mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,731,621 | G→T | M845I (ATG→ATT) | lhr → | putative ATP‑dependent helicase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 3,440,087 | Δ2 bp | coding (942‑943/990 nt) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 4,234,667 | Δ1 bp | intergenic (‑1434/‑499) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,295,641 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| MC JC | 4,319,069 | (CATCGC)2→1 | coding (850‑855/1065 nt) | phnI ← | ribophosphonate triphosphate synthase complex putative catalytic subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_pae_pgi | 241999 | 242022 | 24 | 2 [1] | [0] 3 | fadE | acyl coenzyme A dehydrogenase |
| * | * | ÷ | NC_000913_3_pae_pgi | 365847 | 365940 | 94 | 2 [1] | [1] 2 | lacZ | beta‑D‑galactosidase |
| * | * | ÷ | NC_000913_3_pae_pgi | 366300 | 366339 | 40 | 3 [1] | [0] 3 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913_3_pae_pgi | 510004 | 510027 | 24 | 2 [1] | [1] 2 | copA | copper transporter |
| * | * | ÷ | NC_000913_3_pae_pgi | 1528440–1529173 | 1529187 | 15–748 | 2 [1] | [0] 2 | rhsE | pseudogene, Rhs family |
| * | * | ÷ | NC_000913_3_pae_pgi | 1657722 | 1657729 | 8 | 2 [0] | [1] 2 | ynfD | DUF1161 family periplasmic protein |
| * | * | ÷ | NC_000913_3_pae_pgi | 2826506 | 2826542 | 37 | 4 [1] | [1] 3 | srlE | glucitol/sorbitol‑specific enzyme IIB component of PTS |
| * | * | ÷ | NC_000913_3_pae_pgi | 3423795–3424233 | 3424526–3424247 | 15–732 | 3 [1] | [1] 2 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | 5590 = | NA (NA) | 9 (0.590) | 8/238 | 0.8 | 42.9% | noncoding (26/105 nt) | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | 2304478 = | 12 (0.780) | noncoding (62/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | = 218219 | 9 (0.560) | 4 (0.260) | 4/238 | 1.6 | 31.4% | coding (557/1719 nt) | proS | prolyl‑tRNA synthetase |
| ? | NC_000913_3_pae_pgi | = 218236 | 9 (0.590) | coding (540/1719 nt) | proS | prolyl‑tRNA synthetase | |||||
| * | ? | NC_000913_3_pae_pgi | 228016 = | NA (NA) | 4 (0.260) | 4/238 | 1.6 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_pgi | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_pgi | = 281903 | 21 (1.300) | 7 (0.460) | 7/236 | 0.9 | 26.6% | coding (81/1155 nt) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| ? | NC_000913_3_pae_pgi | = 281914 | 19 (1.250) | coding (70/1155 nt) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913_3_pae_pgi | = 284691 | 16 (0.990) | 3 (0.190) | 3/244 | 1.9 | 20.3% | coding (1491/1968 nt) | yagF | CP4‑6 prophage; dehydratase family protein |
| ? | NC_000913_3_pae_pgi | = 284723 | 8 (0.510) | coding (1523/1968 nt) | yagF | CP4‑6 prophage; dehydratase family protein | |||||
| * | ? | NC_000913_3_pae_pgi | = 540528 | 11 (0.680) | 4 (0.260) | 4/236 | 1.6 | 27.3% | intergenic (+20/‑37) | allB/ybbY | allantoinase/putative uracil/xanthine transporter |
| ? | NC_000913_3_pae_pgi | = 540537 | 11 (0.730) | intergenic (+29/‑28) | allB/ybbY | allantoinase/putative uracil/xanthine transporter | |||||
| * | ? | NC_000913_3_pae_pgi | = 610184 | NA (NA) | 6 (0.390) | 6/238 | 1.1 | NA | noncoding (68/98 nt) | RIP54 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP54 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | 1954429 = | NA (NA) | noncoding (1/98 nt) | RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_pgi | = 1286639 | NA (NA) | 6 (0.390) | 6/242 | 1.1 | NA | noncoding (46/72 nt) | REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_pae_pgi | = 1286665 | NA (NA) | noncoding (72/72 nt) | REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP108 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | = 1299498 | 0 (0.000) | 17 (1.080) | 15/244 | 0.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_pae_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_pae_pgi | 1394851 = | 12 (0.740) | 4 (0.270) | 4/232 | 1.5 | 30.7% | intergenic (+11/+40) | mppA/ynaI | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit/mechanosensitive channel protein, very small conductance |
