mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 37,250 | A→C | 21.8% | V192G (GTG→GGG) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| RA | 71,877 | A→G | 25.4% | E176G (GAG→GGG) | yabI → | DedA family inner membrane protein |
| RA | 75,091 | G→T | 37.4% | D130E (GAC→GAA) | thiB ← | thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein |
| RA | 134,775 | T→C | 15.7% | intergenic (+25/+13) | yacL → / ← speD | UPF0231 family protein/S‑adenosylmethionine decarboxylase |
| RA | 151,821 | A→G | 11.3% | T137T (ACT→ACC) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 159,258 | G→T | 21.7% | V285V (GTC→GTA) | gluQ ← | glutamyl‑Q tRNA(Asp) synthetase |
| RA | 173,427 | A→G | 16.9% | R656G (AGA→GGA) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| RA | 194,997 | C→A | 12.0% | A32E (GCA→GAA) | ispU → | undecaprenyl pyrophosphate synthase |
| RA | 209,270 | T→G | 18.8% | V217G (GTG→GGG) | accA → | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit |
| RA | 246,984 | T→C | 15.3% | A91A (GCT→GCC) | yafL → | putative lipoprotein and C40 family peptidase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 345,302 | C→A | 12.2% | intergenic (+311/‑102) | yahL → / → yahM | uncharacterized protein/uncharacterized protein |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 100% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 501,181 | A→C | 23.1% | T353P (ACT→CCT) | gsk → | inosine/guanosine kinase |
| RA | 685,022 | G→C | 15.3% | R78R (CGC→CGG) | gltL ← | glutamate/aspartate ABC transporter ATPase |
| RA | 742,267 | T→C | 13.9% | E97G (GAG→GGG) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 762,113 | T→C | 25.9% | S198P (TCC→CCC) | sucB → | dihydrolipoyltranssuccinase |
| RA | 830,865 | A→G | 19.7% | intergenic (‑222/‑7) | ybiH ← / → rhlE | DUF1956 domain‑containing tetR family putative transcriptional regulator/ATP‑dependent RNA helicase |
| RA | 842,815 | C→A | 19.1% | Q162K (CAA→AAA) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 954,356 | C→A | 31.3% | L37L (CTG→CTT) | focA ← | formate channel |
| RA | 1,027,203 | T→G | 6.8% | T191P (ACA→CCA) | yccT ← | UPF0319 family protein |
| RA | 1,058,486 | T→C | 23.0% | S135P (TCG→CCG) | torC → | trimethylamine N‑oxide (TMAO) reductase I, cytochrome c‑type subunit |
| RA | 1,074,669 | C→G | 15.2% | A143G (GCG→GGG) | rutR → | rut operon transcriptional repressor for |
| RA | 1,132,071 | T→C | 10.1% | L73P (CTC→CCC) | flgD → | flagellar hook assembly protein |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,289,973 | G→A | 10.8% | E243E (GAG→GAA) | rssA → | putative patatin‑like family phospholipase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,536,735 | A→C | 13.9% | V192G (GTG→GGG) | narW ← | nitrate reductase 2 (NRZ), delta subunit (assembly subunit) |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,054,830 | A→C | 16.5% | T396T (ACA→ACC) | shiA → | shikimate transporter |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,154,491 | T→C | 21.9% | L159P (CTC→CCC) | mdtA → | multidrug efflux system, subunit A |
| RA | 2,169,668 | A→C | 15.6% | intergenic (+57/+25) | yegS → / ← gatR | phosphatidylglycerol kinase, metal‑dependent/pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| 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 | 2,209,353 | T→G | 14.2% | pseudogene (254/2001 nt) | yehQ → | pseudogene |
| RA | 2,507,677 | T→C | 13.5% | E73G (GAG→GGG) | fryC ← | putative enzyme IIC component of PTS |
| RA | 2,509,880 | A→C | 14.2% | D84A (GAC→GCC) | yfeO → | putative ion channel protein |
