mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 85,903:1 | +G | 3.6% | coding (274/1725 nt) | ilvI → | acetolactate synthase 3 large subunit |
| RA | 177,958 | T→A | 2.7% | T169S (ACC→TCC) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
| RA | 203,990 | A→G | 2.7% | T215A (ACG→GCG) | lpxB → | tetraacyldisaccharide‑1‑P synthase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 262,792 | Δ1 bp | 2.6% | intergenic (+36/‑79) | proA → / → thrW | gamma‑glutamylphosphate reductase/tRNA‑Thr |
| RA | 262,793 | Δ1 bp | 2.6% | intergenic (+37/‑78) | proA → / → thrW | gamma‑glutamylphosphate reductase/tRNA‑Thr |
| RA | 339,935 | C→T | 5.9% | intergenic (+192/‑230) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 339,941 | C→T | 5.6% | intergenic (+198/‑224) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 339,958 | G→A | 4.5% | intergenic (+215/‑207) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 370,659 | T→C | 4.6% | L128P (CTG→CCG) | mhpB → | 2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase |
| RA | 375,247 | A→G | 4.7% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,326 | A→G | 5.0% | intergenic (+445/‑133) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 463,633 | T→G | 3.9% | D573E (GAT→GAG) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 509,915 | T→C | 5.0% | M489V (ATG→GTG) | copA ← | copper transporter |
| RA | 580,732 | T→C | 4.3% | intergenic (‑287/‑102) | ylcI ← / → nohD | DUF3950 family protein, DLP12 prophage/DLP12 prophage, DNA packaging protein |
| RA | 715,490 | G→A | 3.1% | E27K (GAA→AAA) | ybfP → | lipoprotein |
| RA | 955,257:1 | +C | 4.1% | coding (1376/1761 nt) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor |
| RA | 1,120,333 | A→G | 3.5% | V85A (GTA→GCA) | solA ← | N‑methyltryptophan oxidase, FAD‑binding |
| RA | 1,172,409 | A→G | 3.6% | L519P (CTG→CCG) | mfd ← | transcription‑repair coupling factor |
| RA | 1,321,321 | G→A | 2.5% | R22C (CGC→TGC) | trpD ← | fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase |
| RA | 1,524,477 | G→A | 2.9% | intergenic (+109/+4) | yncE → / ← ansP | ATP‑binding protein, periplasmic, function unknown/L‑asparagine transporter |
| RA | 1,578,291:1 | +A | 3.6% | coding (1052/1686 nt) | yddA ← | putative multidrug ABC transporter permease/ATPase |
| RA | 1,608,653 | A→G | 3.6% | L124L (TTA→CTA) | yneE ← | bestrophin family putative inner membrane protein |
| RA | 1,612,919 | Δ1 bp | 2.6% | coding (333/927 nt) | glsB ← | glutaminase 2 |
| RA | 1,708,724 | G→A | 5.6% | K602K (AAG→AAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC | 1,709,006 | Δ3 bp | 2.6% | coding (2088‑2090/2223 nt) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,775,317 | T→A | 3.8% | I211N (ATT→AAT) | aroD → | 3‑dehydroquinate dehydratase |
| RA | 1,834,204 | A→G | 3.4% | Q30R (CAA→CGA) | ydjY → | putative ferrodoxin‑like lipoprotein |
| RA | 1,842,914 | A→G | 8.6% | M182V (ATG→GTG) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,858,935 | A→G | 2.8% | V432A (GTC→GCC) | ydjK ← | putative MFS sugar transporter, membrane protein |
| JC | 1,918,979:1 | (GTGAG)1→2 | 4.5% | coding (1470/2634 nt) | yebT → | MCE domain protein |
| 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 | 2,316,391 | T→C | 91.6% | Y73H (TAC→CAC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,409,368 | G→A | 2.7% | R170H (CGT→CAT) | yfbR → | 5'‑nucleotidase |
| RA | 2,435,536 | G→A | 2.6% | R33R (CGC→CGT) | truA ← | tRNA pseudouridine(38‑40) synthase |
| RA | 2,520,272 | A→T | 2.9% | A133A (GCT→GCA) | gltX ← | glutamyl‑tRNA synthetase |
| RA | 2,956,716:1 | +G | 3.0% | coding (2167/2889 nt) | ptrA ← | protease III |
| RA | 3,277,196 | T→A | 2.8% | M66K (ATG→AAG) | prlF → | antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,440,220 | G→A | 5.9% | L270F (CTT→TTT) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,527,604 | Δ1 bp | 7.4% | coding (1138/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| JC | 3,527,656 | Δ5 bp | 92.7% | coding (1190‑1194/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,769,954 | A→G | 6.5% | pseudogene (8/87 nt) | yibU → | pseudogene, H repeat‑associated protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,833,780 | G→T | 3.1% | R253S (CGT→AGT) | yicI ← | putative alpha‑glucosidase |
| RA | 3,865,423 | T→A | 2.6% | T284S (ACG→TCG) | yidE ← | putative transporter |
| JC | 3,992,523 | (CGGGC)2→1 | 89.3% | coding (1372‑1376/2547 nt) | cyaA → | adenylate cyclase |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,014,389 | T→C | 3.7% | D446D (GAT→GAC) | metE → | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,278,911 | C→T | 2.6% | T145M (ACG→ATG) | ghxP → | guanine/hypoxanthine permease, high affinity, guanine/hypoxanthine:H+ symporter |
