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 | 186,409 | C→T | 34.3% | A748T (GCG→ACG) | glnD ← | uridylyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 409,139 | A→T | 5.1% | I294N (ATT→AAT) | rdgC ← | nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function |
| RA | 581,640 | A→T | 5.0% | pseudogene (287/309 nt) | aaaD → | pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related |
| JC | 759,508 | (TGAACGTGCTGG)2→1 | 10.1% | coding (803‑814/2802 nt) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 759,906 | G→A | 15.2% | D401N (GAT→AAT) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| 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 | 1,466,856 | A→G | 5.5% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,735,587 | G→A | 5.1% | Q70Q (CAG→CAA) | sodB → | superoxide dismutase, Fe |
| RA | 1,887,917 | T→A | 7.1% | I25I (ATA→ATT) | rnd ← | ribonuclease D |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,048,541 | A→T | 6.2% | T1202S (ACC→TCC) | yeeJ → | putative adhesin |
| 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 |
| JC JC | 2,269,907 | IS5 (–) +4 bp | 7.9% | intergenic (+340/‑69) | lpxT → / → mepS | lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase |
| RA | 2,304,798 | T→C | 11.8% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,370,205 | G→A | 5.2% | R63H (CGC→CAC) | arnD → | undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase |
| RA | 2,426,951 | A→G | 5.2% | intergenic (‑163/+58) | hisJ ← / ← argT | histidine ABC transporter periplasmic binding protein/lysine/arginine/ornithine transporter subunit |
| RA | 2,876,426 | G→A | 78.1% | intergenic (‑97/‑155) | cysD ← / → iap | sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 3,437,649 | G→A | 9.3% | A378T (GCA→ACA) | trkA → | NAD‑binding component of TrK potassium transporter |
| 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 |
| 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 | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 19.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 26.7% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 20.9% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 13.0% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 11.5% | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 754988 | 758442 | 3455 | 34 [33] | [33] 35 | sdhC–sdhB | sdhC,sdhD,sdhA,sdhB |
| * | * | ÷ | NC_000913 | 1529977 | 1530472 | 496 | 34 [33] | [30] 34 | [ydcD] | [ydcD] |
| * | * | ÷ | NC_000913 | 3423801–3424231 | 3424404–3424239 | 9–604 | 34 [33] | [26] 35 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3769461 | 3770009 | 549 | 35 [33] | [33] 35 | [yibV]–[yibU] | [yibV],yibV,[yibU] |
| * | * | ÷ | NC_000913 | 3798553 | 3800349 | 1797 | 34 [32] | [31] 35 | [waaU]–[waaY] | [waaU],waaZ,[waaY] |
| * | * | ÷ | NC_000913 | 3804143 | 3805220 | 1078 | 36 [33] | [32] 34 | waaS–[waaP] | waaS,[waaP] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 754763 | 21 (0.250) | 8 (0.100) | 8/512 | NT | 28.8% | intergenic (‑295/‑414) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| ? | NC_000913 | 755100 = | 19 (0.230) | intergenic (‑632/‑77) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | NC_000913 | 1207790 = | 37 (0.440) | 46 (0.580) | 34/490 | NT | 53.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 44 (0.550) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 37 (0.440) | 34 (0.430) | 28/490 | NT | 46.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 44 (0.550) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1242578 | 88 (1.040) | 5 (0.060) +T |
5/520 | NT | 5.4% | coding (503/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| ? | NC_000913 | = 1242591 | 87 (1.020) | coding (490/915 nt) | ldcA | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 10 (0.120) | 8/514 | 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 | 1303239 = | 39 (0.460) | 54 (0.640) | 43/522 | NT | 58.1% | coding (341/921 nt) | oppB | oligopeptide ABC transporter permease |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 36 (0.440) | 31/506 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||