| RA | 2,561,294 | T→C | 13.5% | intergenic (+396/‑74) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,590,065 | A→G | 18.2% | E824G (GAG→GGG) | acrD → | aminoglycoside/multidrug efflux system |
| RA | 2,732,138 | A→C | 13.6% | V679G (GTG→GGG) | clpB ← | protein disaggregation chaperone |
| RA | 2,733,167 | A→C | 11.0% | V336G (GTG→GGG) | clpB ← | protein disaggregation chaperone |
| RA | 2,739,684 | T→C | 18.3% | E129G (GAG→GGG) | tyrA ← | fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,744,004 | T→C | 14.2% | L127P (CTC→CCC) | yfiB → | OM lipoprotein putative positive effector of YfiN activity |
| RA | 2,795,328 | T→G | 14.9% | V359G (GTA→GGA) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,796,104 | C→T | 15.0% | S144F (TCT→TTT) | csiR → | transcriptional repressor of csiD |
| RA | 2,819,154 | T→C | 8.0% | intergenic (‑8/+227) | csrA ← / ← alaS | pleiotropic regulatory protein for carbon source metabolism/alanyl‑tRNA synthetase |
| RA | 2,820,820 | G→A | 7.9% | L398L (CTG→TTG) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,822,002 | T→C | 6.8% | S4G (AGC→GGC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,935,069 | A→G | 15.4% | S279G (AGC→GGC) | fucP → | L‑fucose transporter |
| RA | 2,959,174 | A→C | 13.1% | G1085G (GGT→GGG) | recC ← | exonuclease V (RecBCD complex), gamma chain |
| RA | 2,969,479 | T→G | 19.4% | intergenic (‑502/‑183) | rppH ← / → mutH | RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein |
| RA | 2,977,544 | A→C | 16.4% | T316P (ACT→CCT) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,027,731 | A→G | 18.3% | E204G (GAG→GGG) | ghxQ → | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter |
| RA | 3,066,865 | A→T | 8.8% | Y103* (TAT→TAA) | ygfI ← | putative DNA‑binding transcriptional regulator |
| RA | 3,113,957 | T→A | 16.4% | L132F (TTA→TTT) | pppA ← | bifunctional prepilin leader peptidase/ methylase |
| RA | 3,145,643 | T→G | 15.0% | T207P (ACT→CCT) | hybO ← | hydrogenase 2, small subunit |
| RA | 3,265,360 | T→C | 17.2% | G223G (GGA→GGG) | tdcB ← | L‑threonine dehydratase, catabolic |
| RA | 3,293,767 | C→G | 15.8% | A123G (GCG→GGG) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,329,773 | A→G | 16.6% | S271G (AGC→GGC) | dacB → | D‑alanyl‑D‑alanine carboxypeptidase |
| RA | 3,373,350 | A→G | 17.9% | L76P (CTC→CCC) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,373,358 | C→T | 12.3% | K73K (AAG→AAA) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,479,689 | G→A | 15.8% | L307F (CTC→TTC) | kefB ← | potassium:proton antiporter |
| RA | 3,489,862 | A→G | 15.5% | S107P (TCC→CCC) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| RA | 3,523,993 | A→G | 14.6% | S375G (AGT→GGT) | mrcA → | penicillin‑binding protein 1a, murein transglycosylase and transpeptidase |
| JC | 3,525,959 | +GGATCA | 44.8% | coding (191/561 nt) | nudE ← | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase |
| RA | 3,532,595 | C→A | 18.4% | intergenic (‑156/‑223) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| RA | 3,551,917 | A→C | 22.1% | V186G (GTG→GGG) | malP ← | maltodextrin phosphorylase |
| 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 | 3,686,539 | T→C | 14.0% | S879G (AGC→GGC) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,521 | T→C | 18.7% | A28A (GCT→GCC) | yidX → | putative lipoprotein |
| RA | 3,894,501 | T→G | 14.8% | S207R (AGT→AGG) | yieE → | phosphopantetheinyl transferase superfamily protein |
| RA | 3,895,556 | T→C | 19.2% | M352V (ATG→GTG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,966,914 | A→C | 14.2% | S166S (TCA→TCC) | rho → | transcription termination factor |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,017,526 | T→C | 11.3% | L65P (CTC→CCC) | rmuC → | DNA recombination protein |