| ? | NC_000913_3_pae_pgi | 1394881 = | 7 (0.470) | intergenic (+41/+10) | mppA/ynaI | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit/mechanosensitive channel protein, very small conductance | |||||
| * | ? | NC_000913_3_pae_pgi | 1724040 = | 17 (1.050) | 6 (0.390) | 6/238 | 1.1 | 27.9% | coding (1920/2013 nt) | ydhK | putative efflux protein (PET) component of YdhJK efflux pump |
| ? | NC_000913_3_pae_pgi | 1724062 = | 15 (0.980) | coding (1942/2013 nt) | ydhK | putative efflux protein (PET) component of YdhJK efflux pump | |||||
| * | ? | NC_000913_3_pae_pgi | = 1822923 | 13 (0.800) | 3 (0.190) | 3/242 | 1.9 | 21.1% | coding (466/828 nt) | nadE | NAD synthetase, NH3/glutamine‑dependent |
| ? | NC_000913_3_pae_pgi | = 1822933 | 10 (0.640) | coding (476/828 nt) | nadE | NAD synthetase, NH3/glutamine‑dependent | |||||
| * | ? | NC_000913_3_pae_pgi | = 2232735 | NA (NA) | 3 (0.190) | 3/240 | 1.9 | NA | intergenic (+7/‑143) | cdd/sanA | cytidine/deoxycytidine deaminase/DUF218 superfamily vancomycin high temperature exclusion protein |
| ? | NC_000913_3_pae_pgi | = 2232765 | NA (NA) | noncoding (30/34 nt) | REP155 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP155 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | = 2304954 | 10 (0.620) | 5 (0.330) | 5/238 | 1.3 | 27.4% | noncoding (538/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913_3_pae_pgi | 2431013 = | 17 (1.110) | intergenic (‑250/+9) | cvpA/dedD | colicin V production protein/membrane‑anchored periplasmic protein involved in septation | |||||
| * | ? | NC_000913_3_pae_pgi | 2539616 = | NA (NA) | 5 (0.320) | 5/242 | 1.4 | NA | noncoding (10/36 nt) | REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913_3_pae_pgi | 2539630 = | NA (NA) | noncoding (24/36 nt) | REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP175 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | 2728214 = | NA (NA) | 10 (0.640) | 6/244 | 1.2 | NA | noncoding (971/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_pgi | 2728240 = | NA (NA) | noncoding (945/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | 2866514 = | NA (NA) | 3 (0.200) | 3/234 | 1.8 | 37.5% | intergenic (+49/+45) | ygbN/rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| ? | NC_000913_3_pae_pgi | 2866544 = | 5 (0.330) | intergenic (+79/+15) | ygbN/rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor | |||||
| * | ? | NC_000913_3_pae_pgi | = 3123458 | 19 (1.170) | 5 (0.330) | 5/238 | 1.3 | 22.2% | coding (348/2172 nt) | glcB | malate synthase G |
| ? | NC_000913_3_pae_pgi | = 3123472 | 17 (1.110) | coding (334/2172 nt) | glcB | malate synthase G | |||||
| * | ? | NC_000913_3_pae_pgi | 3269740 = | NA (NA) | 4 (0.260) | 4/238 | 1.6 | NA | noncoding (19/98 nt) | RIP237 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP237 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | = 4137879 | NA (NA) | noncoding (91/98 nt) | RIP307 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP307 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_pgi | 3276876 = | 16 (0.990) | 6 (0.400) | 6/232 | 1.1 | 30.2% | intergenic (+23/‑126) | garD/prlF | D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system |
| ? | NC_000913_3_pae_pgi | 3276902 = | 13 (0.870) | intergenic (+49/‑100) | garD/prlF | D‑galactarate dehydrogenase/antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system | |||||
