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 |
| RA | 141,212 | T→A | 5.3% | N5I (AAT→ATT) | gcd ← | glucose dehydrogenase |
| RA | 168,474 | C→T | 79.3% | Q331* (CAG→TAG) | fhuA → | ferrichrome outer membrane transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 392,913 | C→T | 10.6% | intergenic (‑12/‑57) | insE1 ← / → yaiT | IS3 transposase A/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 394,776 | A→G | 7.3% | N91D (AAT→GAT) | yaiV → | putative transcriptional regulator |
| RA | 395,476 | G→T | 75.1% | S271Y (TCT→TAT) | ampH ← | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase |
| RA | 462,737 | C→A | 5.4% | Q275K (CAG→AAG) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 620,790 | G→A | 5.0% | V133V (GTC→GTT) | fepG ← | iron‑enterobactin ABC transporter permease |
| RA | 754,654 | G→T | 13.3% | intergenic (‑186/‑523) | gltA ← / → sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 774,481 | T→G | 6.7% | V58G (GTC→GGC) | ybgE → | putative inner membrane protein in cydABX‑ybgE operon |
| RA | 807,261 | G→A | 5.1% | S7S (TCC→TCT) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 910,542 | C→T | 64.8% | E170K (GAA→AAA) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| JC JC | 911,086 | IS2 (–) +5 bp | 83.9% | intergenic (‑37/+92) | poxB ← / ← hcr | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent |
| RA | 1,158,626 | G→A | 100% | G253D (GGC→GAC) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,164,581 | A→G | 6.1% | K163E (AAA→GAA) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,196,220 | C→T | 11.9% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 9.4% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | 9.3% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | 9.0% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,211,424 | T→C | 6.4% | pseudogene (12/165 nt) | icdC → | pseudogene, isocitrate dehydrogenase C‑terminal gene fragment; idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion |
| RA | 1,270,668 | G→A | 5.1% | intergenic (+208/+81) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| 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 |
| RA | 1,580,004 | A→T | 5.2% | C263S (TGC→AGC) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,624,859 | C→T | 5.7% | I29I (ATC→ATT) | ydeJ → | inactive PncC family protein |
| RA | 1,625,772 | G→A | 5.0% | R537C (CGT→TGT) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,753,767 | C→A | 6.2% | E22* (GAA→TAA) | ydhV ← | putative oxidoreductase subunit |
| RA | 1,819,040 | C→G | 5.3% | L136F (TTG→TTC) | chbR ← | repressor of chb operon for N,N'‑diacetylchitobiose utilization |
| RA | 1,824,688 | G→T | 5.3% | P84T (CCT→ACT) | ves ← | cold‑ and stress‑inducible protein |
| RA | 1,871,089 | G→A | 6.2% | A235A (GCG→GCA) | yeaI → | putative membrane‑anchored diguanylate cyclase |
| RA | 1,905,629 | T→A | 5.1% | intergenic (+370/‑59) | yobD → / → mntP | UPF0266 family inner membrane protein/putative Mn(2+) efflux pump, mntR‑regulated |
| RA | 1,909,592 | T→C | 5.4% | K170E (AAA→GAA) | kdgR ← | KDG regulon transcriptional repressor |
| 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 | 1,984,297 | T→C | 5.1% | E258G (GAG→GGG) | araG ← | L‑arabinose ABC transporter ATPase |
| RA | 2,113,178 | T→C | 6.8% | intergenic (‑117/+256) | rfbB ← / ← wcaN | dTDP‑glucose 4,6 dehydratase, NAD(P)‑binding/putative regulatory subunit for GalU |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,192,183 | A→G | 9.1% | F14L (TTT→CTT) | yehD ← | putative fimbrial‑like adhesin protein |
| RA | 2,257,513 | G→A | 5.3% | S285S (AGC→AGT) | psuG ← | pseudouridine 5'‑phosphate glycosidase |
| RA | 2,319,373 | A→T | 5.6% | D168E (GAT→GAA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,389,029 | T→C | 5.5% | M132T (ATG→ACG) | yfbO → | uncharacterized protein |
| JC JC | 2,413,482 | IS5 (–) +4 bp | 100% | coding (13‑16/1203 nt) | ackA → | acetate kinase A and propionate kinase 2 |
| RA | 2,560,985 | C→A | 20.8% | intergenic (+87/‑383) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,571,486 | T→A | 5.1% | D89V (GAT→GTT) | eutE ← | aldehyde oxidoreductase, ethanolamine utilization protein |
| RA | 2,573,889 | C→T | 5.4% | A139A (GCG→GCA) | eutT ← | cobalamin adenosyltransferase involved in ethanolamine utilization |
| RA | 2,722,202 | T→G | 100% | D750E (GAT→GAG) | pka → | protein lysine acetyltransferase |
| RA | 2,787,427 | G→A | 7.1% | pseudogene (1031/2253 nt) | ygaQ → | uncharacterized protein; putative enzyme |
| JC | 3,176,344 | Δ3 bp | 17.8% | coding (488‑490/828 nt) | cpdA ← | 3',5' cAMP phosphodiesterase |
| RA | 3,260,401 | G→A | 5.9% | S673L (TCA→TTA) | tdcE ← | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase |
| RA | 3,304,475 | C→T | 7.1% | intergenic (+20/+98) | yhbW → / ← mtr | putative luciferase‑like monooxygenase/tryptophan transporter of high affinity |
| RA | 3,322,076 | A→C | 77.6% | noncoding (83/87 nt) | leuU ← | tRNA‑Leu |
| RA | 3,440,282 | C→A | 15.6% | D250Y (GAT→TAT) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,539,816 | T→A | 7.3% | intergenic (+110/‑347) | yhgF → / → feoA | putative transcriptional accessory protein/ferrous iron transporter, protein A |
| 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 | 3,704,334 | G→A | 5.7% | A143V (GCG→GTG) | dppC ← | dipeptide/heme ABC transporter permease |
| RA | 3,781,051 | C→G | 5.1% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,801,032 | C→T | 100% | G323E (GGA→GAA) | waaR ← | lipopolysaccharide 1,2‑glucosyltransferase; UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,943,945 | G→A | 5.1% | noncoding (242/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,966,571 | A→G | 5.2% | D52G (GAT→GGT) | rho → | transcription termination factor |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,238,156 | A→G | 5.5% | S175G (AGT→GGT) | yjbH → | DUF940 family extracellular polysaccharide protein |
| RA | 4,296,060 | C→T | 31.2% | intergenic (+266/+376) | 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 | 4,339,786 | C→T | 5.0% | D246N (GAT→AAT) | adiA ← | arginine decarboxylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 123015 | 127566 | 4552 | 41 [40] | [39] 44 | aceE–[aceF] | aceE,[aceF] |
| * | * | ÷ | NC_000913 | 3423739–3424234 | 3424544–3424238 | 5–806 | 42 [37] | [40] 43 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 258675 | NA (NA) | 17 (0.190) | 14/258 | NT | 20.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1312561 = | 67 (0.730) | coding (330/540 nt) | yciB | IspA family inner membrane protein | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 3 (0.040) | 3/240 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 53 (0.580) | 22 (0.270) | 19/226 | NT | 31.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 51 (0.630) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 51 (0.560) | 21 (0.260) | 20/226 | NT | 30.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 51 (0.630) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 46 (0.520) | 39/250 | 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 | 4542682 = | 26 (0.280) | 51 (0.600) | 44/240 | NT | 64.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 31 (0.360) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 26 (0.280) | 37 (0.430) | 36/240 | NT | 57.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 31 (0.360) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||