| RA | 4,087,251 | T→G | 19.3% | C84G (TGC→GGC) | yiiG → | DUF3829 family lipoprotein |
| RA | 4,146,772 | T→G | 14.5% | V172G (GTG→GGG) | pflC → | putative [formate‑C‑acetyltransferase 2]‑activating enzyme; pyruvate formate‑lyase 1‑activating enzyme |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,240,883 | A→C | 5.8% | F458V (TTT→GTT) | xylE ← | D‑xylose transporter |
| RA | 4,241,829 | T→A | 12.9% | L142F (TTA→TTT) | xylE ← | D‑xylose transporter |
| RA | 4,280,131 | A→G | 12.7% | E51G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,280,577 | A→G | 22.9% | S200G (AGC→GGC) | yjcE → | putative cation/proton antiporter |
| RA | 4,289,531 | T→G | 13.0% | V96G (GTG→GGG) | nrfB → | nitrite reductase, formate‑dependent, penta‑heme cytochrome c |
| RA | 4,296,060 | C→T | 27.7% | intergenic (+266/+376) | 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 | 4,336,951 | A→C | 22.1% | G27G (GGT→GGG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,423,529 | T→G | 12.1% | G228G (GGT→GGG) | ulaE → | L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 4,446,969 | T→G | 17.6% | V953G (GTG→GGG) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,449,045 | T→G | 25.0% | intergenic (+3/+77) | chpB → / ← ppa | toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase |
| RA | 4,487,250 | C→T | 14.2% | L345F (CTC→TTC) | lptF → | lipopolysaccharide export ABC permease |
| RA | 4,530,174 | T→A | 12.7% | I24F (ATC→TTC) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,579,656 | A→C | 24.2% | V62G (GTG→GGG) | symE ← | toxic peptide regulated by antisense sRNA symR |
| RA | 4,628,141 | A→G | 10.8% | E276G (GAG→GGG) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 384787 | 385044 | 258 | 18 [14] | [13] 18 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 584291 | 584589 | 299 | 18 [16] | [16] 17 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 1212036 | 1212633 | 598 | 17 [15] | [14] 17 | iraM/ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| * | * | ÷ | NC_000913 | 1544464 | 1545062 | 599 | 17 [15] | [15] 17 | [yddK]–[yddK] | [yddK],[yddK] |
| * | * | ÷ | NC_000913 | 2103927 | 2104162 | 236 | 18 [16] | [14] 18 | wbbK | lipopolysaccharide biosynthesis protein |
| * | * | ÷ | NC_000913 | 2469155 | 2469855 | 701 | 18 [10] | [13] 17 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 3796978 | 3797746 | 769 | 17 [16] | [16] 17 | waaL | O‑antigen ligase |
| * | * | ÷ | NC_000913 | 4233769 | 4235416 | 1648 | 17 [15] | [16] 18 | [pgi] | [pgi] |
| * | * | ÷ | NC_000913 | 4374222 | 4374420 | 199 | 19 [16] | [16] 22 | [yjeJ] | [yjeJ] |
| * | * | ÷ | NC_000913 | 4542580 | 4542911 | 332 | 17 [16] | [15] 18 | [fimE] | [fimE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 279163 = | NA (NA) | 51 (0.720) | 3/438 | NT | 63.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2760086 | 30 (0.420) | coding (1102/1410 nt) | yfjI | CP4‑57 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | 1207790 = | 9 (0.130) | 59 (0.900) | 46/406 | NT | 82.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 8 (0.110) | 47 (0.720) | 38/406 | NT | 79.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 22 (0.320) | 19/430 | 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 | = 4094333 | 71 (1.010) | 4 (0.060) | 3/432 | NT | 5.8% | noncoding (18/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | = 4094466 | 59 (0.850) | noncoding (151/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||