mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 99,399 | G→A | A333T (GCA→ACA) | ftsW → | putative lipid II flippase; integral membrane protein; FtsZ ring stabilizer |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| RA | 119,744 | (G)6→7 | coding (464/855 nt) | ampE → | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation |
| RA | 216,844 | C→T | E54K (GAA→AAA) | yaeF ← | putative lipoprotein |
| RA | 233,773 | +A | coding (183/1359 nt) | mltD ← | putative membrane‑bound lytic murein transglycosylase D |
| RA | 236,569 | C→T | A168V (GCC→GTC) | dnaQ → | DNA polymerase III epsilon subunit |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 410,479 | A→G | S112S (TCA→TCG) | mak → | manno(fructo)kinase |
| RA | 420,149 | Δ1 bp | coding (559/1320 nt) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 426,471 | G→A | R112H (CGT→CAT) | tgt → | tRNA‑guanine transglycosylase |
| RA | 432,193 | +G | intergenic (‑180/+119) | tsx ← / ← yajI | nucleoside channel, receptor of phage T6 and colicin K/putative lipoprotein |
| RA | 460,056 | A→G | E390G (GAA→GGA) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 508,648 | C→G | intergenic (+89/+227) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator/copper transporter |
| RA | 508,702 | T→C | intergenic (+143/+173) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator/copper transporter |
| RA | 529,036 | A→G | pseudogene (397/491 nt) | ybbD → | pseudogene |
| RA | 561,696 | (G)6→7 | coding (2000/2604 nt) | sfmD → | putative outer membrane export usher protein |
| RA | 715,849 | A→G | L146L (TTA→TTG) | ybfP → | lipoprotein |
| RA | 751,952 | (T)7→6 | coding (218/2448 nt) | ybgQ ← | putative outer membrane protein |
| RA | 758,290 | Δ1 bp | coding (602/717 nt) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 777,575 | T→C | F412L (TTC→CTC) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 883,414 | Δ1 bp | intergenic (‑26/‑259) | ybjG ← / → mdfA | undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein |
| RA | 953,802 | A→G | V222A (GTA→GCA) | focA ← | formate channel |
| RA | 1,053,516 | (G)6→7 | coding (2663/2745 nt) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,097,037 | (G)7→8 | intergenic (+208/+528) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,119,518 | (T)7→6 | coding (1069/1119 nt) | solA ← | N‑methyltryptophan oxidase, FAD‑binding |
| RA | 1,143,641 | G→A | H243Y (CAT→TAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,168,806 | (T)8→9 | coding (27/633 nt) | ycfQ ← | repressor for bhsA(ycfR) |
| RA | 1,197,853 | T→C | N129D (AAT→GAT) | ymfE ← | e14 prophage; putative inner membrane protein |
| RA | 1,204,942 | T→C | pseudogene (539/1134 nt) | aaaE → | pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related |
| RA | 1,207,242 | C→T | G110G (GGC→GGT) | ymfQ → | prohage e14 tail protein homolog |
| RA | 1,246,073 | C→T | G435D (GGC→GAC) | treA ← | periplasmic trehalase |
| RA | 1,255,337 | T→A | S206C (AGT→TGT) | ycgV ← | putative adhesin |
| RA | 1,356,549 | C→T | A188T (GCT→ACT) | sapA ← | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| RA | 1,360,729 | G→T | S60R (AGC→AGA) | puuA ← | glutamate‑‑putrescine ligase |
| RA | 1,364,503 | A→G | D91G (GAC→GGC) | puuB → | gamma‑glutamylputrescine oxidoreductase |
| RA | 1,411,512 | G→A | A146V (GCG→GTG) | ttcA ← | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| RA | 1,489,197 | C→T | D322D (GAC→GAT) | aldA → | aldehyde dehydrogenase A, NAD‑linked |
| RA | 1,594,256 | (C)8→7 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,613,799 | T→C | D302G (GAC→GGC) | sad ← | succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,672,491 | G→A | A178T (GCA→ACA) | ydgD → | putative peptidase |
