mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 11,127 | C→G | 4.8% | S77T (AGT→ACT) | yaaW ← | UPF0174 family protein |
| RA | 188,226 | T→C | 4.7% | intergenic (+31/‑116) | tsf → / → pyrH | translation elongation factor EF‑Ts/uridylate kinase |
| RA | 289,794 | A→G | 7.0% | V239V (GTT→GTC) | yagM ← | CP4‑6 prophage; uncharacterized protein |
| RA | 337,558 | C→G | 6.5% | Y241* (TAC→TAG) | yahJ → | putative metallo‑dependent hydrolase domain deaminase |
| RA | 344,799 | A→T | 7.1% | E136V (GAG→GTG) | prpB → | 2‑methylisocitrate lyase |
| RA | 444,779 | C→T | 72.5% | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 504,372 | T→C | 4.5% | S822G (AGT→GGT) | copA ← | copper transporter |
| RA | 721,831 | A→G | 4.8% | L221P (CTG→CCG) | kdpB ← | potassium translocating ATPase, subunit B |
| RA | 776,421 | T→C | 6.9% | intergenic (+47/‑103) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 777,280 | C→T | 6.1% | intergenic (+172/‑261) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 777,282 | A→T | 6.8% | intergenic (+174/‑259) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 786,387 | C→G | 4.0% | W33C (TGG→TGC) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 796,346 | T→C | 6.9% | D44D (GAT→GAC) | ybhH → | putative PrpF family isomerase |
| RA | 903,388 | A→G | 4.1% | H117H (CAT→CAC) | ybjT ← | putative NAD‑dependent oxidoreductase |
| RA | 916,181 | G→C | 5.5% | E127Q (GAG→CAG) | macB → | fused macrolide transporter subunits of ABC superfamily: ATP‑binding component/membrane component |
| RA | 982,560 | T→A | 24.0% | intergenic (‑122/+481) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 982,566 | C→A | 10.6% | intergenic (‑128/+475) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,191,676 | C→T | 15.5% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 17.8% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | 14.1% | L375L (TTA→CTA) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | 12.5% | L375L (TTA→TTG) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,733 | C→T | 12.3% | N385N (AAC→AAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,736 | G→C | 12.3% | A386A (GCG→GCC) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,739 | A→G | 12.1% | K387K (AAA→AAG) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,748 | C→T | 10.4% | T390T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,760 | G→A | 9.7% | E394E (GAG→GAA) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,282,421 | A→G | 13.9% | intergenic (+439/+122) | narI → / ← tpr | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein |
| RA | 1,432,972 | G→C | 6.0% | T690T (ACC→ACG) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,440,869 | Δ1 bp | 5.3% | coding (672/906 nt) | feaR ← | transcriptional activator for tynA and feaB |
| RA | 1,478,245 | C→A | 8.8% | L310M (CTG→ATG) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,529,302 | G→A | 6.0% | R272C (CGT→TGT) | yddE ← | PhzC‑PhzF family protein |
| RA | 1,695,365 | A→T | 9.3% | N51I (AAT→ATT) | malY → | bifunctional beta‑cystathionase, PLP‑dependent/ regulator of maltose regulon |
| RA | 1,695,395 | A→G | 5.5% | Y61C (TAC→TGC) | malY → | bifunctional beta‑cystathionase, PLP‑dependent/ regulator of maltose regulon |
| RA | 1,702,919 | C→G | 7.4% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| JC | 1,716,881 | (GAT)4→3 | 7.0% | coding (504‑506/2013 nt) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,750,005 | A→G | 5.6% | E17E (GAA→GAG) | pykF → | pyruvate kinase I |
| JC JC | 2,160,620 | IS5 (+) +4 bp | 18.0% | intergenic (+110/+160) | yegQ → / ← ogrK | putative peptidase/positive regulator of P2 growth (insertion of P2 ogr gene into the chromosome) |
| RA | 2,298,564 | A→G | 6.8% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,565 | C→G | 7.3% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,853 | C→T | 35.8% | D126N (GAC→AAC) | ompC ← | outer membrane porin protein C |
| RA | 2,377,435 | A→T | 9.6% | intergenic (+32/+39) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,377,438 | A→T | 8.4% | intergenic (+35/+36) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,384,896 | C→G | 4.2% | W30S (TGG→TCG) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 31.3% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,420,353 | A→C | 28.7% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,421,172 | A→C | 13.1% | D33E (GAT→GAG) | argT ← | lysine/arginine/ornithine transporter subunit |
| RA | 2,506,454 | C→T | 22.7% | intergenic (‑269/‑67) | mntH ← / → nupC | manganese/divalent cation transporter/nucleoside (except guanosine) transporter |
| RA | 2,641,817 | T→G | 8.6% | N1277T (AAC→ACC) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,661,108 | C→G | 5.5% | G33A (GGG→GCG) | hcaT ← | putative 3‑phenylpropionic transporter |
| RA | 2,831,581 | A→T | 7.6% | intergenic (‑117/+32) | hydN ← / ← ascG | formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit/asc operon transcriptional repressor; prpBC operon repressor |
| RA | 2,911,376 | C→T | 7.2% | intergenic (+204/+28) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/(D)‑glucarate dehydratase 1 |
| RA | 2,911,379 | A→C | 8.0% | intergenic (+207/+25) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/(D)‑glucarate dehydratase 1 |
| RA | 2,911,381 | A→G | 7.4% | intergenic (+209/+23) | barA → / ← gudD | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY/(D)‑glucarate dehydratase 1 |
| RA | 2,912,734 | T→C | 6.4% | Q4R (CAA→CGA) | gudD ← | (D)‑glucarate dehydratase 1 |
