mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
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 | 33.9% | A748T (GCG→ACG) | glnD ← | uridylyltransferase |
| RA | 253,776 | A→G | 2.7% | pseudogene (75/501 nt) | prfH → | pseudogene, RF‑1 domain family, probable peptide chain release factor |
| 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 | 508,443 | G→C | 3.3% | A76P (GCG→CCG) | ybaQ → | putative DNA‑binding transcriptional regulator |
| RA | 581,640 | A→T | 5.0% | pseudogene (287/309 nt) | aaaD → | pseudogene, DLP12 prophage, tail fiber assembly protein family,Phage or Prophage Related |
| RA | 705,254 | T→A | 3.9% | S437S (TCT→TCA) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| JC | 759,508 | (TGAACGTGCTGG)2→1 | 10.0% | coding (803‑814/2802 nt) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 759,906 | G→A | 15.0% | D401N (GAT→AAT) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 1,051,652 | A→G | 4.4% | A64A (GCA→GCG) | cspG → | cold shock protein homolog, cold‑inducible |
| RA | 1,182,367 | A→G | 4.4% | W155R (TGG→CGG) | potD ← | spermidine/putrescine ABC transporter periplasmic binding protein |
| RA | 1,449,391 | C→G | 4.8% | P653P (CCG→CCC) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,466,856 | A→G | 6.3% | pseudogene (1465/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,555,923 | T→A | 4.2% | D14V (GAC→GTC) | sra ← | stationary‑phase‑induced ribosome‑associated protein |
| RA | 1,735,587 | G→A | 5.1% | Q70Q (CAG→CAA) | sodB → | superoxide dismutase, Fe |
| RA | 1,887,917 | T→A | 6.9% | I25I (ATA→ATT) | rnd ← | ribonuclease D |
| 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 | 2,304,796 | T→C | 11.3% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,370,203 | G→A | 5.1% | R63H (CGC→CAC) | arnD → | undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase |
| RA | 2,426,949 | A→G | 5.2% | intergenic (‑163/+58) | hisJ ← / ← argT | histidine ABC transporter periplasmic binding protein/lysine/arginine/ornithine transporter subunit |
| RA | 2,876,424 | G→A | 78.1% | intergenic (‑97/‑155) | cysD ← / → iap | sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,956,518:1 | +T | 4.6% | coding (2365/2889 nt) | ptrA ← | protease III |
| RA | 2,956,699 | A→G | 5.0% | G728G (GGT→GGC) | ptrA ← | protease III |
| RA | 2,966,852 | A→G | 3.4% | I527I (ATT→ATC) | ptsP ← | PEP‑protein phosphotransferase enzyme I, GAF domain containing protein |
| RA | 3,269,986 | A→C | 7.7% | intergenic (+386/+228) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,437,647 | G→A | 9.3% | A378T (GCA→ACA) | trkA → | NAD‑binding component of TrK potassium transporter |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,967,801 | T→A | 4.8% | intergenic (+126/‑114) | rho → / → wecA | transcription termination factor/UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| RA | 3,967,963 | A→T | 4.8% | T17S (ACG→TCG) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,047,730 | G→T | 4.7% | V256F (GTT→TTT) | polA → | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease |
| RA | 4,156,202 | G→A | 4.8% | G64D (GGC→GAC) | argB → | acetylglutamate kinase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,059 | C→T | 10.9% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,154 | T→C | 23.2% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 37.5% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 32.6% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,521,015 | Δ1 bp | 4.8% | coding (1007/1350 nt) | yjhF ← | putative transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 754994 | 758417 | 3424 | 34 [33] | [30] 34 | sdhC–sdhB | sdhC, sdhD, sdhA, sdhB |
| * | * | ÷ | NC_000913 | 1529977 | 1530472 | 496 | 34 [33] | [30] 34 | [ydcD] | [ydcD] |
| * | * | ÷ | NC_000913 | 3423803–3424231 | 3424402–3424236 | 6–600 | 34 [33] | [26] 35 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3769460 | 3770008 | 549 | 35 [33] | [33] 35 | [yibV]–[yibU] | [yibV], yibV, [yibU] |
| * | * | ÷ | NC_000913 | 3798552 | 3800348 | 1797 | 34 [32] | [31] 35 | [waaU]–[waaY] | [waaU], waaZ, [waaY] |
| * | * | ÷ | NC_000913 | 3804142 | 3805219 | 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 | 10000 = | 100 (1.170) | 3 (0.040) | 3/512 | NT | 3.0% | coding (495/567 nt) | satP | succinate‑acetate transporter |
| ? | NC_000913 | 10031 = | 99 (1.180) | coding (464/567 nt) | satP | succinate‑acetate transporter | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 58 (0.680) | 46/522 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 754763 | 21 (0.250) | 8 (0.100) | 8/512 | NT | 28.3% | intergenic (‑295/‑414) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| ? | NC_000913 | 755100 = | 20 (0.240) | intergenic (‑632/‑77) | gltA/sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 | |||||
| * | ? | NC_000913 | 1207790 = | 37 (0.430) | 46 (0.570) | 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 (0.430) | 34 (0.420) | 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 | 90 (1.050) | 5 (0.060) +T |
5/520 | NT | 5.3% | coding (503/915 nt) | ldcA | murein tetrapeptide carboxypeptidase, LD‑carboxypeptidase A |
| ? | NC_000913 | = 1242591 | 89 (1.040) | coding (490/915 nt) | ldcA | murein tetrapeptide carboxypeptidase, LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | 1293032 = | 2 (0.020) | 25 (0.290) | 22/522 | NT | 92.6% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | 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 (0.630) | 43/522 | NT | 58.1% | coding (341/921 nt) | oppB | oligopeptide ABC transporter permease |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 37 (0.450) | 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 | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 24 (0.280) | 19/522 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 68 (0.800) | 43/522 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 1987441 | 78 (0.910) | 3 (0.040) | 3/502 | NT | 3.8% | intergenic (+13/+66) | ftnB/yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein |
| ? | NC_000913 | = 1987450 | 78 (0.950) | intergenic (+22/+57) | ftnB/yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein | |||||
| * | ? | NC_000913 | 2269905 = | 58 (0.680) | 3 (0.040) | 3/522 | NT | 4.9% | intergenic (+340/‑72) | 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 |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 2269908 | 58 (0.680) | 7 (0.080) | 7/522 | NT | 10.8% | intergenic (+343/‑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 |
| ? | NC_000913 | 2288917 = | NA (NA) | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 3968569 = | 113 (1.320) | 5 (0.060) | 5/522 | NT | 4.2% | coding (655/1104 nt) | wecA | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+11/+82) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 5 (0.070) | 8/444 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||