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 | 7,069 | A→G | I297I (ATT→ATC) | yaaJ ← | putative transporter YaaJ |
| RA | 50,518 | A→G | G235G (GGT→GGC) | apaH ← | diadenosine tetraphosphatase |
| RA | 60,088 | A→G | F87L (TTC→CTC) | rluA ← | 23S rRNA pseudouridine(746) and tRNA pseudouridine(32) synthase |
| RA | 113,148 | A→T | D24E (GAT→GAA) | coaE ← | dephospho‑CoA kinase |
| RA | 255,174 | (C)6→7 | coding (543/1458 nt) | pepD ← | peptidase D |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 285,052 | A→G | T618A (ACC→GCC) | yagF → | CP4‑6 prophage; D‑xylonate dehydratase |
| RA | 318,945 | C→T | A353T (GCT→ACT) | rclA ← | putative pyridine nucleotide‑disulfide oxidoreductase RclA |
| RA | 339,509 | C→T | R395R (CGC→CGT) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 354,795 | (T)5→4 | intergenic (+203/‑127) | prpE → / → codB | propionyl‑CoA synthetase/cytosine transporter |
| RA | 376,686 | A→G | intergenic (+16/‑86) | mhpT → / → yaiL | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter/DUF2058 domain‑containing protein YaiL |
| RA | 469,571 | (A)8→7 | coding (701/1773 nt) | mdlA → | ABC transporter family protein MdlA |
| RA | 495,775 | A→G | E219G (GAA→GGA) | htpG → | chaperone protein HtpG |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 531,620 | T→C | D201G (GAC→GGC) | allS ← | DNA‑binding transcriptional activator AllS |
| RA | 541,167 | C→T | V201V (GTC→GTT) | ybbY → | putative purine transporter |
| RA | 600,075 | G→A | L454L (CTG→CTA) | cusA → | copper/silver export system RND permease |
| RA | 611,055 | C→T | L480L (CTG→CTA) | fepA ← | ferric enterobactin outer membrane transporter |
| RA | 705,972 | (T)9→8 | intergenic (+82/‑121) | nagE → / → glnS | N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
| RA | 797,869 | T→C | H188R (CAC→CGC) | ybhA ← | pyridoxal phosphate/fructose‑1,6‑bisphosphate phosphatase |
| RA | 804,164 | T→C | V221A (GTC→GCC) | ybhJ → | putative hydratase YbhJ |
| RA | 810,437 | C→T | A19A (GCC→GCT) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 916,326 | A→G | intergenic (‑279/‑147) | aqpZ ← / → ybjD | water channel AqpZ/DUF2813 domain‑containing protein YbjD |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,092,286 | A→G | Y2H (TAT→CAT) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin |
| RA | 1,139,399 | (A)5→4 | coding (1022/1644 nt) | flgK → | flagellar hook‑filament junction protein 1 |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,154,439 | T→C | F110L (TTC→CTC) | mltG → | endolytic murein transglycosylase |
| RA | 1,207,472 | A→G | Y187C (TAC→TGC) | ymfQ → | e14 prophage; conserved protein YmfQ |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,275,844 | A→G | V592A (GTC→GCC) | narX ← | sensory histidine kinase NarX |
| RA | 1,283,563 | T→C | L1234L (TTA→CTA) | narG → | nitrate reductase A subunit alpha |
| RA | 1,297,590 | A→G | S178P (TCT→CCT) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,320,377 | C→T | S336S (TCG→TCA) | trpD ← | anthranilate synthase subunit TrpD |
| RA | 1,334,023 | A→G | T57A (ACG→GCG) | cysB → | DNA‑binding transcriptional dual regulator CysB |
| RA | 1,370,043 | (T)9→7 | intergenic (+40/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,381,781 | A→G | pseudogene (961/969 nt) | ycjV → | putative ABC transporter ATP‑binding protein YcjV |
| RA | 1,420,829 | A→G | N49S (AAC→AGC) | ydaT → | Rac prophage; protein YdaT |
| RA | 1,447,975 | (G)5→4 | coding (457/1500 nt) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,474,861 | (G)5→6 | coding (641/861 nt) | pdxI → | pyridoxine 4‑dehydrogenase |
| RA | 1,494,883 | (C)5→4 | coding (189/924 nt) | ydcI ← | putative DNA‑binding transcriptional repressor YdcI |
