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 | 454,856 | G→A | 5.4% | intergenic (+67/‑277) | bolA → / → tig | stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor) |
| RA | 860,655 | C→T | 5.2% | G651D (GGT→GAT) | ybiW ← | putative pyruvate formate lyase |
| RA | 920,757 | T→C | 6.0% | R137R (CGT→CGC) | macB → | macrolide ABC transporter peremase/ATPase |
| RA | 922,314:1 | +C | 8.0% | intergenic (+21/+52) | macB → / ← cspD | macrolide ABC transporter peremase/ATPase/inhibitor of DNA replication, cold shock protein homolog |
| RA | 1,060,123 | A→T | 5.2% | N290Y (AAC→TAC) ‡ | torA → | trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit |
| RA | 1,060,125 | C→A | 6.0% | N290K (AAC→AAA) ‡ | torA → | trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit |
| RA | 1,100,793 | A→C | 5.1% | intergenic (+6/+58) | ycdZ → / ← csgG | DUF1097 family inner membrane protein/curli production assembly/transport outer membrane lipoprotein |
| RA | 1,127,689 | G→A | 5.1% | R295H (CGT→CAT) | yceM → | putative oxidoreductase |
| RA | 1,277,191 | C→T | 5.7% | R143H (CGC→CAC) | narX ← | sensory histidine kinase in two‑component regulatory system with NarL |
| RA | 1,318,478 | G→T | 6.5% | I437I (ATC→ATA) ‡ | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,318,479 | A→G | 6.3% | I437T (ATC→ACC) ‡ | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,318,480 | T→G | 6.3% | I437L (ATC→CTC) ‡ | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,318,481 | G→C | 6.3% | G436G (GGC→GGG) ‡ | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,318,483 | C→T | 6.3% | G436S (GGC→AGC) ‡ | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| MC JC | 1,402,042 | Δ183,606 bp | 100% | [abgB]–[ydeP] | 176 genes [abgB], abgA, abgR, mcaS, smrA, ydaM, ydaN, fnrS, dbpA, ttcA, intR, ydaQ, ydaC, ralR, recT, recE, racC, ydaE, kilR, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, tmpR, lomR, insH1, lomR, stfR, tfaR, pinR, ynaE, ttcC, uspF, ompN, micC, pfo, ydbJ, hslJ, ldhA, ydbH, ynbE, ydbL, feaR, feaB, tynA, paaZ, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, ynbG, ydbA, insD1, insC1, ydbA, insI1, ydbA, ydbC, ydbD, ynbA, ynbB, ynbC, ynbD, azoR, hrpA, ydcF, aldA, gapC, gapC, cybB, rydC, ydcA, hokB, mokB, sokB, trg, ydcI, ydcJ, opgD, ydcH, rimL, ydcK, tehA, tehB, ydcL, insP, insQ, ydcO, ydcN, ydcP, yncJ, hicA, hicB, ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ydcX, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, rhsE, ydcD, yncI, yncI, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU, yddK, yddK, yddL, yddG, fdnG, fdnH, fdnI, yddM, adhP, maeA, sra, bdm, osmC, ddpF, ddpD, ddpC, ddpB, ddpA, ddpX, dosP, dosC, yddW, gadC, gadB, pqqL, yddB, yddA, ydeM, ydeN, ydeO, safA, [ydeP] |
|
| RA | 1,602,236 | A→T | 6.7% | Q249H (CAA→CAT) | lsrA → | autoinducer 2 import ATP‑binding protein |
| RA | 1,602,239 | A→T | 6.8% | K250N (AAA→AAT) | lsrA → | autoinducer 2 import ATP‑binding protein |
| RA | 1,602,242 | A→T | 6.7% | L251F (TTA→TTT) | lsrA → | autoinducer 2 import ATP‑binding protein |
| RA | 1,615,567 | A→G | 5.8% | E255G (GAG→GGG) | yneJ → | putative DNA‑binding transcriptional regulator |
| RA | 1,674,958 | A→T | 6.6% | intergenic (+11/+14) | tqsA → / ← pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| RA | 1,836,904 | A→G | 5.5% | S278G (AGC→GGC) ‡ | ynjB → | putative ABC transporter periplasmic binding protein |
| RA | 1,836,905 | G→C | 5.1% | S278T (AGC→ACC) ‡ | ynjB → | putative ABC transporter periplasmic binding protein |
| RA | 1,836,906 | C→T | 5.1% | S278S (AGC→AGT) ‡ | ynjB → | putative ABC transporter periplasmic binding protein |
| RA | 1,865,682 | G→C | 5.0% | intergenic (‑46/+44) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| 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 | 2,174,085 | G→A | 100% | pseudogene (194/914 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 | 2,247,030 | G→A | 6.8% | intergenic (‑261/+33) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,247,031 | G→A | 7.0% | intergenic (‑262/+32) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,247,032 | T→C | 6.8% | intergenic (‑263/+31) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,247,033 | T→C | 7.1% | intergenic (‑264/+30) | cirA ← / ← lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| RA | 2,314,800 | A→C | 7.2% | Q438P (CAG→CCG) ‡ | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,314,801 | G→T | 7.1% | Q438H (CAG→CAT) ‡ | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,319,582 | C→G | 5.1% | V99L (GTG→CTG) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,446,813 | G→A | 6.4% | P221S (CCG→TCG) | aroC ← | chorismate synthase |
