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 |
| RA | 1,311,935 | G→T | D36Y (GAT→TAT) | aaeA_2 → | p‑hydroxybenzoic acid efflux pump subunit AaeA |
| JC | 2,191,046 | +CTGAAAATATCTCTTAT | intergenic (‑1/‑313) | PP_RS10045 ← / → purU_3 | LysR family transcriptional regulator/Formyltetrahydrofolate deformylase |
| MC JC | 4,195,579 | Δ105,043 bp | [CJ019_03944]–[CJ019_04036] | 91 genes [CJ019_03944], CJ019_03945, CJ019_03946, CJ019_03947, CJ019_03948, CJ019_03949, CJ019_03950, CJ019_03951, CJ019_03952, CJ019_03953, CJ019_03954, CJ019_03955, CJ019_03956, CJ019_03957, CJ019_03958, CJ019_03959, CJ019_03960, CJ019_03961, CJ019_03962, CJ019_03963, CJ019_03964, CJ019_03965, CJ019_03966, CJ019_03967, CJ019_03968, catA_2, catC, catB, benM_3, CJ019_03973, spuC_4, spuD_3, kefF, aruH, alr, aruI_2, FCS1, acdA_1, CJ019_03982, rocE, rcsC_13, CJ019_03985, arcA_2, betI_2, CJ019_03988, CJ019_03989, CJ019_03990, CJ019_03991, CJ019_03994, nicP_10, pcaK_3, mrdA_1, CJ019_03998, CJ019_03999, glcC, CJ019_04001, CJ019_04002, lutA, CJ019_04004, CJ019_04005, gabR_1, yycB_2, CJ019_04008, CJ019_04009, bktB, hbd, fabR_1, cpdR, rcsC_14, cheB_3, cheR, rcsC_15, cckA_1, CJ019_04019, nicP_11, CJ019_04021, gloA, CJ019_04023, sdhL, CJ019_04025, CJ019_04026, CJ019_04027, CJ019_04028, CJ019_04029, CJ019_04030, soxA_2, rarD_3, prmC_3, proC_1, CJ019_04035, [CJ019_04036] |
|
| RA | 4,627,056 | C→T | G100D (GGC→GAC) | gacA ← | Response regulator GacA |
| 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 |
| RA | 5,390,241 | G→A | G112D (GGC→GAC) | ligH → | 10‑formyltetrahydrofolate synthetase |
| 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 | 87997 | 88052 | 56 | 19 [17] | [17] 19 | [CJ019_00094]–[CJ019_00095] | [CJ019_00094],[CJ019_00095] |
| * | * | ÷ | ACB143 | 329229 | 329369 | 141 | 20 [18] | [18] 20 | [CJ019_00302] | [CJ019_00302] |
| * | * | ÷ | ACB143 | 346081 | 346218 | 138 | 19 [18] | [18] 19 | [hisF]–[btuD_1] | [hisF],[btuD_1] |
| * | * | ÷ | ACB143 | 517190 | 517276 | 87 | 25 [11] | [15] 19 | tyrS/birA | Tyrosine‑‑tRNA ligase/Bifunctional ligase/repressor BirA |
| * | * | ÷ | ACB143 | 661080 | 661224 | 145 | 19 [18] | [18] 19 | [yfhM] | [yfhM] |
| * | * | ÷ | ACB143 | 674241 | 674386 | 146 | 19 [18] | [18] 21 | [nimR_1]–[mcpH_2] | [nimR_1],[mcpH_2] |
| * | * | ÷ | ACB143 | 1149262 | 1149517 | 256 | 19 [18] | [18] 19 | [sasA_4] | [sasA_4] |
| * | * | ÷ | ACB143 | 1585631 | 1585699 | 69 | 19 [17] | [18] 19 | CJ019_01493 | hypothetical protein |
| * | * | ÷ | ACB143 | 1697624 | 1697754 | 131 | 19 [17] | [18] 19 | [CJ019_01593]–[CJ019_01594] | [CJ019_01593],[CJ019_01594] |
