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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 20,896 | N→C | ?61Q (CAN→CAG) | rpsT ← | 30S ribosomal protein S20 |
| RA | 142,348 | N→A | ?254* (TNG→TAG) | fhuA → | ferrichrome porin FhuA |
| RA | 1,386,237 | 2 bp→GT | intergenic (‑60/+16) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional regulator |
| RA | 1,386,240 | 2 bp→AA | intergenic (‑63/+13) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional regulator |
| RA | 2,086,037 | A→C | intergenic (‑173/+57) | sdiA ← / ← yecC | transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein TcyN |
| MC JC | 2,806,542 | 689 bp→71 bp | coding (2‑690/690 nt) | ung → | uracil‑DNA glycosylase |
| RA | 3,917,708 | T→A | M1K (ATG→AAG) † | rpoZ → | DNA‑directed RNA polymerase subunit omega |
| MC JC | 3,917,725 | Δ22 bp | coding (19‑40/276 nt) | rpoZ → | DNA‑directed RNA polymerase subunit omega |
| RA | 4,032,695 | G→T | E271* (GAA→TAA) | rbsB → | ribose ABC transporter substrate‑binding protein RbsB |
| RA | 4,272,972 | +T | intergenic (‑226/‑135) | coaA ← / → ECDH10B_RS21215 | type I pantothenate kinase/tRNA‑Thr |
| MC JC | 4,296,510 | 671 bp→72 bp | coding (2‑672/672 nt) | nfi → | deoxyribonuclease V |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_010473 | 1139614 | 1141026 | 1413 | 14 [13] | [13] 14 | [pgaD]–[pgaB] | [pgaD],pgaC,[pgaB] |
| * | * | ÷ | NC_010473 | 1155447 | 1160082 | 4636 | 14 [13] | [13] 14 | [ycdZ]–[ymdA] | [ycdZ],csgG,csgF,csgE,csgD,csgB,csgA,csgC,[ymdA] |
| * | * | ÷ | NC_010473 | 1380531 | 1382046 | 1516 | 28 [0] | [13] 14 | [lacA]–[lacZ] | [lacA],lacY,[lacZ] |
| * | * | ÷ | NC_010473 | 1384901 | 1385121 | 221 | 15 [13] | [13] 14 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_010473 | 2160525 | 2163778 | 3254 | 14 [13] | [13] 14 | agn43 | agn43 |
| * | * | ÷ | NC_010473 | 3074089 | 3074262 | 174 | 14 [13] | [13] 14 | araE/kduD | arabinose‑proton symporter AraE/2‑dehydro‑3‑deoxy‑D‑gluconate 5‑dehydrogenase KduD |
| * | * | ÷ | NC_010473 | 3170327 | 3171676–3170619 | 293–1350 | 40 [0] | [12] 14 | [cmtA]–ECDH10B_RS15765 | [cmtA],ECDH10B_RS15765 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_010473 | 218238 = | 51 (1.330) | 53 (1.450) | 46/380 | 0.0 | 53.3% | intergenic (+13/‑193) | lpcA/yafJ | D‑sedoheptulose 7‑phosphate isomerase/class II glutamine amidotransferase |
| ? | NC_010473 | = 315947 | 44 (1.200) | intergenic (+81/+143) | yaiL/fghA | DUF2058 domain‑containing protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_010473 | = 262025 | 33 (0.860) | 46 (1.220) | 43/392 | 0.1 | 59.2% | pseudogene (1/294 nt) | xynR | DNA‑binding transcriptional repressor XynR |
| ? | NC_010473 | 263472 = | 31 (0.820) | pseudogene (465/468 nt) | xynR | DNA‑binding transcriptional repressor XynR | |||||
| * | ? | NC_010473 | 276303 = | 25 (0.650) | 56 (1.470) | 49/396 | 0.0 | 69.2% | coding (359/957 nt) | paoB | aldehyde oxidoreductase FAD‑binding subunit PaoB |
| ? | NC_010473 | 3211930 = | NA (NA) | intergenic (‑1/‑106) | nupG/ECDH10B_RS15990 | nucleoside permease NupG/IS4‑like element ISVsa5 family transposase | |||||
| * | ? | NC_010473 | = 276312 | 27 (0.700) | 52 (1.380) | 49/392 | 0.0 | 61.7% | coding (350/957 nt) | paoB | aldehyde oxidoreductase FAD‑binding subunit PaoB |
| ? | NC_010473 | 3199469 = | 38 (1.010) | pseudogene (665/669 nt) | nupG | nucleoside permease NupG | |||||
| * | ? | NC_010473 | 285519 = | 67 (1.750) | 46 (1.200) | 41/398 | 0.1 | 40.7% | intergenic (‑74/+1) | ecpA/ecpR | common pilus major fimbrillin subunit EcpA/ECP biosynthesis operon DNA‑binding transcriptional regulator EcpR |
| ? | NC_010473 | 319815 = | NA (NA) | coding (28/444 nt) | ECDH10B_RS01610 | transferase | |||||
| * | ? | NC_010473 | = 285525 | 67 (1.750) | 41 (1.080) | 35/394 | 0.2 | 38.2% | coding (538/543 nt) | ecpR | ECP biosynthesis operon DNA‑binding transcriptional regulator EcpR |
| ? | NC_010473 | = 321143 | NA (NA) | pseudogene (264/264 nt) | ECDH10B_RS23575 | acetyltransferase | |||||