| RA | 1,534,004 | A→G | intergenic (‑153/‑20) | yddH ← / → nhoA | flavin reductase‑like protein YddH/arylamine N‑acetyltransferase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,597,382 | (T)6→5 | pseudogene (705/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,620,054 | A→G | E22E (GAA→GAG) | marB → | multiple antibiotic resistance protein |
| RA | 1,620,973 | T→C | K55K (AAA→AAG) | eamA ← | cysteine/O‑acetylserine exporter EamA |
| RA | 1,652,044 | T→C | pseudogene (533/1197 nt) | intQ → | Qin prophage; putative defective integrase |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,740,176 | T→C | L89P (CTG→CCG) | ydhC → | putative transporter YdhC |
| RA | 1,755,660 | T→C | intergenic (‑519/‑38) | fumD ← / → pykF | fumarase D/pyruvate kinase I |
| RA | 1,761,092 | A→G | L234L (TTG→CTG) | sufD ← | Fe‑S cluster scaffold complex subunit SufD |
| RA | 1,766,645 | T→C | T681A (ACC→GCC) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,802,756 | (A)7→6 | intergenic (‑186/‑338) | thrS ← / → arpB | threonine‑‑tRNA ligase/putative ankyrin repeat protein B, N‑terminal fragment |
| 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 |
| RA | 1,958,123 | (T)6→5 | coding (10/1101 nt) | torY ← | cytochrome c quinol dehydrogenase TorY |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,028,811 | T→C | T186A (ACC→GCC) | yedI ← | conserved inner membrane protein YedI |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,324,560 | Δ1 bp | coding (452/651 nt) | atoA → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit beta |
| RA | 2,345,512 | T→C | R216R (CGT→CGC) | nrdA → | ribonucleoside‑diphosphate reductase 1 subunit alpha |
| RA | 2,400,358 | G→A | H400Y (CAC→TAC) | nuoF ← | NADH:quinone oxidoreductase subunit F |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,465,409 | Δ1 bp | coding (109/933 nt) | yfdC → | inner membrane protein YfdC |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,626,098 | C→T | I328I (ATC→ATT) | ppx → | exopolyphosphatase |
| RA | 2,696,672 | T→C | L291S (TTA→TCA) | mltF → | membrane‑bound lytic murein transglycosylase F |
| RA | 2,697,293 | A→G | N498S (AAC→AGC) | mltF → | membrane‑bound lytic murein transglycosylase F |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,769,648 | (C)6→7 | intergenic (+162/‑55) | yfjQ → / → yfjR | CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,835,043 | T→C | *378Q (TAG→CAG) | norW → | NADH:flavorubredoxin reductase |
| RA | 2,845,936 | T→C | N179S (AAC→AGC) | hycE ← | formate hydrogenlyase subunit HycE |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,892,397 | T→C | F62L (TTT→CTT) | queD → | 6‑carboxy‑5,6,7,8‑tetrahydropterin synthase |
| RA | 2,892,643 | A→G | intergenic (+64/‑14) | queD → / → ygcN | 6‑carboxy‑5,6,7,8‑tetrahydropterin synthase/putative oxidoreductase with FAD/NAD(P)‑binding domain |
| RA | 2,930,738 | T→C | V388A (GTA→GCA) | sdaB → | L‑serine deaminase II |
| RA | 2,946,315 | A→G | G288G (GGT→GGC) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,042,079 | G→A | S256N (AGC→AAC) | ygfZ → | folate‑binding protein |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,094,406 | T→C | L225L (TTA→TTG) | yggR ← | Type II/IV secretion system family protein |
| RA | 3,172,546 | T→C | I6T (ATT→ACT) | mdaB → | NADPH:quinone oxidoreductase MdaB |
| RA | 3,227,892 | A→G | E31G (GAA→GGA) | ygjJ → | protein YgjJ |
| RA | 3,279,362 | G→A | R150H (CGT→CAT) | kbaZ → | tagatose‑1,6‑bisphosphate aldolase 1 subunit KbaZ |
| RA | 3,280,298 | (G)5→6 | coding (82/474 nt) | agaV → | N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,465,428 | G→A | R116H (CGC→CAC) | gspM → | Type II secretion system protein GspM |
| RA | 3,476,431 | A→G | S4P (TCG→CCG) | yheO ← | putative DNA‑binding transcriptional regulator YheO |
| RA | 3,516,070 | (T)5→6 | coding (1237/1287 nt) | damX ← | cell division protein DamX |
