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 | annotation | gene | description |
| RA | 35,645 | C→T | W173* (TGG→TAG) | caiD ← | crotonobetainyl‑CoA hydratase |
| RA | 44,304 | C→A | A42D (GCC→GAC) | fixC → | putative oxidoreductase FixC |
| RA | 49,370 | T→C | G534G (GGT→GGC) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 71,016 | T→C | R210R (CGT→CGC) | araC → | DNA‑binding transcriptional dual regulator AraC |
| RA | 92,082 | A→G | T224A (ACT→GCT) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 132,433 | C→T | C273C (TGC→TGT) | acnB → | hypothetical protein |
| RA | 145,712 | A→G | Y211C (TAC→TGC) | yadE → | putative polysaccharide deacetylase lipoprotein |
| RA | 172,269 | (G)5→6 | coding (808/1983 nt) | fhuB → | iron(III) hydroxamate ABC transporter membrane subunit |
| RA | 173,839 | A→G | V348V (GTT→GTC) | hemL ← | glutamate‑1‑semialdehyde aminotransferase |
| RA | 175,397 | G→A | V97V (GTG→GTA) | clcA → | chloride:H(+) antiporter ClcA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 284,312 | A→G | H371R (CAC→CGC) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 409,021 | T→C | R25R (CGT→CGC) | ykiD → | protein YkiD |
| RA | 512,765 | T→C | Y64H (TAT→CAT) | ybaT → | putative transporter YbaT |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 566,570 | A→G | intergenic (‑209/‑114) | exoD ← / → renD | DLP12 prophage; putative exonuclease ExoD/DLP12 prophage; protein RenD |
| RA | 582,081 | A→G | N183S (AAC→AGC) | tfaD → | DLP12 prophage; putative tail fiber assembly protein TfaD |
| RA | 642,281 | A→G | E65G (GAA→GGA) | ybdR → | putative Zn(2(+))‑dependent alcohol dehydrogenase YbdR |
| RA | 657,745 | C→T | W65* (TGG→TAG) | crcB ← | F(‑) channel |
| RA | 673,612 | T→C | D391G (GAC→GGC) | leuS ← | leucine‑‑tRNA ligase |
| RA | 685,941 | (C)6→7 | coding (729/741 nt) | gltJ ← | glutamate/aspartate ABC transporter membrane subunit GltJ |
| RA | 701,939 | A→G | V271V (GTT→GTC) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 839,802 | A→G | V577A (GTT→GCT) | fiu ← | putative iron siderophore outer membrane transporter |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,002,129 | A→G | Y108C (TAC→TGC) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,019,564 | A→G | W164R (TGG→CGG) | ompA ← | outer membrane porin A |
| RA | 1,026,152 | A→G | E561G (GAG→GGG) | helD → | DNA helicase IV |
| RA | 1,029,739 | (A)8→9 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase |
| RA | 1,121,231 | (A)8→9 | intergenic (‑276/+11) | bssS ← / ← dinI | regulator of biofilm formation/DNA damage‑inducible protein I |
| RA | 1,134,944 | A→G | V72V (GTA→GTG) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,198,219 | (G)6→7 | coding (19/705 nt) | ymfE ← | e14 prophage; uncharacterized protein YmfE |
| RA | 1,210,436 | T→C | W31R (TGG→CGG) | mcrA → | e14 prophage; 5‑methylcytosine‑specific restriction enzyme McrA |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,292,147 | (A)5→6 | coding (691/909 nt) | galU → | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,313,218 | A→G | V149A (GTT→GCT) | yciC ← | putative inner membrane protein |
| RA | 1,320,624 | C→T | G254E (GGG→GAG) | trpD ← | anthranilate synthase subunit TrpD |
| RA | 1,347,863 | C→T | W350* (TGG→TGA) | rnb ← | RNase II |
| RA | 1,423,583 | T→C | pseudogene (239/300 nt) *62Q (TAA→CAA) |
rzpR → rzoR → |
Rac prophage; putative endopeptidase RzpR Rac prophage; putative lipoprotein |