| RA | 1,694,023 | (A)5→4 | coding (241/1374 nt) | uidB ← | glucuronide transporter |
| RA | 1,698,281 | A→G | V300V (GTT→GTC) | malI ← | transcriptional repressor of Mal regulon |
| RA | 1,755,639 | G→A | intergenic (‑498/‑59) | ydhZ ← / → pykF | uncharacterized protein/pyruvate kinase I |
| RA | 1,868,250 | A→G | Y448C (TAC→TGC) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,898,954 | G→A | L176L (CTG→CTA) | yoaD → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,903,571 | A→G | T164A (ACC→GCC) | manY → | mannose‑specific enzyme IIC component of PTS |
| RA | 1,919,268 | G→A | G587S (GGT→AGT) | yebT → | MCE domain protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,992,339 | G→C | A160G (GCT→GGT) | pgsA ← | phosphatidylglycerophosphate synthetase |
| RA | 2,017,429 | (C)6→7 | coding (876/1374 nt) | fliI → | flagellum‑specific ATP synthase |
| RA | 2,018,260 | (A)8→7 | coding (315/444 nt) | fliJ → | flagellar protein |
| RA | 2,087,983 | T→C | E92E (GAA→GAG) | yeeY ← | LysR family putative transcriptional regulator |
| RA | 2,115,887 | (T)6→7 | coding (10/1395 nt) | wcaM ← | colanic acid biosynthesis protein |
| RA | 2,127,198 | A→G | S373P (TCA→CCA) | gmd ← | GDP‑D‑mannose dehydratase, NAD(P)‑binding |
| RA | 2,147,466 | G→A | S25S (AGC→AGT) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,257,774 | G→A | C198C (TGC→TGT) | psuG ← | pseudouridine 5'‑phosphate glycosidase |
| RA | 2,285,579 | A→G | T402A (ACT→GCT) | yejM → | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor |
| RA | 2,372,870 | T→C | V105A (GTG→GCG) | arnE → | undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit |
| RA | 2,391,343 | C→T | V55I (GTT→ATT) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,416,960 | (T)6→7 | intergenic (+69/‑121) | pta → / → yfcC | phosphate acetyltransferase/putative inner membrane transporter; C4‑dicarboxylate anaerobic carrier family protein |
| RA | 2,455,793 | G→A | intergenic (‑147/+534) | yfcV ← / ← sixA | putative fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,465,945 | G→A | V215V (GTG→GTA) | yfdC → | putative inner membrane protein |
| RA | 2,469,733 | (T)8→7 | coding (603/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,410 | (T)7→6 | coding (1280/1332 nt) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,516,689 | T→C | T382A (ACG→GCG) | yfeA ← | putative diguanylate cyclase |
| RA | 2,553,210 | A→G | K287E (AAA→GAA) | amiA → | N‑acetylmuramoyl‑l‑alanine amidase I |
| RA | 2,614,141 | G→A | G70S (GGC→AGC) | focB → | putative formate transporter |
| RA | 2,652,855 | (G)6→7 | coding (362/846 nt) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,682,175 | C→T | A191T (GCC→ACC) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,731,312 | G→A | intergenic (‑155/+288) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,749,038 | T→C | Y89H (TAC→CAC) | yfjD → | UPF0053 family inner membrane protein |
| RA | 2,762,274 | Δ1 bp | coding (1267/2190 nt) | yfjK ← | radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage |
| RA | 2,764,373 | G→A | H261Y (CAC→TAC) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; RNase LS |
| RA | 2,809,774 | (T)7→8 | coding (158/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 2,866,592 | +C | coding (960/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,889,648 | A→G | M151T (ATG→ACG) | cysI ← | sulfite reductase, beta subunit, NAD(P)‑binding, heme‑binding |
| RA | 3,008,075 | A→G | D189G (GAC→GGC) | ygeX → | 2,3‑diaminopropionate ammonia lyase, PLP‑dependent |
| RA | 3,182,712 | G→A | A55T (GCC→ACC) | zupT → | zinc transporter |
