mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,019 | Δ1 bp | 9.1% | intergenic (+138/‑440) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,020 | T→G | 9.2% | intergenic (+139/‑439) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,060 | C→T | 10.1% | intergenic (+179/‑399) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,065 | G→A | 9.8% | intergenic (+184/‑394) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,066 | G→C | 9.8% | intergenic (+185/‑393) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,067 | A→T | 12.0% | intergenic (+186/‑392) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,069 | G→C | 10.1% | intergenic (+188/‑390) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,072 | Δ1 bp | 9.8% | intergenic (+191/‑387) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,074 | G→C | 10.0% | intergenic (+193/‑385) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,075 | G→A | 9.8% | intergenic (+194/‑384) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,076 | G→T | 11.0% | intergenic (+195/‑383) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,079 | T→A | 10.1% | intergenic (+198/‑380) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,080 | T→C | 10.0% | intergenic (+199/‑379) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,081 | T→C | 10.1% | intergenic (+200/‑378) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,100:1 | +C | 9.1% | intergenic (+219/‑359) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,101 | T→A | 9.2% | intergenic (+220/‑358) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 579,331 | A→G | 7.3% | F88F (TTT→TTC) | ybcV ← | DLP12 prophage, uncharacterized protein |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,504,726:1 | +G | 8.0% | coding (1010/1149 nt) | insQ → | IS609 transposase B |
| RA | 1,909,451 | A→G | 7.2% | F217L (TTT→CTT) | kdgR ← | KDG regulon transcriptional repressor |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 3,050,410 | A→T | 6.2% | S86T (TCG→ACG) | gcvT ← | aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,959,651 | G→A | 7.2% | R54R (CGC→CGT) | ppiC ← | peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,992,437 | T→G | 19.3% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 16.8% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,149,252 | G→T | 5.6% | T338N (ACC→AAC) | eptC ← | LPS heptose I phosphoethanolamine transferase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533767 | 2536350 | 2584 | 17 [15] | [15] 16 | [ptsH]–crr | [ptsH], ptsI, crr |
| * | * | ÷ | NC_000913 | 3423837–3424230 | 3424402–3424236 | 7–566 | 16 [15] | [13] 16 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 43 (0.800) | 41/484 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 1200233 | 38 (0.700) | 3 (0.060) | 3/462 | NT | 8.1% | coding (574/1128 nt) | intE | e14 prophage, putative integrase |
| ? | NC_000913 | = 1200412 | 32 (0.620) | coding (395/1128 nt) | intE | e14 prophage, putative integrase | |||||
| * | ? | NC_000913 | 1207790 = | 14 (0.260) | 25 (0.500) | 21/452 | NT | 62.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.340) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.240) | 21 (0.420) | 19/452 | NT | 59.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 55 (1.020) | 41/484 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1293390 | 60 (1.110) | 3 (0.060) | 3/470 | NT | 4.9% | intergenic (‑468/‑137) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1293504 | 57 (1.090) | intergenic (‑582/‑23) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 1687987 | 31 (0.570) | 3 (0.060) | 3/466 | NT | 6.3% | coding (391/1647 nt) | fumA | fumarate hydratase (fumarase A), aerobic Class I |
| ? | NC_000913 | = 1688218 | 60 (1.150) | coding (160/1647 nt) | fumA | fumarate hydratase (fumarase A), aerobic Class I | |||||
| * | ? | NC_000913 | = 1877275 | 63 (1.170) | 3 (0.060) | 3/468 | NT | 4.8% | intergenic (+19/+3) | yeaO/yoaF | DUF488 family protein/DUF333 family outer membrane lipoprotein |
| ? | NC_000913 | = 1877290 | 59 (1.130) | coding (243/255 nt) | yoaF | DUF333 family outer membrane lipoprotein | |||||
| * | ? | NC_000913 | 1917402 = | 75 (1.390) | 3 (0.060) | 3/474 | NT | 4.0% | coding (1145/1284 nt) | yebS | inner membrane PqiA domain protein |
| ? | NC_000913 | 1917764 = | 71 (1.340) | coding (255/2634 nt) | yebT | MCE domain protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 42 (0.780) | 31/484 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 51 (0.940) | 37/484 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2192868 = | 46 (0.850) | 5 (0.100) | 3/468 | NT | 10.1% | intergenic (‑74/+189) | yehE/mrp | DUF2574 family protein/antiporter inner membrane protein |
| ? | NC_000913 | 2193250 = | 45 (0.860) | coding (917/1110 nt) | mrp | antiporter inner membrane protein | |||||
| * | ? | NC_000913 | = 2692283 | 57 (1.060) | 3 (0.060) | 3/476 | NT | 5.1% | coding (3259/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase |
| ? | NC_000913 | = 2692298 | 55 (1.040) | coding (3244/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase | |||||
| * | ? | NC_000913 | 2887322 = | 47 (0.870) | 3 (0.060) | 3/468 | NT | 7.0% | intergenic (‑105/‑30) | ygcB/sokX | Cascade complex anti‑viral R‑loop helicase‑annealase Cas3/sok‑related sRNA, function unknown |
| ? | NC_000913 | 2887733 = | 34 (0.650) | coding (578/735 nt) | cysH | phosphoadenosine phosphosulfate reductase, PAPS reductase, thioredoxin dependent | |||||
| * | ? | NC_000913 | = 3068490 | 41 (0.760) | 3 (0.060) | 3/472 | NT | 7.1% | coding (317/636 nt) | argO | arginine transporter |
| ? | NC_000913 | = 3068684 | 38 (0.720) | coding (123/636 nt) | argO | arginine transporter | |||||
| * | ? | NC_000913 | = 3154351 | 40 (0.740) | 3 (0.060) | 3/466 | NT | 7.2% | coding (866/957 nt) | yqhC | transcriptional activator of yqhD |
| ? | NC_000913 | = 3154364 | 39 (0.750) | coding (853/957 nt) | yqhC | transcriptional activator of yqhD | |||||