| RA | 1,426,475 | C→T | L8F (CTC→TTC) | ynaA → | Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,633,943 | C→T | P108S (CCA→TCA) | pinQ → | Qin prophage; putative site‑specific recombinase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,635,023 | T→C | A275A (GCA→GCG) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,026 | A→G | H274H (CAT→CAC) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,029 | C→T | A273A (GCG→GCA) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,635,032 | G→A | G272G (GGC→GGT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,647,076 | T→C | intergenic (+339/+98) | flxA → / ← ydfW | Qin prophage; protein FlxA/Qin prophage; uncharacterized protein YdfW |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,713,707 | T→C | G313G (GGT→GGC) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,772,911 | T→C | S134P (TCT→CCT) | ydiN → | putative transporter YdiN |
| RA | 1,850,562 | T→C | F576L (TTC→CTC) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,858,333 | T→C | K167K (AAA→AAG) | ydjJ ← | putative zinc‑binding dehydrogenase YdjJ |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,046,646 | T→C | V570A (GTG→GCG) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,053,628 | A→G | intergenic (‑300/‑15) | yeeL ← / → shiA | putative glycosyltransferase, N‑terminal fragment/shikimate:H(+) symporter |
| RA | 2,059,306 | A→G | F181L (TTT→CTT) | yeeO ← | FMN/FAD exporter |
| RA | 2,080,216 | T→C | T126A (ACG→GCG) | yeeA ← | putative transporter YeeA |
| RA | 2,081,846 | A→C | G234G (GGT→GGG) | dacD ← | D‑alanyl‑D‑alanine carboxypeptidase DacD |
| RA | 2,089,580 | T→C | Y45C (TAC→TGC) | yefM ← | YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor |
| RA | 2,093,886 | Δ1 bp | coding (419/1068 nt) | hisB → | imidazoleglycerol‑phosphate dehydratase/histidinol‑phosphatase |
| RA | 2,108,622 | C→A | G321G (GGG→GGT) | rfbX ← | polyisoprenol‑linked O‑antigen repeat unit flippase |
| RA | 2,127,329 | (T)5→4 | coding (986/1122 nt) | gmd ← | GDP‑mannose 4,6‑dehydratase |
| RA | 2,165,608 | A→G | intergenic (+87/‑60) | yegP → / → yegQ | DUF1508 domain‑containing protein YegP/putative peptidase YegQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,245,536 | (C)5→6 | coding (1234/1992 nt) | cirA ← | ferric dihyroxybenzoylserine outer membrane transporter |
| RA | 2,316,188 | G→A | M4I (ATG→ATA) | rcsB → | DNA‑binding transcriptional activator RcsB |
| RA | 2,356,430 | (A)6→5 | coding (910/1191 nt) | glpC → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C |
| RA | 2,372,711 | T→C | V52A (GTG→GCG) | arnE → | undecaprenyl‑phosphate‑alpha‑L‑Ara4N flippase ‑ ArnE subunit |
| RA | 2,383,720 | (C)5→4 | coding (1008/1212 nt) | elaD → | protease ElaD |
| RA | 2,435,973 | T→C | D226G (GAC→GGC) | usg ← | putative semialdehyde dehydrogenase Usg |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| JC JC | 2,469,515 | IS5 (–) +4 bp | coding (385‑388/1332 nt) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,490,474 | G→A | P493S (CCA→TCA) | oxc ← | oxalyl‑CoA decarboxylase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,638,026 | (C)6→7 | coding (627/1179 nt) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,655,443 | T→C | T306A (ACC→GCC) | pepB ← | aminopeptidase B |
| RA | 2,681,919 | T→C | H276R (CAC→CGC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,707,938 | T→C | T273A (ACC→GCC) | rseB ← | anti‑sigma factor stabilizing protein RseB |
| RA | 2,757,662 | (T)8→7 | coding (939/957 nt) | yfjH ← | CP4‑57 prophage; protein YfjH |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,812,292 | T→C | V289A (GTG→GCG) | emrA → | multidrug efflux pump membrane fusion protein EmrA |
| RA | 2,827,382 | C→T | T7T (ACC→ACT) | srlB → | sorbitol‑specific PTS enzyme IIA component |
| RA | 2,839,466 | T→C | intergenic (‑202/‑58) | ascG ← / → ascF | DNA‑binding transcriptional repressor AscG/beta‑glucoside specific PTS enzyme IIBC component |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,965,300 | G→A | R246R (CGC→CGT) | lgt ← | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase |
| RA | 2,980,583 | T→C | Y18C (TAC→TGC) | ygeA ← | amino acid racemase |
| RA | 3,031,485 | T→C | V40A (GTC→GCC) | uacT → | urate:H(+) symporter |
