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 | freq | annotation | gene | description |
| RA | 123,050 | A→T | 100% | I12F (ATC→TTC) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 125,085 | 2 bp→CA | 100% | coding (2069‑2070/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 835,195 | A→G | 10.5% | K709R (AAA→AGA) | dinG → | ATP‑dependent DNA helicase DinG |
| RA | 953,650 | T→C | 9.6% | T273A (ACA→GCA) | focA ← | formate channel FocA |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,557,343 | C→T | 17.6% | T232T (ACG→ACA) | ddpF ← | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpF |
| RA | 1,559,325 | C→A | 21.6% | A196S (GCG→TCG) | ddpC ← | putative D,D‑dipeptide ABC transporter membrane subunit DdpC |
| RA | 1,816,318 | T→C | 8.3% | intergenic (+190/+68) | katE → / ← chbG | catalase II/chitin disaccharide deacetylase |
| RA | 1,934,850 | C→A | 82.3% | E489* (GAG→TAG) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| RA | 1,935,690 | C→T | 30.5% | V209I (GTT→ATT) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,356,738 | G→A | 12.2% | intergenic (+27/‑166) | glpC → / → rpnE | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C/inactive recombination‑promoting nuclease‑like protein RpnE |
| RA | 2,447,639 | G→A | 100% | H268Y (CAT→TAT) | prmB ← | 50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase |
| RA | 2,512,749 | G→A | 38.2% | intergenic (‑43/‑293) | mntH ← / → nupC | Mn(2(+))/Fe(2(+)): H(+) symporter MntH/nucleoside:H(+) symporter NupC |
| RA | 2,661,840 | A→C | 100% | C98G (TGC→GGC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,866,488 | G→C | 12.5% | intergenic (+23/+71) | ygbN → / ← rpoS | putative transporter YgbN/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,917,603 | T→G | 100% | V849V (GTT→GTG) | barA → | sensory histidine kinase BarA |
| RA | 2,962,561 | G→A | 11.6% | N68N (AAC→AAT) ‡ | ppdC ← | putative YgdA |
| RA | 2,962,562 | T→C | 13.2% | N68S (AAC→AGC) ‡ | ppdC ← | putative YgdA |
| RA | 2,971,151 | T→C | 11.8% | intergenic (+18/‑120) | ygdQ → / → ygdR | UPF0053 inner membrane protein YgdQ/DUF903 domain‑containing lipoprotein YgdR |
| RA | 2,971,159 | G→A | 12.2% | intergenic (+26/‑112) | ygdQ → / → ygdR | UPF0053 inner membrane protein YgdQ/DUF903 domain‑containing lipoprotein YgdR |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,210,838 | A→G | 100% | K20E (AAG→GAG) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,891,502 | C→G | 8.4% | intergenic (+19/‑113) | tnaB → / → mdtL | tryptophan:H(+) symporter TnaB/efflux pump MdtL |
| RA | 3,891,504 | T→A | 7.8% | intergenic (+21/‑111) | tnaB → / → mdtL | tryptophan:H(+) symporter TnaB/efflux pump MdtL |
| RA | 3,891,506 | C→G | 7.5% | intergenic (+23/‑109) | tnaB → / → mdtL | tryptophan:H(+) symporter TnaB/efflux pump MdtL |
| RA | 3,959,515 | T→A | 6.8% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase (NADP(+))/peptidyl‑prolyl cis‑trans isomerase C |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,049,986 | G→T | 7.3% | noncoding (88/109 nt) | spf → | small regulatory RNA Spot 42 |
| RA | 4,049,989 | A→C | 7.0% | noncoding (91/109 nt) | spf → | small regulatory RNA Spot 42 |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 36.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,314,233 | A→T | 6.2% | intergenic (+36/+111) | yjdP → / ← phnP | protein YjdP/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,323,426 | T→C | 15.9% | K309K (AAA→AAG) | phnD ← | phosphonate ABC transporter periplasmic binding protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 365886 | 366142 | 257 | 10 [9] | [9] 10 | lacZ | beta‑galactosidase |
| * | * | ÷ | NC_000913 | 366148 | 366391 | 244 | 10 [9] | [9] 10 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913 | 1196269 | 1211433 | 15165 | 10 [9] | [9] 10 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3621204–3622309 | 3653140–3652031 | 29723–31937 | 11 [9] | [9] 10 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 225281 | NA (NA) | 8 (0.240) | 6/254 | NT | NA | noncoding (1511/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | = 225293 | NA (NA) | noncoding (1523/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 2543861 | 23 (0.660) | 3 (0.090) | 3/252 | NT | 12.3% | coding (763/792 nt) | ucpA | putative oxidoreductase |
| ? | NC_000913 | = 2543865 | 21 (0.630) | coding (759/792 nt) | ucpA | putative oxidoreductase | |||||
| * | ? | NC_000913 | = 3967703 | 53 (1.520) | 4 (0.130) | 4/240 | NT | 7.3% | intergenic (+27/‑213) | rho/rfe | transcription termination factor Rho/UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| ? | NC_000913 | = 3967707 | 53 (1.670) | intergenic (+31/‑209) | rho/rfe | transcription termination factor Rho/UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase | |||||
| * | ? | NC_000913 | = 4168341 | 33 (0.940) | 9 (0.280) | 7/244 | NT | 22.9% | intergenic (+141/‑31) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu |
| ? | NC_000913 | = 4168363 | 30 (0.930) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA/tRNA‑Glu | |||||