mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 40,676 | G→A | T419I (ACC→ATC) | caiT ← | putative transporter |
| RA | 164,205 | A→G | S701G (AGT→GGT) | hrpB → | putative ATP‑dependent helicase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 293,780 | (A)7→6 | coding (139/699 nt) | yagL ← | CP4‑6 prophage, DNA‑binding protein |
| RA | 322,098 | C→T | T164I (ACC→ATC) | ykgE → | cysteine‑rich LutA family protein, putative electron transport chain YkgEFG component |
| RA | 337,217 | T→C | V147A (GTC→GCC) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 678,376 | C→T | P321L (CCG→CTG) | djlB → | putative HscC co‑chaperone, uncharacterized J domain‑containing protein |
| RA | 683,121 | C→T | A91A (GCG→GCA) | hscC ← | Hsp70 family chaperone Hsc62, RpoD‑binding transcription inhibitor |
| RA | 742,336 | C→T | G74D (GGC→GAC) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 924,093 | A→G | D277G (GAC→GGC) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,201,128 | T→C | intergenic (‑96/‑369) | xisE ← / → ymfI | e14 prophage, putative excisionase/e14 prophage, uncharacterized protein |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| JC JC | 1,293,196 | IS5 (+) +4 bp | intergenic (‑274/‑328) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,361,052 | (A)6→7 | intergenic (‑144/‑68) | puuA ← / → puuD | glutamate‑‑putrescine ligase/gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,407,462 | T→C | T112A (ACG→GCG) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,073,094 | T→C | L519P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,141,143 | A→G | L157P (CTG→CCG) | asmA ← | suppressor of OmpF assembly mutants, putative outer membrane protein assembly factor, inner membrane‑anchored periplasmic protein |
| RA | 2,143,783 | T→C | L173P (CTG→CCG) | yegE → | putative diguanylate cyclase |
| 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 | 2,215,997 | A→G | R160R (CGT→CGC) | yehW ← | putative ABC transporter permease |
| RA | 2,227,340 | (C)6→7 | pseudogene (1270/1287 nt) | mdtQ ← | pseudogene, putative channel/filament proteins |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,253,271 | G→A | A292V (GCC→GTC) | nupX ← | nucleoside permease |
| RA | 2,284,097 | T→C | intergenic (‑150/‑32) | yejK ← / → yejL | spermidine nucleoid‑associated protein/UPF0352 family protein |
| RA | 2,313,434 | T→C | intergenic (+258/‑54) | micF → / → rcsD | sRNA antisense regulator affecting ompF expression, Hfq‑dependent/phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,512,258 | (T)5→6 | coding (449/1239 nt) | mntH ← | manganese/divalent cation transporter |
| RA | 2,672,123 | G→A | G26E (GGG→GAG) | hcaD → | phenylpropionate dioxygenase, ferredoxin reductase subunit |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | yfiH ← | UPF0124 family protein |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,830,088 | G→A | V92V (GTG→GTA) | srlQ → | D‑arabinose 5‑phosphate isomerase |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,863,165 | T→C | R277R (CGT→CGC) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,895,747 | C→T | E11E (GAG→GAA) | ygcQ ← | putative flavoprotein |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,218,665 | T→C | T138A (ACC→GCC) | aer ← | fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,342,683 | T→C | G137G (GGT→GGC) | kdsC → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,428,954 | G→A | intergenic (‑192/‑282) | rrsD ← / → yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein |
| RA | 3,451,938 | G→A | R117C (CGT→TGT) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| 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 | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,811 | C→T | intergenic (‑43/+23) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,830,989 | T→C | V178A (GTT→GCT) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,187,838 | A→G | D830G (GAC→GGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,293,898 | A→G | Y119C (TAC→TGC) | nrfG → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 577359 | 607381 | 30023 | 19 [17] | [9] 79 | essD–[ybdK] | 33 genes essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, aaaD, tfaD, ybcY, ybcY, tfaX, appY, ompT, pauD, envY, ybcH, nfrA, nfrB, cusS, cusR, cusC, cusF, cusB, cusA, pheP, ybdG, nfsB, ybdF, ybdJ, [ybdK] |
| * | * | ÷ | NC_000913 | 807329 | 810379 | 3051 | 21 [10] | [15] 19 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2470148 | 2470281 | 134 | 19 [18] | [17] 20 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 2857129 | 2859648 | 2520 | 20 [16] | [16] 19 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423750–3424234 | 3424564–3424241 | 8–815 | 19 [18] | [16] 19 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 575785 | NA (NA) | 69 (0.970) | 45/218 | 0.3 | 88.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 607382 = | 9 (0.130) | coding (2/1119 nt) | ybdK | weak gamma‑glutamyl:cysteine ligase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 69 (1.000) | 39/212 | 0.5 | 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 | |||||