 |
breseq version 0.36.1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 161,041 | T→G | 100% | N313H (AAC→CAC) | pcnB ← | polynucleotide adenylyltransferase PcnB |
| RA | 380,188 | A→C | 100% | F239L (TTT→TTG) | araJ ← | MFS transporter AraJ |
| RA | 430,835 | C→T | 100% | intergenic (‑48/‑108) | ECB_RS02045 ← / → lon | IS4 family transposase/endopeptidase La |
| RA | 475,288:1 | +G | 100% | coding (18/1677 nt) | ybaL ← | Kef family K(+) transporter |
| RA | 649,391 | T→A | 100% | I471F (ATC→TTC) | mrdA ← | peptidoglycan DD‑transpeptidase MrdA |
| RA | 668,787 | A→C | 100% | Y65D (TAC→GAC) | gltI ← | glutamate/aspartate ABC transporter substrate‑binding protein GltI |
| RA | 683,496 | A→C | 100% | V65G (GTT→GGT) | nagC ← | DNA‑binding transcriptional regulator NagC |
| RA | 910,316 | T→C | 100% | intergenic (+176/‑175) | ybjN → / → potF | YbjN domain‑containing protein/spermidine/putrescine ABC transporter substrate‑binding protein PotF |
| RA | 1,248,380 | A→C | 100% | D295E (GAT→GAG) | dhaM ← | dihydroxyacetone kinase subunit DhaM |
| RA | 1,286,699 | C→A | 100% | intergenic (+23/+161) | narI → / ← ECB_RS22925 | respiratory nitrate reductase subunit gamma/RtT sRNA |
| RA | 1,329,516 | C→T | 100% | H33Y (CAC→TAC) | topA → | type I DNA topoisomerase |
| RA | 1,976,879 | T→G | 100% | intergenic (‑57/‑76) | hprR ← / → hiuH | response regulator transcription factor HprR/hydroxyisourate hydrolase |
| RA | 2,082,685 | G→A | 100% | A494V (GCT→GTT) | yegI ← | protein kinase YegI |
| RA | 2,732,014 | C→A | 100% | R91L (CGC→CTC) | hypF ← | carbamoyltransferase HypF |
| RA | 3,045,069 | G→T | 100% | T312N (ACC→AAC) | sslE ← | lipoprotein metalloprotease SslE |
| RA | 3,155,168 | G→A | 100% | G296S (GGC→AGC) | ebgR → | transcriptional regulator EbgR |
| RA | 3,200,643 | C→A | 100% | intergenic (+11/‑245) | tdcR → / → ECB_RS15790 | transcriptional activator TdcR/hypothetical protein |
| RA | 3,248,957 | A→T | 100% | D764E (GAT→GAA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,288,092 | G→A | 100% | R57C (CGT→TGT) | arcB ← | aerobic respiration two‑component sensor histidine kinase ArcB |
| MC JC | 3,289,962 | Δ16 bp | 100% | coding (3‑18/4461 nt) | gltB → | glutamate synthase large subunit |
| RA | 3,339,158 | A→C | 100% | intergenic (+22/‑4) | dusB → / → fis | tRNA dihydrouridine synthase DusB/DNA‑binding transcriptional regulator Fis |
| RA | 3,369,432 | T→C | 100% | D50G (GAC→GGC) | rpsD ← | 30S ribosomal protein S4 |
| RA | 3,370,027 | T→A | 100% | K117M (AAG→ATG) | rpsM ← | 30S ribosomal protein S13 |
| RA | 3,483,047 | C→A | 100% | R455S (CGC→AGC) | malT → | HTH‑type transcriptional regulator MalT |
| RA | 3,490,112 | C→T | 100% | A105T (GCG→ACG) | glpE ← | thiosulfate sulfurtransferase GlpE |