| RA | 3,030,824 | C→T | 31.1% | E214E (GAG→GAA) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 3,135,509 | Δ1 bp | 6.2% | coding (840/1704 nt) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,135,510 | Δ1 bp | 6.2% | coding (839/1704 nt) | hybC ← | hydrogenase 2, large subunit |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 28.4% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,370,777 | C→T | 13.0% | M1M (ATG→ATA) † | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,480,130 | T→C | 8.4% | intergenic (+19/‑20) | crp → / → yhfK | cAMP‑activated global transcription factor, mediator of catabolite repression/putative transporter, FUSC superfamily inner membrane protein, tandem domains |
| RA | 3,522,277 | A→G | 20.3% | M84V (ATG→GTG) | yrfG → | GMP/IMP nucleotidase |
| RA | 3,529,197 | A→G | 69.8% | S11P (TCA→CCA) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,567,248 | G→T | 20.9% | R331S (CGC→AGC) | asd ← | aspartate‑semialdehyde dehydrogenase, NAD(P)‑binding |
| RA | 3,608,704 | C→T | 7.6% | A35V (GCG→GTG) | nikB → | nickel transporter subunit |
| RA | 3,632,525 | T→C | 2.9% | intergenic (+24/+220) | pitA → / ← uspB | phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B |
| RA | 3,632,532 | G→A | 3.1% | intergenic (+31/+213) | pitA → / ← uspB | phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B |
| JC | 3,676,871:1 | +TAA | 86.5% | intergenic (‑64/+119) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,726,790 | T→A | 5.4% | N410K (AAT→AAA) | xylG → | fused D‑xylose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,911,651 | C→T | 8.3% | intergenic (‑26/+25) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,911,656 | C→T | 7.2% | intergenic (‑31/+20) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,911,659 | A→G | 6.7% | intergenic (‑34/+17) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,911,664 | A→G | 8.2% | intergenic (‑39/+12) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 4,127,934 | T→G | 6.5% | T344P (ACG→CCG) | gldA ← | glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase |
| RA | 4,266,916 | G→A | 4.1% | A506A (GCG→GCA) | yjcC → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 4,315,100 | G→C | 6.9% | intergenic (‑118/+15) | phnC ← / ← yjdN | phosphonate ABC transporter ATP‑binding subunit/metalloprotein superfamily protein |
| RA | 4,390,286 | C→A | 77.0% | T61N (ACT→AAT) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| RA | 4,394,665 | T→G | 29.3% | H54Q (CAT→CAG) | purA → | adenylosuccinate synthetase |
| RA | 4,406,114 | A→T | 5.3% | intergenic (‑5/+144) | yjfN ← / ← bsmA | DUF1471 family periplasmic protein/bioflm peroxide resistance protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 19796 = | NA (NA) | 6 (0.090) | 4/276 | NT | 3.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | CP009273 | 3649844 = | 150 (2.140) | coding (257/333 nt) | hdeA | stress response protein acid‑resistance protein | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 88 (1.260) | 49/276 | NT | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 360280 | 88 (1.260) | 65 (1.030) | 5/250 | NT | 59.7% | intergenic (‑214/+381) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 3940171 | 8 (0.130) | noncoding (112/120 nt) | rrfC | 5S ribosomal RNA of rrnC operon | |||||
| * | ? | CP009273 | 627575 = | NA (NA) | 4 (0.060) | 3/262 | NT | NA | noncoding (5/34 nt) | REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP55 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | CP009273 | 627605 = | NA (NA) | intergenic (+150/‑33) | cstA/ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein | |||||
| * | ? | CP009273 | = 777295 | 86 (1.230) | 5 (0.080) | 6/254 | NT | 6.8% | intergenic (+187/‑246) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| ? | CP009273 | = 2514847 | 58 (0.900) | noncoding (575/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | 1045234 = | 98 (1.400) | 49 (0.700) | 36/276 | NT | 45.2% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 21 (0.300) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1046001 | 66 (0.940) | 54 (0.770) | 35/276 | NT | 55.4% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | 1973115 = | 21 (0.300) | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 21 (0.300) | 19 (0.310) | 16/244 | NT | 53.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 14 (0.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 14 (0.200) | 34 (0.550) | 28/244 | NT | 72.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 14 (0.230) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1843546 = | 51 (0.730) | 3 (0.050) | 3/260 | NT | 5.4% | coding (453/1857 nt) | sppA | protease IV (signal peptide peptidase) |
| ? | CP009273 | 1843584 = | 57 (0.870) | coding (491/1857 nt) | sppA | protease IV (signal peptide peptidase) | |||||
| * | ? | CP009273 | = 2298464 | NA (NA) | 6 (0.090) | 4/262 | NT | 5.5% | noncoding (569/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | CP009273 | = 2298494 | 109 (1.560) | noncoding (599/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | CP009273 | 2420388 = | 58 (0.830) | 8 (0.110) | 6/276 | NT | 12.1% | intergenic (‑121/+100) | hisJ/argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2420396 | 56 (0.800) | 9 (0.130) | 6/276 | NT | 13.8% | intergenic (‑129/+92) | hisJ/argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | 3576788 = | NA (NA) | 8 (0.110) | 6/276 | NT | 5.0% | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA |
| ? | CP009273 | = 3649852 | 153 (2.190) | coding (249/333 nt) | hdeA | stress response protein acid‑resistance protein | |||||
| * | ? | CP009273 | = 4145500 | 74 (1.060) | 13 (0.200) | 11/262 | NT | 18.8% | coding (572/1005 nt) | argC | N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding |
| ? | CP009273 | 4145821 = | 42 (0.630) | coding (893/1005 nt) | argC | N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding | |||||