR1/CJ019_02060 | Arsenic resistance transcriptional regulatorArsR1/IS1182 family transposase ISPpu16 |
| ? | ACB143 | 5869157 = | 2 (0.030) | coding (690/2280 nt) | ptsP | Phosphoenolpyruvate‑dependent phosphotransferasesystem | |||||
| * | ? | ACB143 | = 2172433 | 202 (3.370) | 81 (1.350) | 38/262 | 0.2 | 44.3% | intergenic (+175/+93) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | = 5869159 | 2 (0.030) | coding (688/2280 nt) | ptsP | Phosphoenolpyruvate‑dependent phosphotransferasesystem | |||||
| * | ? | ACB143 | = 2172438 | 207 (3.450) | 38 (0.660) | 23/252 | 1.0 | 27.6% | intergenic (+180/+88) | CJ019_02060/CJ019_02061 | IS1182 family transposase ISPpu16/hypothetical protein |
| ? | ACB143 | = 2716441 | 0 (0.000) | coding (191/846 nt) | rhaR_3 | HTH‑type transcriptional activator RhaR | |||||
| * | ? | ACB143 | 3359593 = | 47 (0.780) | 107 (1.780) | 51/262 | 0.0 | 69.0% | intergenic (+219/‑151) | pikAII_1/CJ019_03160 | Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42 |
| ? | ACB143 | 4755885 = | 49 (0.820) | coding (684/1659 nt) | yojI | ABC transporter ATP‑binding/permease proteinYojI | |||||
| * | ? | ACB143 | = 3376605 | 55 (0.920) | 127 (2.120) | 60/262 | 0.0 | 65.8% | coding (501/546 nt) | CJ019_03184 | hypothetical protein |
| ? | ACB143 | = 4765778 | 77 (1.280) | coding (6629/10413 nt) | grsB | Gramicidin S synthase 2 | |||||