| RA | 3,762,741 | A→T | 100% | K662I (AAA→ATA) | spoT → | bifunctional GTP diphosphokinase/guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,875,625:1 | +T | 100% | intergenic (‑59/+294) | glmU ← / ← atpC | bifunctional UDP‑N‑acetylglucosamine diphosphorylase/glucosamine‑1‑phosphate N‑acetyltransferase GlmU/F0F1 ATP synthase subunit epsilon |
| RA | 3,893,550:1 | +G | 100% | intergenic (+5/‑51) | kup → / → ECB_RS25215 | low affinity potassium transporter Kup/IS3 family transposase |
| MC JC | 3,894,998 | Δ6,934 bp | 100% | rbsD–[mdtD] | rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [mdtD] | |
| RA | 4,100,655 | C→T | 100% | M192I (ATG→ATA) | hslU ← | HslU‑‑HslV peptidase ATPase subunit |
| RA | 4,201,911 | C→T | 100% | A217T (GCG→ACG) | iclR ← | glyoxylate bypass operon transcriptional repressor IclR |
| RA | 4,616,396 | G→A | 100% | G290S (GGC→AGC) | nadR → | multifunctional transcriptional regulator/nicotinamide‑nucleotide adenylyltransferase/ribosylnicotinamide kinase NadR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_012967 | 1 | 3 | 3 | NA [0] | [1] 2 | –/thrL | –/thr operon leader peptide |
| * | * | ÷ | NC_012967 | 86799 | 86803 | 5 | 2 [1] | [0] 2 | leuL/leuO | leu operon leader peptide/transcriptional regulator LeuO |
| * | * | ÷ | NC_012967 | 546961–547700 | 553478–553357 | 5658–6518 | 2 [1] | [0] 2 | [ECB_RS02630]–[ECB_RS02685] | [ECB_RS02630],ECB_RS02635,essD,rrrD,rzoD,iss,ylcI,nohD,[ECB_RS02685] |
| * | * | ÷ | NC_012967 | 554554–554670 | 555928–555878 | 1209–1375 | 2 [1] | [1] 2 | [ECB_RS02685]–[ECB_RS02690] | [ECB_RS02685],[ECB_RS02690] |
| * | * | ÷ | NC_012967 | 625409 | 625417 | 9 | 2 [1] | [1] 2 | ybdR/rnk | glutathione‑dependent formaldehyde dehydrogenase/nucleoside diphosphate kinase regulator |
| * | * | ÷ | NC_012967 | 910579 | 910586 | 8 | 2 [1] | [1] 2 | potF | spermidine/putrescine ABC transporter substrate‑binding protein PotF |
| * | * | ÷ | NC_012967 | 1133737 | 1133750 | 14 | 2 [1] | [1] 2 | yceJ/ECB_RS05605 | cytochrome b/YceO family protein |
| * | * | ÷ | NC_012967 | 1256440 | 1256445 | 6 | 2 [0] | [1] 2 | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF |
| * | * | ÷ | NC_012967 | 1739289 | 1739297 | 9 | 3 [1] | [0] 2 | sufC | Fe‑S cluster assembly ATPase SufC |
| * | * | ÷ | NC_012967 | 1756027 | 1756039 | 13 | 2 [1] | [1] 2 | ydiP | AraC family transcriptional regulator |
| * | * | ÷ | NC_012967 | 1868599 | 1868612 | 14 | 3 [1] | [1] 2 | yeaY | Slp family lipoprotein YeaY |
| * | * | ÷ | NC_012967 | 2031681–2031702 | 2054967–2054947 | 23246–23287 | 2 [0] | [1] 2 | [cpsG]–[cpsG] | [cpsG],ECB_RS10255,ECB_RS10260,wbbD,ECB_RS10270,wzy,ECB_RS10280,ECB_RS10285,vioB,vioA,wzx,rfbC,rfbA,rfbD,rfbB,galF,wcaM,wcaL,wcaK,wzxC,wcaJ,[cpsG] |
| * | * | ÷ | NC_012967 | 2198859 | 2198870 | 12 | 2 [1] | [1] 2 | lysP | lysine‑specific permease |