| RA | 3,194,516 | A→G | K551K (AAA→AAG) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,211,972 | C→G | T289S (ACC→AGC) | dnaG → | DNA primase |
| RA | 3,352,673 | T→C | E118G (GAA→GGA) | arcB ← | aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB |
| RA | 3,379,266 | (C)7→9 | coding (732/1128 nt) | zapE ← | divisome ATPase |
| RA | 3,411,299 | T→C | V10A (GTA→GCA) | fis → | global DNA‑binding transcriptional dual regulator |
| RA | 3,429,362 | G→A | V43I (GTT→ATT) | yrdA → | bacterial transferase hexapeptide domain protein |
| RA | 3,468,389 | T→C | S489G (AGT→GGT) | chiA ← | periplasmic endochitinase |
| RA | 3,512,561 | Δ1 bp | intergenic (‑217/+73) | yhfZ ← / ← trpS | putative DNA‑binding transcriptional regulator/tryptophanyl‑tRNA synthetase |
| RA | 3,542,093 | G→A | V563M (GTG→ATG) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane protein |
| RA | 3,560,455 | +G | 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 | 3,567,459 | T→C | N192S (AAC→AGC) | glgA ← | glycogen synthase |
| RA | 3,572,318 | T→C | E395E (GAA→GAG) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| MC JC | 3,582,206 | Δ1,222 bp | IS1‑mediated | [yhhZ]–yrhA | [yhhZ], yrhA |
| RA | 3,594,376 | C→T | A369T (GCA→ACA) | livM ← | branched‑chain amino acid ABC transporter permease |
| RA | 3,595,315 | (A)5→4 | coding (166/1278 nt) | livM ← | branched‑chain amino acid ABC transporter permease |
| RA | 3,618,765 | T→C | Y60H (TAT→CAT) | nikR → | transcriptional repressor, Ni‑binding |
| RA | 3,648,144 | (T)7→6 | intergenic (‑356/‑384) | dinQ ← / → arsR | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/arsenical resistance operon transcriptional repressor; autorepressor |
| RA | 3,657,494 | T→C | L167P (CTG→CCG) | hdeD → | acid‑resistance membrane protein |
| RA | 3,728,118 | (C)8→7 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,952,380 | G→A | L60L (CTG→CTA) | ilvM → | acetolactate synthase 2 small subunit |
| RA | 3,952,569 | C→T | A29V (GCG→GTG) | ilvE → | branched‑chain amino acid aminotransferase |
| RA | 4,122,191 | (T)5→4 | coding (97/531 nt) | hslV ← | peptidase component of the HslUV protease |
| RA | 4,196,250 | T→C | intergenic (‑151/+82) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/stationary phase protein, binds sigma 70 RNA polymerase subunit |
| RA | 4,214,964 | A→G | I229V (ATT→GTT) | metA → | homoserine O‑transsuccinylase |
| RA | 4,296,060 | C→T | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,337,024 | G→A | S3L (TCG→TTG) | adiC ← | arginine:agmatine antiporter |
| RA | 4,341,955 | G→A | T15T (ACG→ACA) | melA → | alpha‑galactosidase, NAD(P)‑binding |
| RA | 4,364,381 | T→C | Y221C (TAC→TGC) | dsbD ← | thiol:disulfide interchange protein and activator of DsbC |
| RA | 4,397,557 | G→T | G49V (GGT→GTT) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,573,528 | A→G | pseudogene (1115/1503 nt) | yjiT → | pseudogene |
| RA | 4,638,193 | (C)6→7 | coding (16/1353 nt) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423712–3424234 | 3424611–3424238 | 5–900 | 68 [65] | [66] 68 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3621150–3622298 | 3622659–3622421 | 124–1510 | 67 [65] | [66] 68 | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 3762295–3764074 | 3765231–3764077 | 4–2937 | 68 [64] | [65] 67 | rhsA | Rhs protein with putative toxin 55 domain; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| * | * | ÷ | NC_000913 | 4094394 | 4094473–4094449 | 56–80 | 68 [65] | [65] 67 | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 156 (1.350) | 93/190 | 0.0 | 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 | |||||