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 |
| RA | 67,887:1 | +G | 71.6% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 67,887:2 | +T | 71.6% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 154,818:1 | +G | 10.0% | coding (609/2598 nt) | htrE ← | putative outer membrane usher protein |
| RA | 222,300 | Δ1 bp | 6.5% | coding (346/1032 nt) | metN ← | DL‑methionine transporter subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 417,301 | T→C | 4.9% | W54R (TGG→CGG) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 711,107 | C→T | 5.3% | W120* (TGG→TAG) | fldA ← | flavodoxin 1 |
| RA | 738,600 | A→C | 6.0% | K170T (AAA→ACA) | ybfD → | H repeat‑associated putative transposase |
| RA | 741,502 | Δ1 bp | 6.2% | coding (1055/1482 nt) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 962,674 | G→A | 5.4% | R227H (CGC→CAC) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,280,405 | Δ1 bp | 4.3% | coding (542/3744 nt) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,280,406 | Δ1 bp | 4.3% | coding (543/3744 nt) | narG → | nitrate reductase 1, alpha subunit |
| 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 | 1,350,329 | Δ1 bp | 5.5% | coding (711/789 nt) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,350,330 | Δ1 bp | 5.6% | coding (710/789 nt) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,430,701 | T→C | 4.7% | P551P (CCT→CCC) | stfR → | Rac prophage, putative tail fiber protein |
| RA | 1,512,664 | A→G | 4.7% | E337E (GAA→GAG) | ydcS → | putative ABC transporter periplasmic binding protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC | 2,023,805 | (CTTTA)2→1 | 67.9% | intergenic (+127/‑159) | fliR → / → rcsA | flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,128,593 | A→G | 9.5% | V99A (GTG→GCG) | wcaF ← | putative acyl transferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,316,679 | A→G | 100% | T169A (ACC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,415,631 | A→G | 4.6% | N296S (AAC→AGC) | pta → | phosphate acetyltransferase |
| RA | 2,655,792 | A→G | 5.3% | Y189H (TAC→CAC) | pepB ← | aminopeptidase B |
| RA | 2,792,347 | A→G | 4.0% | K359K (AAA→AAG) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| RA | 2,967,531 | A→G | 10.8% | L301P (CTG→CCG) | ptsP ← | PEP‑protein phosphotransferase enzyme I, GAF domain containing protein |
| RA | 3,271,984 | Δ1 bp | 4.7% | coding (766/885 nt) | garR ← | tartronate semialdehyde reductase |
| RA | 3,325,804 | T→A | 4.8% | K377I (AAA→ATA) | ftsH ← | protease, ATP‑dependent zinc‑metallo |
| RA | 3,416,047 | A→G | 5.0% | E339E (GAA→GAG) | acrF → | multidrug efflux system protein |
| RA | 3,527,589 | C→T | 100% | Q375* (CAG→TAG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,550,106 | T→C | 5.6% | Q789R (CAG→CGG) | malP ← | maltodextrin phosphorylase |
| JC | 3,628,522 | Δ101 bp | 4.3% | coding (916‑1016/2736 nt) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,883,789 | A→T | 4.8% | intergenic (‑61/‑546) | dnaA ← / → rpmH | chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator/50S ribosomal subunit protein L34 |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,186,261 | G→A | 34.1% | A305T (GCC→ACC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,381,371 | Δ1 bp | 4.2% | coding (949/1809 nt) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,573,988 | G→A | 6.1% | pseudogene (69/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533732 | 2536365 | 2634 | 17 [14] | [14] 19 | ptsH–crr | ptsH, ptsI, crr |
| * | * | ÷ | NC_000913 | 3423853–3424230 | 3424399–3424237 | 8–547 | 16 [15] | [15] 18 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 201043 = | 87 (1.410) | 3 (0.050) | 3/478 | NT | 3.4% | coding (73/1026 nt) | lpxD | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase |
| ? | NC_000913 | 201342 = | 87 (1.460) | coding (372/1026 nt) | lpxD | UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 45 (0.730) | 38/492 | 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 | 327919 = | 81 (1.320) | 3 (0.050) | 3/476 | NT | 3.9% | coding (815/1473 nt) | betB | betaine aldehyde dehydrogenase, NAD‑dependent |
| ? | NC_000913 | 328014 = | 69 (1.160) | coding (720/1473 nt) | betB | betaine aldehyde dehydrogenase, NAD‑dependent | |||||
| * | ? | NC_000913 | = 381460 | 5 (0.080) | 3 (0.050) | 3/486 | NT | 37.8% | coding (110/366 nt) | insC1 | IS2 repressor TnpA |
| ? | NC_000913 | = 381852 | NA (NA) | coding (179/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913 | = 609347 | NA (NA) | 3 (0.050) | 3/486 | NT | 3.2% | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex |
| ? | NC_000913 | 839227 = | 93 (1.510) | intergenic (‑20/+22) | ybiX/fiu | Fe(II)‑dependent oxygenase superfamily protein/catecholate siderophore receptor | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.240) | 28 (0.490) | 27/460 | NT | 57.1% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 28 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.210) | 27 (0.470) | 23/460 | NT | 57.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 44 (0.720) | 38/492 | 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 | = 1644844 | 57 (0.930) | 4 (0.070) | 4/470 | NT | 6.2% | coding (59/252 nt) | rem | Qin prophage, uncharacterized protein |
| ? | NC_000913 | = 1645012 | 67 (1.140) | intergenic (‑110/+107) | rem/hokD | Qin prophage, uncharacterized protein/Qin prophage, small toxic polypeptide | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 28 (0.460) | 25/492 | 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) | 52 (0.850) | 38/492 | 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 | = 2214225 | 59 (0.960) | 4 (0.070) | 4/470 | NT | 5.3% | coding (418/1686 nt) | yehU | inner membrane putative sensory kinase in two‑component system with YehT |
| ? | NC_000913 | = 2214406 | 87 (1.480) | coding (237/1686 nt) | yehU | inner membrane putative sensory kinase in two‑component system with YehT | |||||
| * | ? | NC_000913 | 2288918 = | NA (NA) | 73 (1.190) | 52/490 | NT | 100% | intergenic (‑6/+145) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3992703 = | 0 (0.000) | coding (1552/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 46 (0.750) | 34/490 | NT | 100% | intergenic (‑31/+2) | 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 | = 3992708 | 0 (0.000) | coding (1557/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 2719807 = | 69 (1.120) | 3 (0.050) | 3/474 | NT | 4.1% | coding (587/699 nt) | yfiP | DTW domain protein |
| ? | NC_000913 | 2720261 = | 74 (1.250) | coding (311/2661 nt) | pka | protein lysine acetyltransferase | |||||
| * | ? | NC_000913 | 3620997 = | 48 (0.780) | 3 (0.050) | 3/470 | NT | 10.2% | coding (1807/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3763870 = | 7 (0.120) | coding (1689/4134 nt) | rhsA | Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor | |||||