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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 261,052 | A→G | D222G (GAC→GGC) | proB → | gamma‑glutamate kinase |
| RA | 265,137 | C→T | V24I (GTC→ATC) | yafX ← | CP4‑6 prophage, uncharacterized protein |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 606,927 | C→T | G153S (GGC→AGC) | ybdK ← | weak gamma‑glutamyl:cysteine ligase |
| RA | 635,896 | A→G | L225P (CTC→CCC) | ybdN ← | PAPS reductase‑like domain protein |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 749,989 | A→G | G727G (GGT→GGC) | ybgQ ← | putative outer membrane protein |
| RA | 989,708 | T→C | T217A (ACA→GCA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,002,224 | (G)7→8 | coding (418/1071 nt) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,029,739 | (A)8→7 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase, SAM‑dependent |
| RA | 1,121,680 | C→T | D310N (GAC→AAC) | pyrC ← | dihydro‑orotase |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,372,620 | A→G | T238A (ACT→GCT) | ycjN → | putative ABC sugar transporter periplasmic binding protein |
| RA | 1,393,315 | T→C | V30A (GTA→GCA) | mppA → | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,416,279 | A→G | S370P (TCC→CCC) | recE ← | Rac prophage, exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,520,008 | C→T | L328L (CTG→TTG) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,564,585 | A→G | G383G (GGT→GGC) | dosP ← | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated, cold‑ and stationary phase‑induced bioflim regulator |
| RA | 1,594,132 | (C)8→7 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,688,142 | G→A | A79V (GCC→GTC) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,756,359 | T→C | I221T (ATC→ACC) | pykF → | pyruvate kinase I |
| RA | 1,806,491 | G→A | G41D (GGC→GAC) | pfkB → | 6‑phosphofructokinase II |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,927,241 | (C)6→7 | coding (1599/2061 nt) | ptrB ← | protease II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,000,873 | C→T | R51H (CGC→CAC) | fliZ ← | RpoS antagonist, putative regulator of FliA activity |
| RA | 2,071,500 | A→G | noncoding (184/195 nt) | isrC → | novel sRNA, CP4‑44, putative prophage remnant |
| RA | 2,073,151 | T→C | L538P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| 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 | 2,230,208 | G→A | P60S (CCA→TCA) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,300,364 | G→A | A797V (GCC→GTC) | napA ← | nitrate reductase, periplasmic, large subunit |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,408,553 | G→A | A331A (GCG→GCA) | alaA → | glutamate‑pyruvate aminotransferase, glutamic‑pyruvic transaminase (GPT), alanine transaminase |
| RA | 2,607,273 | C→T | F119F (TTC→TTT) | hyfF → | hydrogenase 4, membrane subunit |
| RA | 2,619,314 | T→C | T283A (ACG→GCG) | uraA ← | uracil permease |
| RA | 2,620,907 | (A)8→7 | intergenic (‑35/‑290) | upp ← / → purM | uracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,852,122 | G→A | G87S (GGC→AGC) | hypC → | hydrogenase maturation protein |
| RA | 2,863,567 | (T)7→8 | intergenic (+66/‑26) | ygbK → / → ygbL | FliA‑regulated DUF1537 family protein/putative class II aldolase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,972,909 | (C)6→7 | coding (954/1194 nt) | lplT ← | lysophospholipid transporter |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,350,675 | Δ1 bp | noncoding (99/121 nt) | arcZ → | sRNA positive antisense regulator of rpoS, binds Hfq |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,530,091 | G→A | T106T (ACG→ACA) | hslO → | heat shock protein Hsp33 |