| RA | 2,772,226 | C→T | 5.2% | pseudogene (841/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein |
| RA | 2,772,227 | A→T | 5.3% | pseudogene (840/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein |
| RA | 2,777,571 | A→G | 5.7% | D40G (GAC→GGC) | ypjF → | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,846,376 | C→T | 5.5% | Q32Q (CAG→CAA) | hycE ← | hydrogenase 3, large subunit |
| RA | 3,269,967 | C→T | 6.1% | intergenic (+365/+249) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,968 | G→T | 6.2% | intergenic (+366/+248) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA 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 |
| MC JC | 3,936,337 | Δ902 bp | 100% | [rbsB] | [rbsB] | |
| RA | 3,937,351 | A→T | 100% | N20Y (AAT→TAT) | rbsK → | ribokinase |
| JC JC | 3,938,845 | IS2 (+) +5 bp | 100% | coding (619‑623/993 nt) | rbsR → | transcriptional repressor of ribose metabolism |
| RA | 3,967,666 | A→T | 100% | K417I (AAA→ATA) | rho → | transcription termination factor |
| RA | 4,040,827 | T→G | 5.8% | intergenic (+191/+79) | rrfA → / ← mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| RA | 4,070,413 | T→G | 7.4% | intergenic (‑12/+102) | yihR ← / ← yihS | putative sulphoquinovose mutarotase/sulphoquinovose isomerase |
| RA | 4,229,394 | G→T | 5.1% | intergenic (+32/+59) | yjbB → / ← pepE | putative Na+/Pi‑cotransporter/peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,229,396 | C→G | 5.1% | intergenic (+34/+57) | yjbB → / ← pepE | putative Na+/Pi‑cotransporter/peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,229,398 | A→C | 5.2% | intergenic (+36/+55) | yjbB → / ← pepE | putative Na+/Pi‑cotransporter/peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,229,404 | G→T | 5.1% | intergenic (+42/+49) | yjbB → / ← pepE | putative Na+/Pi‑cotransporter/peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,229,405 | C→T | 5.2% | intergenic (+43/+48) | yjbB → / ← pepE | putative Na+/Pi‑cotransporter/peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,245,110 | T→G | 6.7% | intergenic (‑35/+119) | malF ← / ← malE | maltose transporter subunit/maltose transporter subunit |
| RA | 4,296,190 | A→G | 19.4% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 21.6% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 37.9% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 22.6% | intergenic (+492/+150) | 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 | 4,335,655 | T→A | 5.2% | intergenic (‑65/+39) | eptA ← / ← adiC | lipid A phosphoethanolamine transferase/arginine:agmatine antiporter |
| RA | 4,383,872 | G→A | 5.4% | G12R (GGA→AGA) | yjeM → | putative transporter |
| RA | 4,552,833 | T→C | 6.2% | intergenic (+13/‑68) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| RA | 4,552,837 | Δ1 bp | 5.3% | intergenic (+17/‑64) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| RA | 4,552,841:1 | +A | 5.5% | intergenic (+21/‑60) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| RA | 4,552,845 | G→A | 5.8% | intergenic (+25/‑56) | uxuA → / → uxuB | mannonate hydrolase/D‑mannonate oxidoreductase, NAD‑dependent |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423844–3424483 | 3424483 | 1–640 | 39 [38] | [38] 39 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 57 (0.570) | 30 (0.320) | 28/530 | NT | 40.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 36 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 57 (0.570) | 40 (0.430) | 38/530 | NT | 47.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 36 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 183 (1.870) | 140/554 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 3304484 | NA (NA) | 4 (0.040) | 3/540 | NT | NA | intergenic (+29/+89) | yhbW/mtr | putative luciferase‑like monooxygenase/tryptophan transporter of high affinity |
| ? | NC_000913 | = 3304553 | NA (NA) | intergenic (+98/+20) | yhbW/mtr | putative luciferase‑like monooxygenase/tryptophan transporter of high affinity | |||||
| * | ? | NC_000913 | = 4542690 | 263 (2.650) | 25 (0.260) | 23/544 | NT | 9.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 236 (2.460) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||