| RA | 4,296,189 | A→G | 40.5% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 44.9% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 11.3% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,302 | A→G | 5.9% | intergenic (+509/+135) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | C→T | 3.5% | intergenic (+587/+57) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,309,627 | A→G | 2.5% | M452T (ATG→ACG) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,628 | T→A | 2.6% | M452L (ATG→TTG) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,629 | C→A | 2.9% | V451V (GTG→GTT) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,631 | C→G | 3.0% | V451L (GTG→CTG) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,633 | T→C | 2.8% | K450R (AAA→AGA) | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,636 | T→A | 2.6% | Y449F (TAC→TTC) | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,639 | A→T | 2.6% | I448N (ATT→AAT) | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,642 | T→A | 2.6% | E447V (GAA→GTA) | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,644 | G→A | 2.6% | A446A (GCC→GCT) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,645 | G→A | 2.6% | A446V (GCC→GTC) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,646 | C→A | 2.6% | A446S (GCC→TCC) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,647 | T→G | 2.6% | K445N (AAA→AAC) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,309,649 | T→G | 2.6% | K445Q (AAA→CAA) ‡ | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,315,559:1 | +G | 3.4% | coding (525/558 nt) | phnN ← | ribose 1,5‑bisphosphokinase |
| RA | 4,333,593 | T→C | 2.8% | N120S (AAT→AGT) | basR ← | response regulator in two‑component regulatory system with BasS |
| RA | 4,343,451 | Δ1 bp | 2.8% | coding (82/1422 nt) | melB → | melibiose:sodium symporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533632 | 2536444 | 2813 | 65 [61] | [61] 64 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 123 (0.930) | 68/510 | NT | 99.2% | 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 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 405054 | 116 (0.880) | 3 (0.020) | 3/496 | NT | 2.5% | coding (591/810 nt) | proC | pyrroline‑5‑carboxylate reductase, NAD(P)‑binding |
| ? | NC_000913 | = 405064 | 118 (0.920) | coding (581/810 nt) | proC | pyrroline‑5‑carboxylate reductase, NAD(P)‑binding | |||||
| * | ? | NC_000913 | 477337 = | 110 (0.840) | 4 (0.030) | 3/498 | NT | 3.4% | coding (1281/1551 nt) | ylaB | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| ? | NC_000913 | 477527 = | 117 (0.910) | coding (1091/1551 nt) | ylaB | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase | |||||
| * | ? | NC_000913 | 1045201 = | 185 (1.400) | 5 (0.040) | 5/492 | NT | 2.6% | coding (603/1140 nt) | gfcE | putative O‑antigen capsule outer membrane auxillary protein export channel |
| ? | NC_000913 | 1045310 = | 192 (1.510) | coding (494/1140 nt) | gfcE | putative O‑antigen capsule outer membrane auxillary protein export channel | |||||
| * | ? | NC_000913 | 1207790 = | 66 (0.500) | 61 (0.490) | 47/478 | NT | 51.1% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 55 (0.450) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 66 (0.500) | 57 (0.460) | 46/478 | NT | 49.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 55 (0.450) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 137 (1.040) | 88/510 | 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 | = 1299498 | 1 (0.010) | 87 (0.670) | 61/502 | NT | 98.3% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 2 (0.020) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 89 (0.680) | 49/510 | 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) | 124 (0.940) | 77/510 | 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 | 2306058 = | 143 (1.090) | 4 (0.030) | 4/496 | NT | 2.8% | coding (695/1647 nt) | mqo | malate dehydrogenase, FAD/NAD(P)‑binding domain |
| ? | NC_000913 | 2306078 = | 141 (1.100) | coding (675/1647 nt) | mqo | malate dehydrogenase, FAD/NAD(P)‑binding domain | |||||
| * | ? | NC_000913 | 3845530 = | 96 (0.730) | 12 (0.090) | 12/490 | NT | 10.9% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 103 (0.810) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 4309626 | 142 (1.080) | 6 (0.050) | 6/494 | NT | 4.1% | coding (1356/1533 nt) | alsA | D‑allose ABC transporter ATPase |
| ? | NC_000913 | = 4309650 | 144 (1.130) | coding (1332/1533 nt) | alsA | D‑allose ABC transporter ATPase | |||||
| * | ? | NC_000913 | 4345645 = | 126 (0.960) | 4 (0.030) +CGA |
4/504 | NT | 3.0% | intergenic (‑86/+36) | yjdF/fumB | DUF2238 family inner membrane protein/anaerobic class I fumarate hydratase (fumarase B) |
| ? | NC_000913 | 4345668 = | 134 (1.020) | intergenic (‑109/+13) | yjdF/fumB | DUF2238 family inner membrane protein/anaerobic class I fumarate hydratase (fumarase B) | |||||