| * | ? | NC_010473 | 306751 = | 35 (0.910) | 37 (0.970) | 31/398 | 0.4 | 51.4% | intergenic (+101/‑394) | ECDH10B_RS25865/pdeL | protein YahV/DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| ? | NC_010473 | 4640589 = | NA (NA) | intergenic (‑1257/+13) | nanC/ECDH10B_RS23035 | N‑acetylneuraminic acid outer membrane channel NanC/IS4‑like element ISVsa5 family transposase | |||||
| * | ? | NC_010473 | = 306759 | 38 (0.990) | 46 (1.200) | 40/398 | 0.1 | 54.8% | intergenic (+109/‑386) | ECDH10B_RS25865/pdeL | protein YahV/DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| ? | NC_010473 | 3211929 = | NA (NA) | pseudogene (1/603 nt) | nupG | nucleoside permease NupG | |||||
| * | ? | NC_010473 | 1118030 = | 1 (0.030) | 31 (0.810) | 28/396 | 0.6 | 59.6% | coding (844/1257 nt) | yccE | YccE family protein |
| ? | NC_010473 | = 3213256 | 41 (1.080) | intergenic (+12/+1) | ECDH10B_RS15990/ECDH10B_RS15995 | IS4‑like element ISVsa5 family transposase/DUF4092 domain‑containing protein | |||||
| * | ? | NC_010473 | = 1118039 | 3 (0.080) | 31 (0.810) | 29/396 | 0.6 | 91.2% | coding (853/1257 nt) | yccE | YccE family protein |
| ? | NC_010473 | 3211929 = | NA (NA) | pseudogene (1/603 nt) | nupG | nucleoside permease NupG | |||||
| * | ? | NC_010473 | = 1380530 | 0 (0.000) | 14 (0.600) +78 bp |
13/242 | 1.1 | 58.2% | coding (91/612 nt) | lacA | galactoside O‑acetyltransferase |
| ? | NC_010473 | = 4471165 | 33 (0.860) | intergenic (+109/‑29) | groL/yjeI | chaperonin GroEL/DUF4156 domain‑containing protein | |||||
| * | ? | NC_010473 | 1455332 = | 43 (1.120) | 31 (0.870) +CGTTACTGGTTTCAT |
23/368 | 0.9 | 45.6% | coding (1/978 nt) | pspF | phage shock protein operon transcriptional activator |
| ? | NC_010473 | 3365613 = | 37 (0.970) | intergenic (+244/+370) | yhaC/rnpB | YhaC family protein/RNase P RNA component class A | |||||
| * | ? | NC_010473 | 1823174 = | 1 (0.030) | 30 (0.780) | 27/398 | 0.7 | 60.6% | coding (145/816 nt) | mepH | peptidoglycan DD‑endopeptidase MepH |
| ? | NC_010473 | 3199469 = | 38 (0.990) | pseudogene (665/669 nt) | nupG | nucleoside permease NupG | |||||
| * | ? | NC_010473 | = 1823182 | 1 (0.030) | 32 (0.840) | 28/398 | 0.6 | 97.0% | coding (153/816 nt) | mepH | peptidoglycan DD‑endopeptidase MepH |
| ? | NC_010473 | = 3200797 | NA (NA) | pseudogene (2/2952 nt) | ECDH10B_RS15940 | SslE/AcfD family lipoprotein zinc metalloprotease | |||||
| * | ? | NC_010473 | = 3170326 | 0 (0.000) | 40 (1.050) | 37/396 | 0.2 | 100% | pseudogene (294/1257 nt) | cmtA | PTS mannitol transporter subunit IICB |
| ? | NC_010473 | 3225914 = | NA (NA) | coding (33/1137 nt) | yghO | protein YghO | |||||
| * | ? | NC_010473 | = 3200797 | NA (NA) | 33 (0.860) | 30/398 | 0.5 | 97.1% | pseudogene (2/2952 nt) | ECDH10B_RS15940 | SslE/AcfD family lipoprotein zinc metalloprotease |
| ? | NC_010473 | = 3632463 | 1 (0.030) | intergenic (‑112/‑116) | ompR/greB | two‑component system response regulator OmpR/transcription elongation factor GreB | |||||
| * | ? | NC_010473 | 3211929 = | NA (NA) | 30 (0.790) | 27/396 | 0.7 | 93.8% | pseudogene (1/603 nt) | nupG | nucleoside permease NupG |
| ? | NC_010473 | 3632455 = | 2 (0.050) | intergenic (‑104/‑124) | ompR/greB | two‑component system response regulator OmpR/transcription elongation factor GreB | |||||
| * | ? | NC_010473 | 3816235 = | NA (NA) | 36 (0.950) | 33/394 | 0.3 | 94.8% | intergenic (‑35/‑45) | hokA/ECDH10B_RS25725 | type I toxin‑antitoxin system toxin HokA/IS3‑like element IS150 family transposase |
| ? | NC_010473 | 4028795 = | 2 (0.050) | intergenic (+4/‑163) | kup/rbsD | low affinity potassium transporter Kup/D‑ribose pyranase | |||||
| * | ? | NC_010473 | = 3817675 | NA (NA) | 25 (0.650) | 25/398 | 0.9 | 100% | intergenic (+26/+253) | ECDH10B_RS25725/glyS | IS3‑like element IS150 family transposase/glycine‑‑tRNA ligase subunit beta |
| ? | NC_010473 | = 4028799 | 0 (0.000) | intergenic (+8/‑159) | kup/rbsD | low affinity potassium transporter Kup/D‑ribose pyranase | |||||