| * | ? | NC_000913_3_pae_pgi | 3570872 = | 14 (0.860) | 4 (0.260) | 4/240 | 1.6 | 27.3% | coding (448/1974 nt) | glgX | glycogen debranching enzyme |
| ? | NC_000913_3_pae_pgi | 3570898 = | 8 (0.520) | coding (422/1974 nt) | glgX | glycogen debranching enzyme | |||||
| * | ? | NC_000913_3_pae_pgi | = 3621525 | NA (NA) | 3 (0.190) | 3/244 | 1.9 | 100% | coding (2334/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913_3_pae_pgi | = 3621561 | 0 (0.000) | coding (2370/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913_3_pae_pgi | = 3628298 | 14 (0.860) | 6 (0.390) | 6/240 | 1.1 | 30.5% | coding (1241/2736 nt) | rbbA | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| ? | NC_000913_3_pae_pgi | = 3628309 | 14 (0.910) | coding (1230/2736 nt) | rbbA | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein | |||||
| * | ? | NC_000913_3_pae_pgi | = 3749147 | 15 (0.930) | 4 (0.260) | 4/240 | 1.6 | 20.9% | coding (571/663 nt) | sgbH | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase |
| ? | NC_000913_3_pae_pgi | = 3749165 | 16 (1.040) | coding (589/663 nt) | sgbH | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase | |||||
| * | ? | NC_000913_3_pae_pgi | 3749440 = | 9 (0.560) | 3 (0.190) | 3/248 | 1.9 | 23.2% | coding (209/861 nt) | sgbU | putative L‑xylulose 5‑phosphate 3‑epimerase |
| ? | NC_000913_3_pae_pgi | 3749468 = | 11 (0.690) | coding (237/861 nt) | sgbU | putative L‑xylulose 5‑phosphate 3‑epimerase | |||||
| * | ? | NC_000913_3_pae_pgi | = 4028187 | 11 (0.680) | 4 (0.260) | 4/244 | 1.6 | 27.0% | coding (586/1164 nt) | fadA | 3‑ketoacyl‑CoA thiolase (thiolase I) |
| ? | NC_000913_3_pae_pgi | = 4028202 | 11 (0.700) | coding (571/1164 nt) | fadA | 3‑ketoacyl‑CoA thiolase (thiolase I) | |||||
| * | ? | NC_000913_3_pae_pgi | 4094379 = | 19 (1.170) | 4 (0.280) | 4/222 | 1.5 | 23.0% | noncoding (64/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913_3_pae_pgi | 4094422 = | 10 (0.700) | noncoding (107/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | = 4150413 | 7 (0.430) | 6 (0.400) | 6/234 | 1.1 | 39.4% | intergenic (‑148/+34) | eptC/ppc | LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase |
| ? | NC_000913_3_pae_pgi | = 4150423 | 12 (0.800) | intergenic (‑158/+24) | eptC/ppc | LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase | |||||
| * | ? | NC_000913_3_pae_pgi | = 4192177 | 6 (0.370) | 4 (0.260) | 4/242 | 1.6 | 35.1% | coding (459/771 nt) | thiG | thiamine biosynthesis ThiGH complex subunit |
| ? | NC_000913_3_pae_pgi | = 4192203 | 9 (0.580) | coding (433/771 nt) | thiG | thiamine biosynthesis ThiGH complex subunit | |||||
| * | ? | NC_000913_3_pae_pgi | = 4295404 | 3 (0.190) | 6 (0.390) | 6/238 | 1.1 | 67.3% | noncoding (310/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913_3_pae_pgi | = 4295420 | 3 (0.200) | noncoding (326/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913_3_pae_pgi | = 4415221 | NA (NA) | 6 (0.390) | 6/240 | 1.1 | NA | noncoding (4/34 nt) | REP332 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP332 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913_3_pae_pgi | = 4415251 | NA (NA) | noncoding (34/34 nt) | REP332 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP332 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | 4569207 = | NA (NA) | 4 (0.260) | 4/240 | 1.6 | NA | noncoding (2/99 nt) | RIP347 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP347 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | 4569230 = | NA (NA) | noncoding (25/99 nt) | RIP347 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP347 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||