| RA | 3,525,052 | T→C | F728L (TTC→CTC) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,532,985 | C→T | A56A (GCC→GCT) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,550,076 | T→C | intergenic (‑6/+4) | malQ ← / ← malP | 4‑alpha‑glucanotransferase/maltodextrin phosphorylase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,582,314 | T→C | L151P (CTC→CCC) | yhhZ → | putative endonuclease YhhZ |
| RA | 3,629,462 | A→G | V26A (GTT→GCT) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,682,126 | A→G | intergenic (‑186/+35) | yhjJ ← / ← dctA | peptidase M16 family protein/C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,746,518 | A→G | Y142C (TAC→TGC) | yiaO → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ periplasmic binding protein |
| RA | 3,770,066 | A→G | intergenic (+386/+177) | yibV → / ← yibH | PF15596 family protein YibV/inner membrane protein YibH |
| 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 | 3,878,762 | A→G | V453A (GTC→GCC) | gyrB ← | DNA gyrase subunit B |
| RA | 3,944,115 | A→G | noncoding (412/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,969,628 | G→A | A200T (GCG→ACG) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| JC | 3,982,684 | (C)8→11 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,040,676 | C→T | intergenic (+40/+230) | rrfA → / ← mobB | 5S ribosomal RNA/molybdopterin‑guanine dinucleotide biosynthesis adaptor protein |
| RA | 4,106,387 | (T)8→7 | noncoding (58/58 nt) | cpxQ → | small regulatory RNA CpxQ |
| RA | 4,144,442 | A→G | T150A (ACG→GCG) | pflD → | putative formate acetyltransferase 2 |
| RA | 4,249,344 | C→T | intergenic (+33/‑210) | lamB → / → malM | maltose outer membrane channel/phage lambda receptor protein/maltose regulon periplasmic protein |
| RA | 4,296,268 | T→C | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,334,454 | T→C | L379L (TTA→TTG) | eptA ← | phosphoethanolamine transferase EptA |
| RA | 4,339,041 | T→C | D494G (GAC→GGC) | adiA ← | arginine decarboxylase, degradative |
| RA | 4,361,448 | (A)8→7 | coding (487/1539 nt) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,381,821 | A→G | G166G (GGT→GGC) | frdA ← | fumarate reductase flavoprotein subunit |
| RA | 4,443,268 | Δ1 bp | coding (887/1734 nt) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,473,205 | A→G | V2A (GTA→GCA) | yjgH ← | RutC family protein YjgH |
| RA | 4,473,852 | C→T | D68N (GAT→AAT) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,597,074 | (T)8→7 | intergenic (+62/+76) | lgoD → / ← opgB | L‑galactonate oxidoreductase/phosphoglycerol transferase I |
| RA | 4,625,637 | A→G | Y248C (TAC→TGC) | serB → | phosphoserine phosphatase |
| RA | 4,626,677 | A→G | S256G (AGC→GGC) | radA → | DNA recombination protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1552081–1552189 | 1552316–1552213 | 25–236 | 76 [74] | [74] 76 | fdnI/yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM |
| * | * | ÷ | NC_000913 | 1634022–1634638 | 1634916–1634640 | 3–895 | 77 [74] | [74] 75 | [pinQ]–[ydfN] | [pinQ],tfaQ,[ydfN] |
| * | * | ÷ | NC_000913 | 3423751–3424234 | 3424544–3424238 | 5–794 | 75 [72] | [74] 76 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 0 (0.000) | 251 (1.390) | 101/244 | 0.1 | 98.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 7 (0.040) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 0 (0.000) | 176 (0.970) | 71/244 | 0.7 | 98.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 7 (0.040) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 199 (1.000) | 97/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 277 (1.350) | 303 (1.490) | 111/274 | 0.1 | 68.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 7 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 234 (1.140) | 105/276 | 0.2 | 97.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 6 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||