| 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 | 3,664,360 | G→A | P87S (CCC→TCC) | gadW ← | transcriptional activator of gadA and gadBC, repressor of gadX |
| RA | 3,769,260 | (A)6→5 | intergenic (+4/‑85) | yibW → / → yibV | pseudogene, rhsA‑linked/pseudogene, putative cryptic Rhs immunity protein |
| 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 | 3,849,229 | C→T | S303N (AGC→AAC) | uhpB ← | sensory histidine kinase in two‑component regulatory sytem with UhpA |
| 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 | 3,950,468 | (G)5→4 | intergenic (+48/‑39) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 4,077,129 | G→A | E39K (GAA→AAA) | dtd → | D‑tyr‑tRNA(Tyr) deacylase |
| 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 | 4,283,098 | G→T | intergenic (‑23/+155) | yjcF ← / ← actP | pentapeptide repeats protein/acetate transporter |
| 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 | 4,586,393 | A→G | T123T (ACT→ACC) | hsdR ← | endonuclease R Type I restriction enzyme |
| RA | 4,606,215 | (G)8→10 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 84039 | 84071 | 33 | 5 [2] | [2] 3 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | NC_000913 | 246593 | 246631 | 39 | 6 [2] | [2] 4 | dinJ/yafL | antitoxin of YafQ‑DinJ toxin‑antitoxin system/putative lipoprotein and C40 family peptidase |
| * | * | ÷ | NC_000913 | 708023 | 708065 | 43 | 3 [1] | [2] 6 | glnS/chiP | glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars |
| * | * | ÷ | NC_000913 | 732326–732524 | 734236–734149 | 1626–1911 | 3 [2] | [2] 3 | [rhsC]–[rhsO] | [rhsC], ybfB, [rhsO] |
| * | * | ÷ | NC_000913 | 807343 | 810366 | 3024 | 5 [1] | [1] 3 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1640988 | 1641029 | 42 | 5 [2] | [1] 14 | essQ/cspB | Qin prophage, putative S lysis protein/Qin prophage, cold shock protein |
| * | * | ÷ | NC_000913 | 2033854 | 2033897 | 44 | 4 [2] | [0] 3 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein |
| * | * | ÷ | NC_000913 | 2056700 | 2056765 | 66 | 3 [0] | [2] 3 | amn/yeeN | AMP nucleosidase/UPF0082 family protein |
| * | * | ÷ | NC_000913 | 2306846 | 2306883 | 38 | 3 [1] | [2] 3 | mqo/yojI | malate dehydrogenase, FAD/NAD(P)‑binding domain/microcin J25 efflux ABC transporter permease/ATPase |
| * | * | ÷ | NC_000913 | 2470181 | 2470271 | 91 | 3 [0] | [2] 5 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 2857138 | 2859629 | 2492 | 6 [0] | [1] 3 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3287268 | 3287350 | 83 | 4 [2] | [2] 3 | agaI/yraH | galactosamine‑6‑phosphate isomerase/putative fimbrial‑like adhesin protein |
| * | * | ÷ | NC_000913 | 3413567 | 3413614 | 48 | 5 [2] | [2] 3 | acrS/acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| * | * | ÷ | NC_000913 | 3423765–3424234 | 3426728–3424657 | 424–2964 | 3 [2] | [2] 3 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3455419 | 3455487 | 69 | 3 [1] | [2] 4 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | NC_000913 | 3727848 | 3727876 | 29 | 6 [2] | [0] 3 | yiaB/xylB | YiaAB family inner membrane protein/xylulokinase |
| * | * | ÷ | NC_000913 | 3757939 | 3758018 | 80 | 5 [2] | [0] 4 | [selB] | [selB] |
| * | * | ÷ | NC_000913 | 3793691 | 3793745 | 55 | 3 [2] | [1] 6 | yibB/hldD | YibB family protein, function unknown/ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
| * | * | ÷ | NC_000913 | 3946647 | 3946850–3946690 | 44–204 | 4 [2] | [2] 4 | rrfC | rrfC |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 5 (0.200) | 32 (1.530) | 22/180 | 0.1 | 91.1% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 2 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.200) | 16 (0.770) | 16/180 | 0.3 | 83.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 2 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||