| * | * | ÷ | NC_012967 | 2610962 | 2610999 | 38 | 2 [1] | [1] 2 | qseE | two component system sensor histidine kinase QseE/GlrK |
| * | * | ÷ | NC_012967 | 2625791 | 2625803 | 13 | 2 [0] | [1] 2 | rnc/lepB | ribonuclease III/signal peptidase I |
| * | * | ÷ | NC_012967 | 3357546 | 3357557 | 12 | 2 [1] | [1] 2 | yrdA | gamma carbonic anhydrase family protein |
| * | * | ÷ | NC_012967 | 3493584 | 3493589 | 6 | 2 [1] | [1] 2 | ECB_RS17340 | PstS family phosphate ABC transporter substrate‑binding protein |
| * | * | ÷ | NC_012967 | 4046323 | 4046325 | 3 | 2 [0] | [0] 2 | yihQ | sulfoquinovosidase |
| * | * | ÷ | NC_012967 | 4607056 | 4607069 | 14 | 2 [1] | [1] 2 | deoC | deoxyribose‑phosphate aldolase |
| * | * | ÷ | NC_012967 | 4629803 | 4629812 | 10 | 2 [1] | [0] NA | yjtD/– | tRNA/rRNA methyltransferase/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_012967 | 16972 = | 0 (0.000) | 9 (0.940) | 3/50 | NT | 100% | intergenic (‑71/‑516) | mokC/nhaA | type I toxin‑antitoxin system toxin MokC/Na+/H+ antiporter NhaA |
| ? | NC_012967 | 588495 = | NA (NA) | intergenic (‑222/‑47) | ybdK/ECB_RS24840 | YbdK family carboxylate‑amine ligase/IS3‑like element IS150 family transposase | |||||
| * | ? | NC_012967 | = 16976 | 0 (0.000) | 6 (0.680) | 6/46 | NT | 100% | intergenic (‑75/‑512) | mokC/nhaA | type I toxin‑antitoxin system toxin MokC/Na+/H+ antiporter NhaA |
| ? | NC_012967 | = 590469 | NA (NA) | intergenic (+24/‑74) | ECB_RS24845/hokE | IS3 family transposase/type I toxin‑antitoxin system toxin HokE | |||||
| * | ? | NC_012967 | 589884 = | NA (NA) | 4 (0.450) | 3/46 | NT | NA | pseudogene (384/698 nt) | ECB_RS23205 | IS1 family transposase |
| ? | NC_012967 | = 590469 | NA (NA) | intergenic (+24/‑74) | ECB_RS24845/hokE | IS3 family transposase/type I toxin‑antitoxin system toxin HokE | |||||
| * | ? | NC_012967 | 664690 = | NA (NA) | 11 (1.240) | 9/46 | NT | 100% | intergenic (‑3/‑45) | gltL/ECB_RS24860 | glutamate/aspartate ABC transporter ATP‑binding protein GltL/IS3 family transposase |
| ? | NC_012967 | 1270658 = | 0 (0.000) | intergenic (‑165/+240) | ECB_RS06335/chaA | type I toxin‑antitoxin system toxin Ldr family protein/sodium‑potassium/proton antiporter ChaA | |||||
| * | ? | NC_012967 | 1460160 = | NA (NA) | 9 (0.970) | 7/48 | NT | 100% | intergenic (‑115/‑55) | gap/ECB_RS07290 | type I glyceraldehyde‑3‑phosphate dehydrogenase/IS1 family transposase |
| ? | NC_012967 | = 1604671 | 0 (0.000) | coding (1212/2379 nt) | ECB_RS07985 | prophage tail fiber N‑terminal domain‑containing protein | |||||
| * | ? | NC_012967 | 1733645 = | 0 (0.000) | 14 (1.580) | 13/46 | NT | 100% | coding (681/1413 nt) | pykF | pyruvate kinase PykF |
| ? | NC_012967 | = 2775875 | NA (NA) | intergenic (‑45/+204) | ECB_RS25125/cysH | IS3 family transposase/phosphoadenosine phosphosulfate reductase | |||||
