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 | 55,482 | T→C | D543G (GAC→GGC) | lptD ← | lipopolysaccharide assembly protein LptD |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 311,002 | Δ1 bp | coding (335/591 nt) | ecpR ← | DNA‑binding transcriptional dual regulator MatA |
| RA | 325,935 | G→A | P438L (CCC→CTC) | betA ← | choline dehydrogenase |
| RA | 386,360 | C→T | P52S (CCT→TCT) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 417,596 | C→T | P152L (CCG→CTG) | phoB → | DNA‑binding transcriptional dual regulator PhoB |
| RA | 428,722 | A→G | D359G (GAC→GGC) | secD → | Sec translocon accessory complex subunit SecD |
| RA | 514,566 | G→A | G98G (GGC→GGT) | ybbJ ← | NfeD‑like family protein |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 630,889 | C→T | T332T (ACC→ACT) | cstA → | carbon starvation protein A |
| RA | 700,166 | T→C | N54S (AAC→AGC) | umpH ← | UMP phosphatase |
| RA | 743,909 | C→T | A106V (GCG→GTG) | pxpB → | 5‑oxoprolinase component B |
| RA | 751,895 | C→T | G92D (GGT→GAT) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 773,407 | C→T | G122G (GGC→GGT) | cydB → | cytochrome bd‑I ubiquinol oxidase subunit II |
| RA | 867,051 | A→G | T162A (ACC→GCC) | iaaA → | isoaspartyl dipeptidase proenzyme |
| 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 | 972,557 | A→G | D269G (GAT→GGT) | ycbJ → | putative phosphotransferase YcbJ |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,022,012 | A→C | G624G (GGT→GGG) | yccS ← | putative transporter YccS |
| RA | 1,093,358 | (G)6→7 | coding (483/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,124,719 | C→T | R203H (CGC→CAC) | mdtH ← | multidrug efflux pump MdtH |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,198,052 | T→C | A62A (GCA→GCG) | ymfE ← | e14 prophage; uncharacterized protein YmfE |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,288,055 | A→G | H190H (CAT→CAC) | purU ← | formyltetrahydrofolate deformylase |
| RA | 1,372,756 | G→A | G283D (GGT→GAT) | ycjN → | putative ABC transporter periplasmic binding protein YcjN |
| RA | 1,485,167 | A→G | T703A (ACC→GCC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,516,460 | A→G | T295A (ACG→GCG) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,618,444 | T→C | V155V (GTA→GTG) | marC ← | inner membrane protein MarC |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,085 | T→C | G439G (GGT→GGC) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,720,255 | T→C | V127A (GTA→GCA) | slyB → | outer membrane lipoprotein SlyB |
| RA | 1,723,167 | C→T | G349G (GGC→GGT) | ydhK → | putative transporter YdhK |
| RA | 1,780,993 | T→C | V198A (GTT→GCT) | ydiR → | putative electron transfer flavoprotein subunit YdiR |
| RA | 1,846,333 | C→T | D210N (GAT→AAT) | topB ← | DNA topoisomerase III |
| RA | 1,849,454 | T→C | G206G (GGT→GGC) | sppA → | protease IV, a signal peptide peptidase |
| 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 | 1,901,792 | G→A | intergenic (‑10/‑256) | yoaL ← / → manX | protein YoaL/mannose‑specific PTS enzyme IIAB component |
| RA | 1,924,381 | T→C | T71A (ACG→GCG) | yebZ ← | putative inner membrane protein |
| RA | 1,946,025 | (A)7→6 | intergenic (‑49/+90) | ruvA ← / ← yobI | Holliday junction branch migration complex subunit RuvA/uncharacterized protein YobI |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,015,676 | C→T | A266V (GCC→GTC) | fliG → | flagellar motor switch protein FliG |
| RA | 2,051,365 | T→C | V2143A (GTA→GCA) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,066,175 | T→C | intergenic (‑411/+130) | cobU ← / ← insH‑6 | cobinamide‑P guanylyltransferase/cobinamide kinase/CP4‑44 prophage; IS5 transposase and trans‑activator |
| RA | 2,086,480 | A→G | S195P (TCT→CCT) | plaP ← | putrescine:H(+) symporter PlaP |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,188,043 | (C)6→5 | coding (372/1035 nt) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,202,057 | C→T | T593T (ACC→ACT) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,242,011 | A→G | C319C (TGT→TGC) | yeiB ← | DUF418 domain‑containing protein YeiB |
| RA | 2,288,561 | (C)7→8 | pseudogene (354/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,303,802 | T→C | intergenic (+32/‑103) | yojO → / → eco | uncharacterized protein YojO/serine protease inhibitor ecotin |
| RA | 2,307,508 | T→C | T370A (ACG→GCG) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,405,158 | (A)8→7 | intergenic (‑86/+545) | nuoA ← / ← lrhA | NADH:quinone oxidoreductase subunit A/DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,424,506 | A→G | S2P (TCC→CCC) | hisP ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, ATP binding subunit |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,755,800 | G→A | noncoding (208/363 nt) | ssrA → | tmRNA |
| RA | 2,765,794 | (C)7→6 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,792,661 | A→G | E463E (GAA→GAG) | gabD → | NADP(+)‑dependent succinate‑semialdehyde dehydrogenase |
| RA | 2,798,154 | A→G | R114R (CGT→CGC) | stpA ← | DNA‑binding transcriptional repressor StpA with RNA chaperone activity |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,867,700 | T→C | T352A (ACC→GCC) | nlpD ← | murein hydrolase activator NlpD |
