mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| JC JC | 156,143 | IS5 (–) +4 bp | coding (56‑59/741 nt) | yadV ← | putative fimbrial chaperone YadV |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 258,999 | Δ14,956 bp | IS5‑mediated | [crl]–[ykfC] | 21 genes [crl], phoE, proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,085 | C→T | Q108* (CAG→TAG) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| JC JC | 1,399,590 | IS5 (+) +4 bp | intergenic (‑64/+128) | fnr ← / ← ogt | DNA‑binding transcriptional dual regulator FNR/methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| RA | 1,922,115 | G→T | intergenic (+99/‑6) | yebV → / → yebW | DUF1480 domain‑containing protein YebV/DUF1482 domain‑containing protein YebW |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC | 2,173,675 | (ATTCGGTTAACGCCTGG)1→2 | intergenic (‑802/+607) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| JC JC | 2,406,440 | IS5 (–) +4 bp | coding (199‑202/939 nt) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| JC JC | 2,698,402 | IS30 (+) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| JC JC | 2,717,292 | IS30 (–) +2 bp | coding (539‑540/690 nt) | ung → | uracil‑DNA glycosylase |
| RA | 2,778,018 | C→T | intergenic (+236/+128) | ypjF → / ← ypjA | toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,779,776 | G→A | S984L (TCG→TTG) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,533,776 | IS30 (+) +2 bp | coding (959‑960/1623 nt) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,939,212 | C→T | S329L (TCG→TTG) P467P (CCG→CCA) |
rbsR → hsrA ← |
DNA‑binding transcriptional dual regulator RbsR putative transporter HsrA |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| JC JC | 4,476,959 | IS5 (+) +4 bp | coding (1523‑1526/1815 nt) | yjgL → | protein YjgL |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423806–3424459 | 3424459 | 1–654 | 41 [37] | [36] 38 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 270541 = | NA (NA) | 103 (0.990) | 67/594 | 0.3 | 79.2% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 998144 = | 27 (0.260) | coding (277/540 nt) | elfA | putative laminin‑binding fimbrial subunit | |||||
| * | ? | NC_000913 | 270541 = | NA (NA) | 82 (0.790) | 53/598 | 0.8 | 68.3% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1855666 = | 38 (0.360) | coding (306/981 nt) | ydjG | NADH‑dependent methylglyoxal reductase | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 85 (0.810) | 56/598 | 0.6 | 49.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 735612 | 87 (0.830) | intergenic (+1510/‑38) | ybfB/ybfC | uncharacterized protein YbfB/uncharacterized protein YbfC | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 65 (0.620) | 49/598 | 1.0 | 42.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 735609 = | 87 (0.830) | intergenic (+1507/‑41) | ybfB/ybfC | uncharacterized protein YbfB/uncharacterized protein YbfC | |||||
| * | ? | NC_000913 | = 998145 | 27 (0.260) | 98 (0.940) | 76/598 | 0.1 | 78.4% | coding (278/540 nt) | elfA | putative laminin‑binding fimbrial subunit |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 27 (0.260) | 82 (0.830) | 62/566 | 0.3 | 73.4% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 34 (0.340) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.300) | 58 (0.590) | 46/566 | 1.0 | 64.7% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 34 (0.340) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 2 (0.020) | 121 (1.180) | 78/590 | 0.1 | 99.2% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 74 (0.710) | 54/594 | 0.7 | 58.3% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 4123473 = | 53 (0.510) | coding (984/1026 nt) | cytR | DNA‑binding transcriptional repressor CytR | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 87 (0.830) | 63/598 | 0.4 | 70.2% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1855667 | 37 (0.350) | coding (305/981 nt) | ydjG | NADH‑dependent methylglyoxal reductase | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 87 (0.830) | 60/598 | 0.5 | 75.6% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4578641 | 28 (0.270) | coding (214/897 nt) coding (697/1380 nt) |
mcrB mcrB |
5‑methylcytosine‑specific restriction enzyme subunit McrB 5‑methylcytosine‑specific restriction enzyme subunit McrB |
|||||
| * | ? | NC_000913 | = 4123474 | 49 (0.470) | 99 (0.950) | 71/598 | 0.2 | 66.9% | coding (983/1026 nt) | cytR | DNA‑binding transcriptional repressor CytR |
| ? | NC_000913 | 4507459 = | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 4498181 = | NA (NA) | 104 (1.000) | 61/598 | 0.5 | 78.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 4578637 = | 29 (0.280) | coding (218/897 nt) coding (701/1380 nt) |
mcrB mcrB |
5‑methylcytosine‑specific restriction enzyme subunit McrB 5‑methylcytosine‑specific restriction enzyme subunit McrB |
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