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 | 7,686 | C→T | V92I (GTC→ATC) | yaaJ ← | putative transporter |
| RA | 105,107 | T→C | Y376H (TAT→CAT) | ftsA → | ATP‑binding cell division FtsK recruitment protein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 424,284 | C→T | D589D (GAC→GAT) | malZ → | maltodextrin glucosidase |
| RA | 427,630 | (T)5→4 | intergenic (+11/‑17) | yajC → / → secD | SecYEG protein translocase auxillary subunit/SecYEG protein translocase auxillary subunit |
| RA | 529,055 | (T)8→7 | pseudogene (416/491 nt) | ybbD → | pseudogene |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 585,217 | C→T | W139* (TGG→TGA) | ompT ← | DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 632,923 | A→G | A185A (GCT→GCC) | ybdH ← | putative oxidoreductase |
| RA | 671,531 | A→G | G25G (GGT→GGC) | holA ← | DNA polymerase III, delta subunit |
| RA | 685,425 | T→C | T169A (ACC→GCC) | gltK ← | glutamate/aspartate ABC transporter permease |
| RA | 865,423 | A→G | P314P (CCT→CCC) | moeA ← | molybdopterin molybdenumtransferase, molybdopterin biosynthesis protein |
| RA | 992,344 | T→C | Y575H (TAC→CAC) | pepN → | aminopeptidase N |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,181,782 | A→G | intergenic (‑57/+1) | ymfA ← / ← potD | DUF3592 family inner membrane protein/spermidine/putrescine ABC transporter periplasmic binding protein |
| RA | 1,209,412 | T→C | pseudogene (208/501 nt) | stfE ← | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,334,893 | A→G | intergenic (+64/‑231) | cysB → / → ymiA | N‑acetylserine‑responsive cysteine regulon transcriptional activator, autorepressor/uncharacterized protein |
| RA | 1,351,693 | A→G | L23P (CTC→CCC) | ycjD ← | DUF559 family endonuclease‑related protein |
| RA | 1,377,088 | A→G | Y86C (TAC→TGC) | ycjS → | putative NADH‑binding oxidoreductase |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,585,424 | A→G | Y355H (TAT→CAT) | ydeP ← | putative oxidoreductase |
| RA | 1,594,256 | (C)8→9 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,644,142 | G→A | Q55* (CAG→TAG) | ydfU ← | Qin prophage, uncharacterized protein |
| RA | 1,657,767 | G→A | C68Y (TGC→TAC) | ynfD → | DUF1161 family periplasmic protein |
| RA | 1,719,281 | C→T | V108M (GTG→ATG) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,751,030 | G→A | intergenic (‑17/+47) | ydhX ← / ← ydhW | putative 4Fe‑4S ferridoxin‑type protein, FNR, Nar, NarP‑regulated protein, putative subunit of YdhYVWXUT oxidoreductase complex/FNR, Nar, NarP‑regulated protein, putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,825,480 | T→C | D49G (GAC→GGC) | spy ← | periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,905,787 | T→C | S34P (TCT→CCT) | mntP → | putative Mn(2+) efflux pump, mntR‑regulated |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,988,106 | (C)6→7 | intergenic (‑147/‑116) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,995,769 | T→C | intergenic (‑410/‑49) | uvrY ← / → yecF | response regulator in two‑component regulatory system with BarA/DUF2594 family protein |
| RA | 2,072,728 | G→A | G397D (GGT→GAT) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,073,225 | T→C | W563R (TGG→CGG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,149,300 | C→T | Q562Q (CAG→CAA) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| 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 | 2,203,362 | A→G | I1028M (ATA→ATG) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,228,728 | C→T | pseudogene (31/150 nt) | mdtQ ← | pseudogene, putative channel/filament proteins |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,298,294 | G→A | T142I (ACC→ATC) | napB ← | nitrate reductase, small, cytochrome C550 subunit, periplasmic |
| RA | 2,314,992 | T→C | L502P (CTG→CCG) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,340,022 | C→T | G152G (GGC→GGT) | ubiG → | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
