mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 526,792 | A→C | 16.7% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,796 | C→G | 14.9% | A1179G (GCG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 14.3% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 551,372 | C→A | 5.1% | intergenic (+40/+155) | ybcF → / ← purK | putative carbonate kinase/N5‑carboxyaminoimidazole ribonucleotide synthase |
| JC | 712,853 | +GTGCCACAGG | 100% | intergenic (‑51/‑134) | ybfF ← / → seqA | acyl‑CoA esterase/negative modulator of initiation of replication |
| RA | 1,117,876 | C→G | 5.4% | intergenic (+17/+25) | yceA → / ← yceI | putative rhodanese‑related sulfurtransferase/periplasmic high pH‑inducible lipid‑binding protein |
| RA | 1,117,877 | G→C | 5.4% | intergenic (+18/+24) | yceA → / ← yceI | putative rhodanese‑related sulfurtransferase/periplasmic high pH‑inducible lipid‑binding protein |
| RA | 1,117,878 | T→A | 5.3% | intergenic (+19/+23) | yceA → / ← yceI | putative rhodanese‑related sulfurtransferase/periplasmic high pH‑inducible lipid‑binding protein |
| RA | 1,117,879 | G→C | 5.3% | intergenic (+20/+22) | yceA → / ← yceI | putative rhodanese‑related sulfurtransferase/periplasmic high pH‑inducible lipid‑binding protein |
| RA | 1,169,380 | T→C | 5.8% | intergenic (+50/+32) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,382 | C→G | 5.2% | intergenic (+52/+30) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,169,384 | G→A | 5.3% | intergenic (+54/+28) | bhsA → / ← ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| RA | 1,529,175 | T→C | 100% | pseudogene (1274/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,180 | T→C | 100% | pseudogene (1279/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,185 | C→T | 100% | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,950,306 | C→G | 5.0% | G73R (GGC→CGC) | aspS ← | aspartyl‑tRNA synthetase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,630,921 | A→T | 5.1% | intergenic (+56/+37) | yfgI → / ← guaA | nalidixic acid resistance protein, putative periplasmic protein/GMP synthetase (glutamine aminotransferase) |
| RA | 2,911,007 | G→A | 5.1% | R29C (CGT→TGT) | mazF ← | mRNA interferase toxin, antitoxin is MazE |
| RA | 2,911,008 | A→T | 5.2% | H28Q (CAT→CAA) ‡ | mazF ← | mRNA interferase toxin, antitoxin is MazE |
| RA | 2,911,009 | T→C | 5.2% | H28R (CAT→CGT) ‡ | mazF ← | mRNA interferase toxin, antitoxin is MazE |
| RA | 3,233,708 | A→G | 5.3% | intergenic (+25/+20) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,233,709 | A→T | 5.0% | intergenic (+26/+19) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,233,710 | C→T | 5.0% | intergenic (+27/+18) | fadH → / ← higA | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system |
| RA | 3,477,345 | A→T | 5.3% | A25A (GCT→GCA) | fkpA ← | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,831,757 | C→T | 6.3% | A434V (GCC→GTC) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,831,761 | C→G | 6.3% | A435A (GCC→GCG) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,831,764 | C→G | 6.4% | A436A (GCC→GCG) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,831,768 | A→G | 6.2% | T438A (ACA→GCA) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,875,522 | C→G | 6.8% | L29V (CTG→GTG) | yidX → | putative lipoprotein |
| RA | 4,296,190 | A→G | 29.9% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 30.3% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 34.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 22.5% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 12.4% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 10.8% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,472,236 | T→G | 12.3% | T54P (ACC→CCC) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423742–3424503 | 3424503 | 1–762 | 90 [89] | [89] 90 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 271133 | NA (NA) | 4 (0.030) | 4/554 | NT | NA | noncoding (593/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 271141 | NA (NA) | noncoding (601/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 274347 = | NA (NA) | 8 (0.050) | 6/550 | NT | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1096961 = | 140 (0.920) | 29 (0.270) | 10/404 | NT | 23.9% | intergenic (+132/+604) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 84 (0.770) | intergenic (+674/+62) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.100) | 126 (0.880) | 112/532 | NT | 88.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 19 (0.130) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 14 (0.090) | 122 (0.850) | 105/532 | NT | 88.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 19 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 177 (1.180) | 140/556 | NT | 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 | |||||
| * | ? | NC_000913 | = 3620350 | NA (NA) | 9 (0.060) | 8/552 | NT | 100% | coding (1159/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3620425 | 0 (0.000) | coding (1234/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||