| * | ? | NC_012967 | = 1733649 | 0 (0.000) | 7 (0.730) | 7/50 | NT | 100% | coding (685/1413 nt) | pykF | pyruvate kinase PykF |
| ? | NC_012967 | 2774435 = | NA (NA) | intergenic (‑67/+26) | ECB_RS13765/ECB_RS25125 | type I toxin‑antitoxin system Hok family toxin/IS3 family transposase | |||||
| * | ? | NC_012967 | 1821523 = | 0 (0.000) | 10 (1.130) | 9/46 | NT | 100% | coding (577/1041 nt) | ynjI | DUF1266 domain‑containing protein |
| ? | NC_012967 | = 2775875 | NA (NA) | intergenic (‑45/+204) | ECB_RS25125/cysH | IS3 family transposase/phosphoadenosine phosphosulfate reductase | |||||
| * | ? | NC_012967 | = 1821528 | 0 (0.000) | 7 (0.760) | 6/48 | NT | 100% | coding (572/1041 nt) | ynjI | DUF1266 domain‑containing protein |
| ? | NC_012967 | 2774436 = | NA (NA) | intergenic (‑68/+25) | ECB_RS13765/ECB_RS25125 | type I toxin‑antitoxin system Hok family toxin/IS3 family transposase | |||||
| * | ? | NC_012967 | 2772857 = | NA (NA) | 13 (1.540) | 7/44 | NT | 93.7% | intergenic (+378/‑54) | iap/ECB_RS13760 | alkaline phosphatase isozyme conversion aminopeptidase/IS4 family transposase |
| ? | NC_012967 | = 4524530 | 1 (0.100) | coding (502/549 nt) | fimA | type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_012967 | = 2774193 | NA (NA) | 13 (1.540) | 11/44 | NT | 93.7% | intergenic (+170/+23) | ECB_RS13760/ECB_RS13765 | IS4 family transposase/type I toxin‑antitoxin system Hok family toxin |
| ? | NC_012967 | 4524519 = | 1 (0.100) | coding (491/549 nt) | fimA | type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_012967 | 2774435 = | NA (NA) | 8 (0.870) | 7/48 | NT | 100% | intergenic (‑67/+26) | ECB_RS13765/ECB_RS25125 | type I toxin‑antitoxin system Hok family toxin/IS3 family transposase |
| ? | NC_012967 | = 3015774 | 0 (0.000) | coding (1195/1677 nt) | ECB_RS14885 | polysaccharide export protein | |||||
| * | ? | NC_012967 | = 2775875 | NA (NA) | 9 (1.020) | 7/46 | NT | 100% | intergenic (‑45/+204) | ECB_RS25125/cysH | IS3 family transposase/phosphoadenosine phosphosulfate reductase |
| ? | NC_012967 | 3015769 = | 0 (0.000) | coding (1190/1677 nt) | ECB_RS14885 | polysaccharide export protein | |||||
| * | ? | NC_012967 | = 3630716 | NA (NA) | 11 (1.140) | 9/50 | NT | NA | intergenic (‑171/‑305) | ECB_RS25605/yhjV | type I toxin‑antitoxin system toxin Ldr family protein/amino acid permease |
| ? | NC_012967 | = 3652533 | NA (NA) | intergenic (+26/+253) | ECB_RS25190/glyS | IS3 family transposase/glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_012967 | 3651091 = | NA (NA) | 8 (0.830) | 7/50 | NT | NA | intergenic (‑33/‑47) | hokA/ECB_RS25190 | type I toxin‑antitoxin system toxin HokA/IS3 family transposase |
| ? | NC_012967 | = 3741531 | NA (NA) | pseudogene (380/698 nt) | ECB_RS18445 | IS1‑like element IS1A family transposase | |||||