| RA | 2,905,768 | A→G | T20A (ACT→GCT) | ygcG → | protein YgcG |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,973,345 | G→A | A173V (GCC→GTC) | lplT ← | lysophospholipid transporter |
| RA | 2,974,911 | C→T | A368A (GCG→GCA) | aas ← | acyltransferase |
| RA | 3,009,716 | T→C | V318A (GTG→GCG) | ygeY → | putative peptidase YgeY |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,072,812 | T→C | S294G (AGT→GGT) | epd ← | D‑erythrose‑4‑phosphate dehydrogenase |
| RA | 3,097,936 | G→A | G224R (GGG→AGG) | yggW → | putative coproporphyrinogen‑III oxidase‑like protein YggW |
| RA | 3,102,751 | Δ1 bp | coding (102/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase |
| RA | 3,155,039 | T→C | A60A (GCA→GCG) | yqhC ← | DNA‑binding transcriptional activator YqhC |
| RA | 3,177,509 | (C)6→7 | coding (402/630 nt) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,180,822 | G→A | W134* (TGG→TGA) | ygiC → | putative enzyme with ATPase activity |
| RA | 3,194,843 | (G)6→7 | noncoding (23/145 nt) | sibD ← | small RNA SibD |
| JC | 3,216,481 | (G)6→9 | coding (11/765 nt) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,351,634 | T→C | K464K (AAA→AAG) | arcB ← | sensory histidine kinase ArcB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,385,829 | G→A | intergenic (+28/+28) | yhcN → / ← yhcO | DUF1471 domain‑containing stress‑induced protein YhcN/putative barnase inhibitor |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,490,764 | (C)5→6 | coding (66/564 nt) | pabA ← | aminodeoxychorismate synthase subunit 2 |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,627,869 | T→A | D557V (GAT→GTT) | rbbA ← | ribosome‑associated ATPase |
| RA | 3,639,879 | (T)8→7 | intergenic (‑159/‑232) | uspB ← / → uspA | putative universal stress (ethanol tolerance) protein B/universal stress global stress response regulator |
| RA | 3,686,902 | T→C | T758A (ACC→GCC) | bcsC ← | cellulose biosynthesis protein BcsC |
| RA | 3,728,110 | T→C | D421G (GAT→GGT) | xylB ← | xylulokinase |
| RA | 3,762,260 | G→A | V26V (GTG→GTA) | rhsA → | rhs element protein RhsA |
| RA | 3,762,263 | C→T | R27R (CGC→CGT) | rhsA → | rhs element protein RhsA |
| RA | 3,794,338 | G→A | A118T (GCC→ACC) | rfaD → | ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,828,023 | A→G | L215L (TTG→CTG) | gltS ← | glutamate:sodium symporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 4,060,843 | (G)6→7 | coding (397/711 nt) | yihL → | putative transcriptional regulator YihL |
| RA | 4,074,228 | A→G | T164A (ACG→GCG) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,131,717 | G→A | G628E (GGG→GAG) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,179,333 | C→T | A152V (GCG→GTG) | rplA → | 50S ribosomal subunit protein L1 |
| RA | 4,201,586 | G→A | Q35* (CAA→TAA) | zraP ← | zinc responsive, periplasmic protein with chaperone activity |
| RA | 4,230,452 | G→A | V33V (GTG→GTA) | rluF → | 23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase |
| RA | 4,274,165 | A→G | N14S (AAT→AGT) | ssb → | ssDNA‑binding protein |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,310,086 | C→T | G299S (GGT→AGT) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,310,436 | T→C | D182G (GAC→GGC) | alsA ← | D‑allose ABC transporter ATP binding subunit |
| RA | 4,400,982 | C→T | T104I (ACC→ATC) | hflX → | ribosome rescue factor HflX |
| RA | 4,409,574 | C→T | L100L (CTC→CTT) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| RA | 4,419,389 | A→G | G79G (GGT→GGC) | ulaG ← | L‑ascorbate‑6‑phosphate lactonase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,473,559 | T→C | G165G (GGA→GGG) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,492,189 | (A)6→7 | coding (337/1320 nt) | idnT ← | L‑idonate/5‑ketogluconate/gluconate transporter |
| RA | 4,556,804 | (T)6→5 | intergenic (+7/‑109) | ytiD → / → idlP | protein YtiD/iraD leader peptide |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 433043 | 433110 | 68 | 11 [9] | [9] 10 | nrdR | NrdR transcriptional repressor |
| * | * | ÷ | NC_000913 | 738216–738306 | 738559 | 254–344 | 10 [9] | [9] 10 | ybfD | H repeat‑associated putative transposase YbfD |
| * | * | ÷ | NC_000913 | 3423770–3424232 | 3424523–3424242 | 11–754 | 14 [9] | [9] 10 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3762282–3764070 | 3765545–3765414 | 1345–3264 | 10 [9] | [9] 10 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 18 (0.370) | 64 (1.480) | 44/244 | 0.1 | 84.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 7 (0.160) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 18 (0.370) | 44 (1.010) | 32/244 | 0.3 | 79.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 7 (0.160) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 56 (1.180) | 43/268 | 0.1 | 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 = | 73 (1.490) | 90 (1.850) | 55/274 | 0.0 | 70.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.060) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 43 (0.880) | 34/276 | 0.3 | 97.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||