mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 62,822 | Δ16 bp | 100% | coding (428‑443/2907 nt) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 92,250 | T→C | 6.4% | S280P (TCA→CCA) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 349,642 | A→G | 6.5% | intergenic (+70/‑370) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 425,955 | C→T | 5.1% | A315A (GCC→GCT) | queA → | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase |
| RA | 701,362 | G→T | 7.2% | S78Y (TCC→TAC) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 801,946 | T→C | 5.7% | G20G (GGT→GGC) | ybhI → | putative DASS family tricarboxylate or dicarboxylate transporter |
| JC JC | 973,271 | IS5 (+) +4 bp | 68.6% | coding (128‑131/780 nt) | elyC ← | envelope biogenesis factor; DUF218 superfamily protein |
| RA | 1,031,646 | A→G | 5.7% | noncoding (67/88 nt) | serT ← | tRNA‑Ser |
| RA | 1,073,967 | T→G | 6.5% | E15D (GAA→GAC) | rutA ← | pyrimidine oxygenase, FMN‑dependent |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,402,502 | G→T | 5.5% | Q252K (CAG→AAG) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,407,779 | A→G | 5.6% | F6S (TTC→TCC) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,466,210 | G→A | 8.1% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 7.1% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,529,430 | G→T | 5.2% | pseudogene (1529/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,854,576:1 | +T | 5.6% | coding (279/759 nt) | ydjF ← | putative DNA‑binding transcriptional regulator |
| RA | 1,936,308 | C→T | 100% | V3I (GTA→ATA) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,985,718 | G→A | 5.3% | G137G (GGC→GGT) | araF ← | L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,046,044 | Δ1 bp | 7.3% | coding (1107/7077 nt) | yeeJ → | putative adhesin |
| RA | 2,113,831 | C→T | 6.3% | R166H (CGT→CAT) | wcaN ← | putative regulatory subunit for GalU |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,137,960 | A→T | 7.1% | E20V (GAA→GTA) | yegH → | inner membrane protein |
| 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 | 2,185,975 | C→A | 5.9% | A20D (GCC→GAC) | rcnA → | membrane protein conferring nickel and cobalt resistance |
| RA | 2,272,636 | C→A | 7.1% | S91S (TCC→TCA) | yejA → | microcin C ABC transporter periplasmic binding protein |
| RA | 2,304,798 | T→C | 8.6% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,514,258 | A→G | 5.4% | intergenic (+14/‑73) | nupC → / → insL1 | nucleoside (except guanosine) transporter/IS186 transposase |
| RA | 2,625,212 | G→A | 5.7% | G33D (GGT→GAT) | ppx → | exopolyphosphatase |
| RA | 2,963,184 | G→A | 5.6% | A178V (GCC→GTC) | ppdB ← | putative prepilin peptidase‑dependent protein |
| RA | 3,267,747:1 | +G | 6.0% | intergenic (+149/‑107) | tdcR → / → yhaB | L‑threonine dehydratase operon activator protein/uncharacterized protein |
| RA | 3,486,708 | A→T | 11.2% | I197F (ATC→TTC) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| JC JC | 3,553,103 | IS5 (+) +4 bp | 100% | coding (19‑22/2706 nt) | malT → | mal regulon transcriptional activator |
| 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 | 3,655,363:1 | +T | 5.5% | coding (540/648 nt) | yhiD ← | putative Mg(2+) transport ATPase, inner membrane protein |
| RA | 3,744,991 | T→C | 5.8% | V63A (GTG→GCG) | yiaN → | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,004,945 | G→A | 6.9% | V28V (GTG→GTA) | pldA → | outer membrane phospholipase A |
| JC JC | 4,049,903 | IS2 (–) +5 bp | 100% | noncoding (5‑9/109 nt) | spf → | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 14.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 24.9% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 25.4% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 30.4% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 13.6% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 8.7% | 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 | 4,583,907 | T→A | 5.8% | H952L (CAC→CTC) | hsdR ← | endonuclease R Type I restriction enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423879–3424232 | 3424414–3424238 | 7–536 | 24 [22] | [22] 24 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4233745 | 4235413 | 1669 | 25 [23] | [21] 24 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 382153 | NA (NA) | 9 (0.120) | 4/490 | NT | NA | noncoding (894/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382246 | NA (NA) | noncoding (987/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 50 (0.660) | 44 (0.620) | 35/470 | NT | 57.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 18 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.640) | 55 (0.780) | 51/470 | NT | 63.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 18 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1491823 = | 46 (0.610) | 4 (0.050) | 4/492 | NT | 5.7% | coding (147/174 nt) | ydcA | putative periplasmic protein |
| ? | NC_000913 | 1492363 = | 87 (1.180) | intergenic (+189/‑107) | sokB/trg | sRNA antisense regulator blocking mokB, and hence hokB, translation/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor | |||||
| * | ? | NC_000913 | = 2498108 | 61 (0.810) | 6 (0.080) | 5/480 | NT | 10.4% | coding (188/1239 nt) | alaC | glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase |
| ? | NC_000913 | = 2498315 | 45 (0.620) | intergenic (‑20/‑356) | alaC/ypdA | glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase/sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system | |||||