| RA | 3,063,297 | A→G | D104G (GAT→GGT) | argK → | methylmalonyl‑CoA mutase‑interacting GTPase YgfD |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,118,539 | A→G | F192L (TTC→CTC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,175,797 | (C)6→7 | coding (210/582 nt) | yqiA ← | esterase YqiA |
| RA | 3,179,935 | T→C | C64C (TGT→TGC) | ygiB → | DUF1190 domain‑containing protein YgiB |
| RA | 3,194,843 | (G)6→7 | noncoding (23/145 nt) | sibD ← | small RNA SibD |
| RA | 3,198,142 | T→C | G500G (GGA→GGG) | glnE ← | fused glutamine synthetase deadenylase/glutamine synthetase adenylyltransferase |
| RA | 3,211,722 | T→C | F206L (TTC→CTC) | dnaG → | DNA primase |
| RA | 3,250,097 | T→C | R7R (CGT→CGC) | yqjK → | conserved protein YqjK |
| RA | 3,293,659 | A→G | N87S (AAC→AGC) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,335,010 | T→C | S34S (AGT→AGC) | sfsB → | putative transcriptional regulator SfsB |
| RA | 3,336,920 | T→C | intergenic (‑117/+43) | ibaG ← / ← mlaB | acid stress protein IbaG/intermembrane phospholipid transport system protein MlaB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,359,226 | A→G | D10G (GAC→GGC) | gltD → | glutamate synthase subunit GltD |
| RA | 3,379,266 | (C)7→9 | coding (732/1128 nt) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,546,932 | T→C | V125A (GTG→GCG) | gntT → | high‑affinity gluconate transporter |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,583,506 | T→C | C8C (TGT→TGC) | insA‑6 → | IS1 protein InsA |
| RA | 3,803,322 | T→C | L272L (CTA→CTG) | waaB ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 4,201,660 | A→G | V10A (GTA→GCA) | zraP ← | zinc responsive, periplasmic protein with chaperone activity |
| RA | 4,221,040 | T→C | Y483C (TAC→TGC) | arpA ← | regulator of acetyl CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,305,163 | A→G | S479P (TCG→CCG) | yjcS ← | alkyl sulfatase |
| RA | 4,392,261 | (A)8→9 | intergenic (+112/‑99) | orn → / → glyV | oligoribonuclease/tRNA‑Gly |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,472,426 | (A)8→9 | coding (108/135 nt) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,500,253 | (C)5→6 | pseudogene (539/1199 nt) | yjgX ← | KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment |
| RA | 4,531,749 | A→G | intergenic (‑98/+688) | sgcX ← / ← yjhP | KpLE2 phage‑like element; putative endoglucanase with Zn‑dependent exopeptidase domain/KpLE2 phage‑like element; putative methyltransferase YjhP |
| RA | 4,545,466 | T→C | V124A (GTC→GCC) | fimD → | type I fimbriae usher protein |
| RA | 4,560,459 | (C)5→4 | coding (222/684 nt) | yjiH ← | Gate family protein YjiH |
| RA | 4,566,166 | A→G | F361L (TTT→CTT) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1432396–1432653 | 1433538–1433373 | 721–1143 | 9 [8] | [6] 9 | [stfR]–[pinR] | [stfR],tfaR,[pinR] |
| * | * | ÷ | NC_000913 | 3423787–3424234 | 3424523–3424242 | 9–737 | 11 [8] | [6] 13 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 31 (0.770) | 10/260 | 2.3 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 8 (0.260) | 6/202 | 2.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 22 (0.750) | 13/190 | 1.0 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 18 (0.600) | 6/192 | 2.4 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 1207790 = | 13 (0.300) | 56 (1.480) | 41/244 | 0.0 | 77.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 22 (0.580) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.300) | 24 (0.630) | 16/244 | 1.2 | 58.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 22 (0.580) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 69 (1.610) | 75 (1.760) | 40/274 | 0.1 | 68.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 42 (0.980) | 33/276 | 0.3 | 91.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 4 (0.090) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||