| RA | 2,388,713 | T→C | L27L (TTA→CTA) | yfbO → | uncharacterized protein |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,489,435 | G→A | A251V (GCA→GTA) | yfdV ← | putative transporter |
| RA | 2,563,520 | G→T | intergenic (+403/‑72) | yffP → / → yffQ | CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized 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 | 2,774,632 | (A)7→8 | coding (1315/1704 nt) | yfjW → | CP4‑57 prophage, putative inner membrane protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,933,613 | T→C | T26A (ACA→GCA) | fucA ← | L‑fuculose‑1‑phosphate aldolase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,946,757 | T→C | Y141C (TAC→TGC) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 3,007,295 | T→C | V345A (GTG→GCG) | ygeW → | putative carbamoyltransferase |
| RA | 3,138,483 | T→C | T14A (ACA→GCA) | gss ← | glutathionylspermidine amidase and glutathionylspermidine synthetase |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,142,833 | C→T | A53T (GCA→ACA) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,447,579 | G→A | A63A (GCC→GCT) | rplX ← | 50S ribosomal subunit protein L24 |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,478,883 | G→A | A575A (GCC→GCT) | kefB ← | potassium:proton antiporter |
| 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 | 3,624,198 | T→C | pseudogene (312/351 nt) | yrhC → | pseudogene fragment |
| RA | 3,634,940 | A→G | S34G (AGC→GGC) | yhiM → | acid resistance protein, inner membrane |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,844,805 | T→C | L281P (CTC→CCC) | adeD → | cryptic adenine deaminase |
| RA | 3,865,112 | Δ1 bp | coding (1162/1662 nt) | yidE ← | putative transporter |
| RA | 3,897,086 | T→C | C105R (TGT→CGT) | yieH → | phosphoenolpyruvate and 6‑phosphogluconate phosphatase |
| 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 | 4,090,709 | C→T | D73N (GAC→AAC) | frvX ← | putative peptidase |
| RA | 4,095,367 | C→T | A206T (GCA→ACA) | rhaA ← | L‑rhamnose isomerase |
| RA | 4,185,540 | C→T | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,312,566 | T→C | R142R (AGA→AGG) | alsR ← | d‑allose‑inducible als operon transcriptional repressor, autorepressor, repressor of rpiR |
| RA | 4,340,898 | C→T | R244H (CGC→CAC) | melR ← | melibiose operon transcriptional regulator, autoregulator |
| 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 | 4,384,052 | T→C | Y72H (TAT→CAT) | yjeM → | putative transporter |
| RA | 4,403,556 | A→G | D86G (GAC→GGC) | hflC → | HflB protease modulator specific for phage lambda cII repressor |
| RA | 4,431,613 | T→C | E124G (GAA→GGA) | ytfE ← | iron‑sulfur cluster repair protein RIC |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,513,332 | C→T | L26L (CTG→CTA) | fecC ← | ferric citrate ABC transporter permease |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,544,191 | A→G | K155R (AAA→AGA) | fimI → | fimbrial protein involved in type 1 pilus biosynthesis |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,585,984 | C→T | A260T (GCC→ACC) | hsdR ← | endonuclease R Type I restriction enzyme |
| 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 | 807329 | 810363 | 3035 | 18 [9] | [10] 13 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2033824 | 2033954 | 131 | 19 [12] | [11] 13 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein |
| * | * | ÷ | NC_000913 | 2629603 | 2629719 | 117 | 18 [12] | [12] 14 | yfgG/yfgH | uncharacterized protein/outer membrane integrity lipoprotein |
| * | * | ÷ | NC_000913 | 2857129 | 2859661 | 2533 | 13 [11] | [11] 13 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423750–3424233 | 3424529–3424239 | 7–780 | 15 [10] | [12] 13 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 3623948–3624038 | 3624168 | 131–221 | 13 [12] | [12] 13 | yrhC | pseudogene fragment |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 51 (1.020) | 35/212 | 0.3 | 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 | |||||