| * | * | ÷ | ACB143 | 1914570 | 1914679 | 110 | 19 [14] | [18] 21 | [ppsC_1]–[CJ019_01830] | [ppsC_1],[CJ019_01830] |
| * | * | ÷ | ACB143 | 2092960 | 2093067 | 108 | 19 [15] | [7] 21 | rcsC_3/CJ019_01993 | Sensor histidine kinase RcsC/hypothetical protein |
| * | * | ÷ | ACB143 | 2288860 | 2288927 | 68 | 19 [17] | [17] 19 | [CJ019_02172] | [CJ019_02172] |
| * | * | ÷ | ACB143 | 2830072 | 2830233 | 162 | 24 [17] | [18] 19 | [gabD1] | [gabD1] |
| * | * | ÷ | ACB143 | 3046197 | 3046345 | 149 | 19 [17] | [18] 20 | [rcsC_5]–[degU_2] | [rcsC_5],[degU_2] |
| * | * | ÷ | ACB143 | 3459837 | 3459920 | 84 | 19 [16] | [17] 20 | CJ019_03284 | hypothetical protein |
| * | * | ÷ | ACB143 | 3769361 | 3769481 | 121 | 21 [16] | [16] 19 | CJ019_03581/CJ019_03582 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 3944670 | 3944836 | 167 | 19 [16] | [17] 20 | CJ019_03729/CJ019_03730 | hypothetical protein/hypothetical protein |
| * | * | ÷ | ACB143 | 4163765 | 4163846 | 82 | 21 [18] | [16] 19 | katG/leuO_2 | Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO |
| * | * | ÷ | ACB143 | 4666867 | 4666980 | 114 | 19 [18] | [7] 20 | [btuB_4] | [btuB_4] |
| * | * | ÷ | ACB143 | 4732385 | 4732479 | 95 | 20 [18] | [17] 19 | [CJ019_04468] | [CJ019_04468] |
| * | * | ÷ | ACB143 | 4845743 | 4845798 | 56 | 19 [18] | [18] 19 | recR/ybaB | Recombination protein RecR/Nucleoid‑associated protein YbaB |
| * | * | ÷ | ACB143 | 4944201 | 4944340 | 140 | 19 [17] | [18] 20 | [CJ019_04642] | [CJ019_04642] |
| * | * | ÷ | ACB143 | 5482295 | 5482392 | 98 | 20 [18] | [18] 19 | purH/purD | Bifunctional purine biosynthesis protein PurH/Phosphoribosylamine‑‑glycine ligase |
| * | * | ÷ | ACB143 | 5503639 | 5503826 | 188 | 20 [18] | [18] 21 | [CJ019_05176] | [CJ019_05176] |
| * | * | ÷ | ACB143 | 5534178 | 5534316 | 139 | 19 [18] | [18] 21 | [nadE]–[CJ019_05208] | [nadE],[CJ019_05208] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | ACB143 | 3359593 = | 47 (0.780) | 96 (1.600) | 53/260 | 0.0 | 62.9% | intergenic (+219/‑151) | pikAII_1/CJ019_03160 | Narbonolide/10‑deoxymethynolide synthase PikA2,modules 3 and 4/Tn3 family transposase ISPa42 |
| ? | ACB143 | 4740816 = | 66 (1.100) | coding (903/1665 nt) | CJ019_04477 | Electron transfer flavoprotein‑ubiquinoneoxidoreductase | |||||
| * | ? | ACB143 | = 3376605 | 53 (0.880) | 167 (2.780) | 63/260 | 0.0 | 74.4% | coding (501/546 nt) | CJ019_03184 | hypothetical protein |
| ? | ACB143 | = 4850748 | 62 (1.030) | coding (435/489 nt) | CJ019_04550 | hypothetical protein | |||||