mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
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 | 526,792 | A→C | 15.0% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,796 | C→G | 15.8% | A1179G (GCG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 16.5% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 805,959 | A→G | 5.5% | intergenic (+195/+39) | ybhJ → / ← ybhC | aconitase family protein/acyl‑CoA thioesterase, lipoprotein |
| RA | 805,960 | A→C | 5.5% | intergenic (+196/+38) | ybhJ → / ← ybhC | aconitase family protein/acyl‑CoA thioesterase, lipoprotein |
| 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 | 1,529,175 | T→C | 100% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 100% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 100% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,620,224 | C→G | 5.0% | intergenic (+17/+14) | marB → / ← eamA | periplasmic mar operon regulator/cysteine and O‑acetyl‑L‑serine efflux system |
| RA | 1,666,466 | T→G | 7.8% | Y384* (TAT→TAG) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,666,468 | A→T | 7.7% | Q385L (CAG→CTG) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,666,470 | C→A | 7.9% | L386I (CTA→ATA) | clcB → | H(+)/Cl(‑) exchange transporter |
| RA | 1,788,336 | A→T | 6.9% | intergenic (+58/‑99) | ppsR → / → aroH | PEP synthase kinase and PEP synthase pyrophosphorylase/3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,356,734 | G→C | 6.4% | intergenic (+23/‑170) | glpC → / → yfaD | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein |
| RA | 2,356,737 | T→C | 6.5% | intergenic (+26/‑167) | glpC → / → yfaD | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein |
| RA | 2,356,738 | G→A | 6.2% | intergenic (+27/‑166) | glpC → / → yfaD | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein |
| RA | 2,356,741 | G→C | 6.4% | intergenic (+30/‑163) | glpC → / → yfaD | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster/transposase_31 family protein |
| RA | 2,581,669 | G→A | 5.3% | intergenic (+30/+65) | tktB → / ← ypfG | transketolase 2, thiamine triphosphate‑binding/DUF1176 family protein |
| RA | 2,581,670 | C→A | 5.4% | intergenic (+31/+64) | tktB → / ← ypfG | transketolase 2, thiamine triphosphate‑binding/DUF1176 family protein |
| RA | 3,038,277 | A→C | 5.0% | S182R (AGT→AGG) ‡ | dsbC ← | protein disulfide isomerase II |
| RA | 3,038,279 | T→A | 5.0% | S182C (AGT→TGT) ‡ | dsbC ← | protein disulfide isomerase II |
| RA | 3,038,281 | G→C | 5.0% | A181G (GCC→GGC) | dsbC ← | protein disulfide isomerase II |
| RA | 3,038,283 | T→A | 5.0% | P180P (CCA→CCT) ‡ | dsbC ← | protein disulfide isomerase II |
| RA | 3,038,285 | G→T | 5.8% | P180T (CCA→ACA) ‡ | dsbC ← | protein disulfide isomerase II |
| RA | 3,042,319 | T→A | 5.0% | intergenic (+26/+170) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,042,320 | C→T | 5.0% | intergenic (+27/+169) | ygfZ → / ← yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| RA | 3,233,708 | A→G | 6.1% | intergenic (+25/+20) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,233,709 | A→T | 6.1% | intergenic (+26/+19) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,233,710 | C→T | 6.0% | intergenic (+27/+18) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,234,506 | G→A | 5.5% | intergenic (‑51/+233) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,234,507 | A→T | 5.5% | intergenic (‑52/+232) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,234,508 | T→C | 5.5% | intergenic (‑53/+231) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,291,109 | A→T | 5.1% | K766* (AAA→TAA) ‡ | yraJ → | putative outer membrane protein |
| RA | 3,291,110 | A→T | 5.1% | K766I (AAA→ATA) ‡ | yraJ → | putative outer membrane protein |
| RA | 3,388,283 | T→C | 5.0% | T282A (ACA→GCA) | aaeA ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 4,070,413 | T→G | 5.1% | intergenic (‑12/+102) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,070,814 | G→A | 100% | R315C (CGT→TGT) | yihS ← | sulphoquinovose isomerase |
| RA | 4,070,817 | C→A | 100% | V314L (GTA→TTA) | yihS ← | sulphoquinovose isomerase |
| RA | 4,075,135 | T→G | 100% | I156S (ATC→AGC) | yihW → | putative transcriptional regulator for sulphoquinovose utilization |
| RA | 4,296,190 | A→G | 24.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 24.7% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 24.2% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.0% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 9.8% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 12.0% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,315,437 | A→T | 5.0% | F34L (TTT→TTA) ‡ | phnO ← | aminoalkylphosphonate N‑acetyltransferase |
| RA | 4,315,438 | A→T | 5.4% | F34Y (TTT→TAT) ‡ | phnO ← | aminoalkylphosphonate N‑acetyltransferase |
| RA | 4,315,439 | A→T | 5.7% | F34I (TTT→ATT) ‡ | phnO ← | aminoalkylphosphonate N‑acetyltransferase |
| RA | 4,323,257 | A→G | 5.7% | intergenic (‑27/+79) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,323,258 | A→C | 5.1% | intergenic (‑28/+78) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,323,264 | T→A | 5.3% | intergenic (‑34/+72) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,323,265 | T→A | 6.0% | intergenic (‑35/+71) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,323,271 | G→T | 5.2% | intergenic (‑41/+65) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,323,272 | C→T | 5.2% | intergenic (‑42/+64) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,444,191 | G→T | 5.9% | G27V (GGC→GTC) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,444,193 | A→C | 5.5% | T28P (ACC→CCC) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,472,236 | T→G | 13.9% | T54P (ACC→CCC) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423715–3424504 | 3424504 | 1–790 | 63 [62] | [62] 64 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 41 (0.300) | 63 (0.490) | 53/532 | NT | 61.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 41 (0.320) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 41 (0.300) | 55 (0.430) | 51/532 | NT | 58.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 41 (0.320) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1768798 | 88 (0.640) | 5 (0.040) | 3/552 | NT | 5.5% | intergenic (‑113/‑276) | ydiJ/ydiK | putative FAD‑linked oxidoreductase/UPF0118 family inner membrane protein |
| ? | NC_000913 | = 1768874 | 87 (0.650) | intergenic (‑189/‑200) | ydiJ/ydiK | putative FAD‑linked oxidoreductase/UPF0118 family inner membrane protein | |||||
| * | ? | NC_000913 | = 1879834 | 126 (0.930) | 7 (0.050) | 7/558 | NT | 5.3% | coding (115/360 nt) | yeaR | DUF1971 family protein, nitrate‑inducible |
| ? | NC_000913 | 2514274 = | NA (NA) | noncoding (2/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 1979270 | NA (NA) | 621 (4.540) | 330/564 | NT | 83.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3844640 | 127 (0.930) | coding (677/1767 nt) | adeD | cryptic adenine deaminase | |||||
| * | ? | NC_000913 | 2066607 = | 103 (0.750) | 6 (0.050) | 3/550 | NT | 5.6% | noncoding (747/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2102148 = | NA (NA) | noncoding (796/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 641 (4.690) | 341/564 | NT | 87.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3712115 = | 96 (0.700) | intergenic (‑108/+121) | yhjX/yhjY | pyruvate‑inducible inner membrane protein, putative transporter/autotransporter beta‑domain protein | |||||
| * | ? | NC_000913 | 3621436 = | NA (NA) | 4 (0.030) | 3/558 | NT | 100% | coding (2245/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3621558 = | 0 (0.000) | coding (2367/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||